Starting phenix.real_space_refine on Wed May 21 23:23:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jqm_36575/05_2025/8jqm_36575.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jqm_36575/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jqm_36575/05_2025/8jqm_36575.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jqm_36575/05_2025/8jqm_36575.map" model { file = "/net/cci-nas-00/data/ceres_data/8jqm_36575/05_2025/8jqm_36575.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jqm_36575/05_2025/8jqm_36575.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLU:plan': 3, 'ARG:plan': 2, '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: {'GLU:plan': 3, 'ARG:plan': 2, '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: {'GLU:plan': 3, 'ARG:plan': 2, '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: {'GLU:plan': 3, 'ARG:plan': 2, '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: 13.36, per 1000 atoms: 0.93 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: 3.55 Conformation dependent library (CDL) restraints added in 3.2 seconds 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: 1.80 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: 4.55 Time building geometry restraints manager: 4.15 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: 3.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 40.590 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.080 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:12.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.670 ------------------------------------------------------------------------------- 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 : 5.07 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (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 TRP 0.015 0.001 TRP a 168 HIS 0.004 0.001 HIS b 216 PHE 0.019 0.002 PHE M 104 TYR 0.016 0.002 TYR M 105 ARG 0.007 0.001 ARG b 14 Details of bonding type rmsd hydrogen bonds : bond 0.21690 ( 419) hydrogen bonds : angle 8.37160 ( 1087) SS BOND : bond 0.00410 ( 28) SS BOND : angle 2.15290 ( 56) covalent geometry : bond 0.00388 (14762) covalent geometry : angle 0.64754 (20061) *********************** 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 : 1.540 Fit side-chains REVERT: L 61 ARG cc_start: 0.7494 (ptt-90) cc_final: 0.7290 (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: 0.6169 (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: 0.7960 (m110) outliers start: 11 outliers final: 0 residues processed: 231 average time/residue: 1.3941 time to fit residues: 350.0708 Evaluate side-chains 170 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 151 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 162 optimal weight: 0.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 286 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.126832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.094880 restraints weight = 96572.895| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 5.50 r_work: 0.2685 rms_B_bonded: 5.07 restraints_weight: 2.0000 r_work (final): 0.2685 ------------------------------------------------------------------------------- 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 = 0.50 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 = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 14790 Z= 0.248 Angle : 0.746 12.878 20117 Z= 0.393 Chirality : 0.049 0.182 2151 Planarity : 0.005 0.036 2575 Dihedral : 5.768 26.367 1995 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.19 % Favored : 94.70 % Rotamer: Outliers : 2.86 % Allowed : 8.19 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.20), residues: 1824 helix: 1.33 (0.42), residues: 157 sheet: -0.10 (0.24), residues: 485 loop : -0.58 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP M 36 HIS 0.018 0.002 HIS a 2 PHE 0.020 0.002 PHE M 104 TYR 0.026 0.003 TYR M 105 ARG 0.008 0.001 ARG a 99 Details of bonding type rmsd hydrogen bonds : bond 0.05881 ( 419) hydrogen bonds : angle 6.23476 ( 1087) SS BOND : bond 0.00663 ( 28) SS BOND : angle 2.55755 ( 56) covalent geometry : bond 0.00610 (14762) covalent geometry : angle 0.73442 (20061) *********************** 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 209 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 1.706 Fit side-chains REVERT: L 81 GLU cc_start: 0.6809 (pm20) cc_final: 0.6406 (pm20) REVERT: A 29 ARG cc_start: 0.7210 (OUTLIER) cc_final: 0.6328 (ptm-80) REVERT: B 220 MET cc_start: 0.9065 (mmt) cc_final: 0.8813 (mpp) REVERT: B 276 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.8027 (mtp180) REVERT: B 326 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8550 (tttp) REVERT: b 48 GLN cc_start: 0.7567 (tt0) cc_final: 0.7261 (tt0) REVERT: N 24 ARG cc_start: 0.7843 (tpt170) cc_final: 0.7521 (tpt170) REVERT: N 30 THR cc_start: 0.8876 (OUTLIER) cc_final: 0.8646 (p) REVERT: a 75 LEU cc_start: 0.7326 (tp) cc_final: 0.7092 (tp) REVERT: a 102 GLN cc_start: 0.8105 (mm-40) cc_final: 0.7750 (mm-40) REVERT: a 234 ASP cc_start: 0.8257 (p0) cc_final: 0.8005 (p0) REVERT: a 271 