Starting phenix.real_space_refine on Thu Jun 19 04:55:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jqm_36575/06_2025/8jqm_36575.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jqm_36575/06_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_36575/06_2025/8jqm_36575.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jqm_36575/06_2025/8jqm_36575.map" model { file = "/net/cci-nas-00/data/ceres_data/8jqm_36575/06_2025/8jqm_36575.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jqm_36575/06_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-5710/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: 12.45, per 1000 atoms: 0.87 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: 3.20 Conformation dependent library (CDL) restraints added in 2.9 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: 1.85 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: 4.35 Time building geometry restraints manager: 3.86 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: 3.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 39.650 Find NCS groups from input model: 0.630 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:12.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.440 ------------------------------------------------------------------------------- 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 : 1.759 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: 1.3882 time to fit residues: 349.5821 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 : 1.664 ------------------------------------------------------------------------------- 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 = 0.126833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.094879 restraints weight = 96572.037| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 5.50 r_work: 0.2685 rms_B_bonded: 5.09 restraints_weight: 2.0000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2676 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2676 ------------------------------------------------------------------------------- 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 2.55750 ( 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 : 1.618 Fit side-chains REVERT: L 81 GLU cc_start: 0.6808 (pm20) cc_final: 0.6405 (pm20) REVERT: A 29 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.6320 (ptm-80) REVERT: B 220 MET cc_start: 0.9063 (mmt) cc_final: 0.8811 (mpp) REVERT: B 276 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8033 (mtp180) REVERT: B 326 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8554 (tttp) REVERT: b 48 GLN cc_start: 0.7567 (tt0) cc_final: 0.7260 (tt0) REVERT: N 24 ARG cc_start: 0.7844 (tpt170) cc_final: 0.7521 (tpt170) REVERT: N 30 THR cc_start: 0.8882 (OUTLIER) cc_final: 0.8647 (p) REVERT: a 75 LEU cc_start: 0.7332 (tp) cc_final: 0.7097 (tp) REVERT: a 102 GLN cc_start: 0.8108 (mm-40) cc_final: 0.7752 (mm-40) REVERT: a 234 ASP cc_start: 0.8256 (p0) cc_final: 0.8004 (p0) REVERT: a 271 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8168 (tt0) REVERT: a 279 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7496 (mt-10) REVERT: a 326 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7295 (ptmm) REVERT: a 340 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7282 (mm-30) outliers start: 33 outliers final: 15 residues processed: 194 average time/residue: 1.5465 time to fit residues: 324.5361 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 : 1.622 ------------------------------------------------------------------------------- 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: 10.0000 chunk 109 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 11 optimal weight: 0.1980 chunk 138 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 69 optimal weight: 0.0870 chunk 149 optimal weight: 0.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- 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 = 0.3483 r_free = 0.3483 target = 0.131152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.098742 restraints weight = 88848.839| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 5.17 r_work: 0.2753 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14790 Z= 0.092 Angle : 0.543 9.866 20117 Z= 0.287 Chirality : 0.042 0.163 2151 Planarity : 0.004 0.037 2575 Dihedral : 4.977 22.242 1995 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.41 % Favored : 95.48 % Rotamer: Outliers : 1.90 % Allowed : 10.41 % Favored : 87.68 % 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: 2.03 (0.43), residues: 151 sheet: 0.22 (0.25), residues: 497 loop : -0.31 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 118 HIS 0.006 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 0.03488 ( 419) hydrogen bonds : angle 5.48844 ( 1087) SS BOND : bond 0.00257 ( 28) SS BOND : angle 1.23814 ( 56) covalent geometry : bond 0.00206 (14762) covalent geometry : angle 0.53935 (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 212 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 194 time to evaluate : 1.709 Fit side-chains REVERT: H 92 THR cc_start: 0.8326 (m) cc_final: 0.7955 (t) REVERT: b 48 GLN cc_start: 0.7434 (tt0) cc_final: 0.7096 (tt0) REVERT: b 261 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.8280 (mpp-170) REVERT: N 24 ARG cc_start: 0.7698 (tpt170) cc_final: 0.7350 (tpt170) REVERT: a 75 LEU cc_start: 0.7348 (tp) cc_final: 0.7075 (tp) REVERT: a 102 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7717 (mm-40) REVERT: a 157 ASP cc_start: 0.5573 (OUTLIER) cc_final: 0.5307 (t0) REVERT: a 340 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7350 (tp30) outliers start: 18 outliers final: 9 residues processed: 203 average time/residue: 1.4914 time to fit residues: 329.4115 Evaluate side-chains 188 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 177 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 129 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 159 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 153 optimal weight: 10.0000 chunk 151 optimal weight: 6.9990 chunk 118 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 overall best weight: 3.1384 ------------------------------------------------------------------------------- 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 = 0.3454 r_free = 0.3454 target = 0.128612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.096899 restraints weight = 94729.800| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 5.67 r_work: 0.2653 rms_B_bonded: 5.04 restraints_weight: 2.0000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2653 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2653 r_free = 0.2653 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2653 r_free = 0.2653 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2653 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 14790 Z= 0.211 Angle : 0.684 10.972 20117 Z= 0.360 Chirality : 0.047 0.161 2151 Planarity : 0.005 0.039 2575 Dihedral : 5.536 26.151 1995 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.97 % Favored : 94.92 % Rotamer: Outliers : 3.37 % Allowed : 10.73 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.31 (0.20), residues: 1824 helix: 1.58 (0.42), residues: 156 sheet: 0.03 (0.25), residues: 483 loop : -0.54 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP b 168 HIS 0.012 0.001 HIS b 2 PHE 0.017 0.002 PHE B 323 TYR 0.022 0.002 TYR M 105 ARG 0.005 0.001 ARG a 99 Details of bonding type rmsd hydrogen bonds : bond 0.04870 ( 419) hydrogen bonds : angle 5.69155 ( 1087) SS BOND : bond 0.00554 ( 28) SS BOND : angle 2.65777 ( 56) covalent geometry : bond 0.00521 (14762) covalent geometry : angle 0.67071 (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 221 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 180 time to evaluate : 1.939 Fit side-chains REVERT: A 29 ARG cc_start: 0.7206 (OUTLIER) cc_final: 0.6301 (ptm-80) REVERT: A 347 ARG cc_start: 0.8351 (ptp-110) cc_final: 0.7980 (ptm160) REVERT: B 276 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7958 (mtp180) REVERT: b 7 ASP cc_start: 0.8404 (t70) cc_final: 0.8184 (t0) REVERT: b 48 GLN cc_start: 0.7541 (tt0) cc_final: 0.7198 (tt0) REVERT: b 261 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8405 (mpp-170) REVERT: N 30 THR cc_start: 0.8835 (OUTLIER) cc_final: 0.8626 (p) REVERT: a 75 LEU cc_start: 0.7332 (tp) cc_final: 0.7044 (tp) REVERT: a 102 GLN cc_start: 0.8141 (mm-40) cc_final: 0.7702 (mm-40) REVERT: a 279 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7535 (mt-10) REVERT: a 340 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7356 (tp30) outliers start: 41 outliers final: 16 residues processed: 205 average time/residue: 1.7185 time to fit residues: 383.8606 Evaluate side-chains 192 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 132 SER Chi-restraints excluded: chain b residue 178 GLU Chi-restraints excluded: chain b residue 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 239 SER Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain a residue 287 VAL Chi-restraints excluded: chain a residue 350 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 167 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 62 optimal weight: 9.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 ** a 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.130140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.094037 restraints weight = 94877.217| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 4.46 r_work: 0.2764 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2704 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2704 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 14790 Z= 0.151 Angle : 0.621 10.888 20117 Z= 0.328 Chirality : 0.044 0.156 2151 Planarity : 0.004 0.040 2575 Dihedral : 5.330 24.370 1995 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.97 % Favored : 94.92 % Rotamer: Outliers : 3.11 % Allowed : 11.56 % Favored : 85.33 % 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: -0.27 (0.20), residues: 1824 helix: 1.67 (0.43), residues: 157 sheet: 0.13 (0.25), residues: 481 loop : -0.55 (0.18), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP b 168 HIS 0.009 0.001 HIS b 2 PHE 0.013 0.002 PHE B 323 TYR 0.015 0.002 TYR M 105 ARG 0.003 0.000 ARG a 99 Details of bonding type rmsd hydrogen bonds : bond 0.04152 ( 419) hydrogen bonds : angle 5.50289 ( 1087) SS BOND : bond 0.00421 ( 28) SS BOND : angle 2.17493 ( 56) covalent geometry : bond 0.00369 (14762) covalent geometry : angle 0.61166 (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 209 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 172 time to evaluate : 1.913 Fit side-chains REVERT: A 347 ARG cc_start: 0.8366 (ptp-110) cc_final: 0.8023 (ptm160) REVERT: B 276 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7895 (mtp180) REVERT: b 48 GLN cc_start: 0.7569 (tt