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8165 (tt0) REVERT: a 279 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7495 (mt-10) REVERT: a 326 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7296 (ptmm) REVERT: a 340 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7282 (mm-30) outliers start: 33 outliers final: 15 residues processed: 194 average time/residue: 1.4948 time to fit residues: 314.4528 Evaluate side-chains 192 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 1.613 ------------------------------------------------------------------------------- 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 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 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 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 Chi-restraints excluded: chain a residue 326 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 160 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 11 optimal weight: 0.0670 chunk 138 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 69 optimal weight: 0.5980 chunk 149 optimal weight: 0.9990 overall best weight: 0.9324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 16 GLN B 2 HIS b 344 ASN a 1 HIS a 82 ASN a 131 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.131893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.099716 restraints weight = 88193.864| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 5.09 r_work: 0.2786 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2732 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2732 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14790 Z= 0.103 Angle : 0.558 9.986 20117 Z= 0.295 Chirality : 0.043 0.161 2151 Planarity : 0.004 0.038 2575 Dihedral : 5.066 22.733 1995 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.24 % Favored : 95.65 % Rotamer: Outliers : 2.10 % Allowed : 10.35 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.20), residues: 1824 helix: 2.01 (0.43), residues: 151 sheet: 0.21 (0.25), residues: 497 loop : -0.35 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 118 HIS 0.007 0.001 HIS b 2 PHE 0.011 0.001 PHE L 98 TYR 0.013 0.001 TYR M 35 ARG 0.003 0.000 ARG b 69 Details of bonding type rmsd hydrogen bonds : bond 0.03668 ( 419) hydrogen bonds : angle 5.54503 ( 1087) SS BOND : bond 0.00303 ( 28) SS BOND : angle 1.37376 ( 56) covalent geometry : bond 0.00235 (14762) covalent geometry : angle 0.55366 (20061) *********************** 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 209 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 1.735 Fit side-chains REVERT: H 92 THR cc_start: 0.8350 (m) cc_final: 0.7969 (t) REVERT: b 48 GLN cc_start: 0.7482 (tt0) cc_final: 0.7131 (tt0) REVERT: b 261 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8280 (mpp-170) REVERT: N 24 ARG cc_start: 0.7720 (tpt170) cc_final: 0.7383 (tpt170) REVERT: a 75 LEU cc_start: 0.7369 (tp) cc_final: 0.7097 (tp) REVERT: a 102 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7616 (mm-40) REVERT: a 157 ASP cc_start: 0.5633 (OUTLIER) cc_final: 0.5323 (t0) REVERT: a 234 ASP cc_start: 0.8111 (p0) cc_final: 0.7859 (p0) REVERT: a 340 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7320 (tp30) outliers start: 21 outliers final: 10 residues processed: 198 average time/residue: 1.4113 time to fit residues: 304.0411 Evaluate side-chains 188 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 176 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 287 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 17 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 159 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 153 optimal weight: 0.9990 chunk 151 optimal weight: 0.7980 chunk 118 optimal weight: 0.4980 chunk 29 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 3 GLN L 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.131181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.099077 restraints weight = 96502.164| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 5.67 r_work: 0.2739 rms_B_bonded: 5.04 restraints_weight: 2.0000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2696 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2696 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 14790 Z= 0.125 Angle : 0.584 10.202 20117 Z= 0.308 Chirality : 0.043 0.154 2151 Planarity : 0.004 0.040 2575 Dihedral : 5.112 24.019 1995 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.69 % Favored : 95.20 % Rotamer: Outliers : 2.67 % Allowed : 11.30 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.20), residues: 1824 helix: 2.10 (0.43), residues: 151 sheet: 0.28 (0.25), residues: 480 loop : -0.35 (0.18), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP b 168 HIS 0.008 0.001 HIS b 2 PHE 0.011 0.001 PHE B 323 TYR 0.013 0.001 TYR M 35 ARG 0.003 0.000 ARG a 99 Details of bonding type rmsd hydrogen bonds : bond 0.03833 ( 419) hydrogen bonds : angle 5.40916 ( 1087) SS BOND : bond 0.00369 ( 28) SS BOND : angle 1.96442 ( 56) covalent geometry : bond 0.00299 (14762) covalent geometry : angle 0.57581 (20061) *********************** 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 208 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 178 time to evaluate : 1.665 Fit side-chains REVERT: B 276 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7920 (mtp180) REVERT: b 48 GLN cc_start: 0.7517 (tt0) cc_final: 0.7164 (tt0) REVERT: b 168 TRP cc_start: 0.6744 (m100) cc_final: 0.5961 (m100) REVERT: b 261 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8329 (mpp-170) REVERT: a 75 LEU cc_start: 0.7352 (tp) cc_final: 0.7056 (tp) REVERT: a 102 GLN cc_start: 0.8143 (mm-40) cc_final: 0.7681 (mm-40) REVERT: a 157 ASP cc_start: 0.5680 (OUTLIER) cc_final: 0.5376 (t0) REVERT: a 279 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7394 (mt-10) REVERT: a 340 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7309 (tp30) outliers start: 30 outliers final: 13 residues processed: 198 average time/residue: 1.4530 time to fit residues: 312.2798 Evaluate side-chains 182 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 1.647 ------------------------------------------------------------------------------- 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 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 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 239 SER 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 167 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 146 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- 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 ** a 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.127696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.104170 restraints weight = 94038.198| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 6.25 r_work: 0.2572 rms_B_bonded: 6.15 restraints_weight: 2.0000 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2553 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2553 r_free = 0.2553 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2553 r_free = 0.2553 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2553 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.116 14790 Z= 0.302 Angle : 0.792 14.628 20117 Z= 0.416 Chirality : 0.051 0.166 2151 Planarity : 0.005 0.044 2575 Dihedral : 5.911 27.338 1995 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.36 % Favored : 94.59 % Rotamer: Outliers : 3.62 % Allowed : 11.11 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.20), residues: 1824 helix: 1.28 (0.42), residues: 158 sheet: -0.01 (0.25), residues: 480 loop : -0.66 (0.18), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP M 36 HIS 0.015 0.002 HIS b 2 PHE 0.022 0.003 PHE B 323 TYR 0.029 0.003 TYR M 105 ARG 0.008 0.001 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.05718 ( 419) hydrogen bonds : angle 5.87899 ( 1087) SS BOND : bond 0.00747 ( 28) SS BOND : angle 2.87663 ( 56) covalent geometry : bond 0.00745 (14762) covalent geometry : angle 0.77837 (20061) *********************** 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 219 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 174 time to evaluate : 1.729 Fit side-chains REVERT: L 79 ARG cc_start: 0.7283 (mmm-85) cc_final: 0.6847 (mtp180) REVERT: A 29 ARG cc_start: 0.7246 (OUTLIER) cc_final: 0.6236 (ptm-80) REVERT: B 276 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8106 (mtp180) REVERT: b 48 GLN cc_start: 0.7688 (tt0) cc_final: 0.7365 (tt0) REVERT: b 261 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8544 (mpp-170) REVERT: b 343 SER cc_start: 0.8461 (m) cc_final: 0.8141 (p) REVERT: N 81 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6097 (pm20) REVERT: a 35 HIS cc_start: 0.6263 (m90) cc_final: 0.5923 (m90) REVERT: a 102 GLN cc_start: 0.8163 (mm-40) cc_final: 0.7709 (mm-40) REVERT: a 271 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8262 (tt0) REVERT: a 279 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7316 (mt-10) REVERT: a 340 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7321 (mm-30) outliers start: 45 outliers final: 23 residues processed: 202 average time/residue: 1.5397 time to fit residues: 336.0960 Evaluate side-chains 204 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 1.522 ------------------------------------------------------------------------------- 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 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 276 ARG Chi-restraints excluded: chain B residue 326 LYS 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 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 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 236 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 32 optimal weight: 0.0170 chunk 123 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 113 optimal weight: 0.0670 chunk 74 optimal weight: 0.9990 chunk 50 optimal weight: 8.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- 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** a 147 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.132927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.109352 restraints weight = 88335.353| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 6.28 r_work: 0.2714 rms_B_bonded: 6.09 restraints_weight: 2.0000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2677 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2677 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14790 Z= 0.097 Angle : 0.552 10.770 20117 Z= 0.290 Chirality : 0.042 0.158 2151 Planarity : 0.004 0.038 2575 Dihedral : 4.992 21.878 1995 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.52 % Favored : 95.42 % Rotamer: Outliers : 2.35 % Allowed : 12.83 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.20), residues: 1824 helix: 2.08 (0.43), residues: 151 sheet: 0.26 (0.25), residues: 463 loop : -0.37 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 118 HIS 0.004 0.001 HIS B 195 PHE 0.012 0.001 PHE L 98 TYR 0.013 0.001 TYR M 35 ARG 0.005 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.03133 ( 419) hydrogen bonds : angle 5.27063 ( 1087) SS BOND : bond 0.00272 ( 28) SS BOND : angle 1.63424 ( 56) covalent geometry : bond 0.00225 (14762) covalent geometry : angle 0.54597 (20061) *********************** 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 209 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 1.774 Fit side-chains REVERT: b 41 ARG cc_start: 0.7096 (ttt180) cc_final: 0.6844 (ttt180) REVERT: b 48 GLN cc_start: 0.7590 (tt0) cc_final: 0.7247 (tt0) REVERT: a 75 LEU cc_start: 0.7188 (tp) cc_final: 0.6986 (tp) REVERT: a 102 GLN cc_start: 0.8117 (mm-40) cc_final: 0.7651 (mm-40) REVERT: a 279 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7314 (mt-10) REVERT: a 340 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7306 (tp30) outliers start: 25 outliers final: 15 residues processed: 200 average time/residue: 1.5112 time to fit residues: 329.6263 Evaluate side-chains 182 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain b residue 55 CYS 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 129 THR Chi-restraints excluded: chain a residue 134 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 80 optimal weight: 1.9990 chunk 13 optimal weight: 20.0000 chunk 74 optimal weight: 7.9990 chunk 105 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 140 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 103 optimal weight: 0.4980 overall best weight: 2.6986 ------------------------------------------------------------------------------- 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 = 0.3477 r_free = 0.3477 target = 0.130292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.106501 restraints weight = 79133.831| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 5.42 r_work: 0.2650 rms_B_bonded: 5.34 restraints_weight: 2.0000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2631 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2631 r_free = 0.2631 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2631 r_free = 0.2631 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2631 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 14790 Z= 0.186 Angle : 0.662 10.870 20117 Z= 0.347 Chirality : 0.046 0.154 2151 Planarity : 0.004 0.040 2575 Dihedral : 5.387 23.540 1995 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.25 % Favored : 94.70 % Rotamer: Outliers : 2.67 % Allowed : 13.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.20), residues: 1824 helix: 1.59 (0.42), residues: 157 sheet: 0.04 (0.25), residues: 462 loop : -0.52 (0.18), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP b 168 HIS 0.010 0.001 HIS b 2 PHE 0.016 0.002 PHE B 323 TYR 0.019 0.002 TYR M 105 ARG 0.005 0.001 ARG L 61 Details of bonding type rmsd hydrogen bonds : bond 0.04449 ( 419) hydrogen bonds : angle 5.46801 ( 1087) SS BOND : bond 0.00498 ( 28) SS BOND : angle 2.55168 ( 56) covalent geometry : bond 0.00460 (14762) covalent geometry : angle 0.64923 (20061) *********************** 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 197 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 1.697 Fit side-chains REVERT: B 340 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7522 (mm-30) REVERT: b 48 GLN cc_start: 0.7587 (tt0) cc_final: 0.7272 (tt0) REVERT: b 343 SER cc_start: 0.8409 (m) cc_final: 0.8162 (p) REVERT: N 30 THR cc_start: 0.8818 (OUTLIER) cc_final: 0.8608 (p) REVERT: N 81 GLU cc_start: 0.7093 (pp20) cc_final: 0.6889 (pp20) REVERT: a 75 LEU cc_start: 0.7257 (tp) cc_final: 0.7007 (tp) REVERT: a 102 GLN cc_start: 0.8155 (mm-40) cc_final: 0.7703 (mm-40) REVERT: a 224 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8410 (mt-10) REVERT: a 279 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7519 (mt-10) REVERT: a 340 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7350 (tp30) outliers start: 30 outliers final: 18 residues processed: 185 average time/residue: 1.5206 time to fit residues: 304.8092 Evaluate side-chains 184 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 143 CYS 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 278 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 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 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 28 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 83 optimal weight: 0.0980 chunk 147 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 142 optimal weight: 9.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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 = 0.3480 r_free = 0.3480 target = 0.130550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.107145 restraints weight = 90439.096| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 5.53 r_work: 0.2638 rms_B_bonded: 5.49 restraints_weight: 2.0000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2627 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2627 r_free = 0.2627 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2627 r_free = 0.2627 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2627 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 14790 Z= 0.171 Angle : 0.650 11.224 20117 Z= 0.341 Chirality : 0.045 0.154 2151 Planarity : 0.004 0.040 2575 Dihedral : 5.416 23.409 1995 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.13 % Favored : 94.81 % Rotamer: Outliers : 2.60 % Allowed : 13.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.20), residues: 1824 helix: 1.56 (0.42), residues: 157 sheet: 0.03 (0.24), residues: 493 loop : -0.52 (0.18), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP b 168 HIS 0.009 0.001 HIS b 2 PHE 0.015 0.002 PHE B 323 TYR 0.017 0.002 TYR M 105 ARG 0.004 0.000 ARG L 61 Details of bonding type rmsd hydrogen bonds : bond 0.04330 ( 419) hydrogen bonds : angle 5.46558 ( 1087) SS BOND : bond 0.00474 ( 28) SS BOND : angle 2.34450 ( 56) covalent geometry : bond 0.00421 (14762) covalent geometry : angle 0.63877 (20061) *********************** 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: 29 poor density : 165 time to evaluate : 1.597 Fit side-chains REVERT: H 112 GLN cc_start: 0.7542 (OUTLIER) cc_final: 0.7267 (mt0) REVERT: L 79 ARG cc_start: 0.7193 (mmm-85) cc_final: 0.6760 (mtp-110) REVERT: B 340 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7474 (mm-30) REVERT: b 48 GLN cc_start: 0.7598 (tt0) cc_final: 0.7296 (tt0) REVERT: b 343 SER cc_start: 0.8383 (m) cc_final: 0.8130 (p) REVERT: N 30 THR cc_start: 0.8856 (OUTLIER) cc_final: 0.8651 (p) REVERT: a 75 LEU cc_start: 0.7311 (tp) cc_final: 0.7051 (tp) REVERT: a 102 GLN cc_start: 0.8145 (mm-40) cc_final: 0.7702 (mm-40) REVERT: a 279 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7501 (mt-10) REVERT: a 340 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7226 (mm-30) outliers start: 29 outliers final: 18 residues processed: 183 average time/residue: 1.5118 time to fit residues: 299.4084 Evaluate side-chains 183 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain L residue 74 THR 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 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 278 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 129 THR Chi-restraints excluded: chain a residue 134 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 148 optimal weight: 6.9990 chunk 168 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 147 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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** ** b 147 HIS ** 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 = 0.3496 r_free = 0.3496 target = 0.131894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.108794 restraints weight = 88608.177| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 5.59 r_work: 0.2669 rms_B_bonded: 5.58 restraints_weight: 2.0000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2656 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2656 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14790 Z= 0.120 Angle : 0.588 10.496 20117 Z= 0.308 Chirality : 0.043 0.153 2151 Planarity : 0.004 0.040 2575 Dihedral : 5.115 22.869 1995 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.85 % Favored : 95.09 % Rotamer: Outliers : 2.41 % Allowed : 13.78 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.20), residues: 1824 helix: 2.11 (0.43), residues: 149 sheet: 0.21 (0.25), residues: 461 loop : -0.39 (0.18), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP b 168 HIS 0.006 0.001 HIS b 2 PHE 0.011 0.001 PHE H 80 TYR 0.014 0.001 TYR M 35 ARG 0.003 0.000 ARG L 61 Details of bonding type rmsd hydrogen bonds : bond 0.03624 ( 419) hydrogen bonds : angle 5.27913 ( 1087) SS BOND : bond 0.00341 ( 28) SS BOND : angle 1.81580 ( 56) covalent geometry : bond 0.00288 (14762) covalent geometry : angle 0.58068 (20061) *********************** 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 190 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 1.752 Fit side-chains REVERT: H 112 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.7234 (mt0) REVERT: B 340 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7460 (mm-30) REVERT: b 48 GLN cc_start: 0.7547 (tt0) cc_final: 0.7253 (tt0) REVERT: b 309 GLU cc_start: 0.8058 (tp30) cc_final: 0.7290 (pm20) REVERT: b 343 SER cc_start: 0.8379 (m) cc_final: 0.8134 (p) REVERT: a 75 LEU cc_start: 0.7284 (tp) cc_final: 0.7023 (tp) REVERT: a 102 GLN cc_start: 0.8139 (mm-40) cc_final: 0.7674 (mm-40) REVERT: a 279 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7323 (mt-10) REVERT: a 340 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7325 (tp30) outliers start: 26 outliers final: 20 residues processed: 181 average time/residue: 1.5614 time to fit residues: 305.2912 Evaluate side-chains 187 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain A residue 37 ASP 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 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 278 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 129 THR Chi-restraints excluded: chain a residue 134 VAL 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 149 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 126 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 175 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 13 optimal weight: 20.0000 chunk 174 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 160 optimal weight: 9.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 16 GLN ** b 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.131925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.108637 restraints weight = 89262.527| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 5.64 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14790 Z= 0.130 Angle : 0.598 10.603 20117 Z= 0.313 Chirality : 0.044 0.150 2151 Planarity : 0.004 0.041 2575 Dihedral : 5.123 23.006 1995 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.91 % Favored : 95.03 % Rotamer: Outliers : 2.22 % Allowed : 14.16 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.20), residues: 1824 helix: 2.08 (0.43), residues: 149 sheet: 0.18 (0.25), residues: 469 loop : -0.37 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP b 168 HIS 0.007 0.001 HIS b 2 PHE 0.011 0.001 PHE H 80 TYR 0.014 0.002 TYR M 35 ARG 0.003 0.000 ARG L 61 Details of bonding type rmsd hydrogen bonds : bond 0.03746 ( 419) hydrogen bonds : angle 5.27827 ( 1087) SS BOND : bond 0.00367 ( 28) SS BOND : angle 1.89337 ( 56) covalent geometry : bond 0.00314 (14762) covalent geometry : angle 0.59072 (20061) ********************** 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 184 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 1.740 Fit side-chains REVERT: H 112 GLN cc_start: 0.7211 (OUTLIER) cc_final: 0.6897 (mt0) REVERT: B 192 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7295 (mm-30) REVERT: B 340 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7162 (mm-30) REVERT: b 48 GLN cc_start: 0.7293 (tt0) cc_final: 0.7043 (tt0) REVERT: b 309 GLU cc_start: 0.7483 (tp30) cc_final: 0.7177 (pm20) REVERT: b 343 SER cc_start: 0.8362 (m) cc_final: 0.8101 (p) REVERT: a 75 LEU cc_start: 0.7412 (tp) cc_final: 0.7139 (tp) REVERT: a 102 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7741 (mm-40) REVERT: a 279 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6905 (mt-10) REVERT: a 340 GLU cc_start: 0.7312 (mm-30) cc_final: 0.7053 (tp30) outliers start: 23 outliers final: 19 residues processed: 175 average time/residue: 1.5440 time to fit residues: 293.1521 Evaluate side-chains 179 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 112 GLN 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 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 278 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 129 THR Chi-restraints excluded: chain a residue 134 VAL 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 50 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 169 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 176 optimal weight: 0.0370 chunk 89 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 95 optimal weight: 0.4980 chunk 14 optimal weight: 9.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 16 GLN L 6 GLN b 147 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.134412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.111417 restraints weight = 95263.780| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 6.44 r_work: 0.2730 rms_B_bonded: 6.23 restraints_weight: 2.0000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14790 Z= 0.090 Angle : 0.539 10.067 20117 Z= 0.281 Chirality : 0.042 0.151 2151 Planarity : 0.004 0.039 2575 Dihedral : 4.746 21.463 1995 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.52 % Favored : 95.42 % Rotamer: Outliers : 2.22 % Allowed : 14.22 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.20), residues: 1824 helix: 2.32 (0.43), residues: 149 sheet: 0.37 (0.25), residues: 469 loop : -0.24 (0.19), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 118 HIS 0.004 0.001 HIS b 2 PHE 0.011 0.001 PHE L 98 TYR 0.013 0.001 TYR M 35 ARG 0.003 0.000 ARG b 69 Details of bonding type rmsd hydrogen bonds : bond 0.03026 ( 419) hydrogen bonds : angle 5.04899 ( 1087) SS BOND : bond 0.00274 ( 28) SS BOND : angle 1.37326 ( 56) covalent geometry : bond 0.00210 (14762) covalent geometry : angle 0.53445 (20061) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10332.70 seconds wall clock time: 178 minutes 37.15 seconds (10717.15 seconds total)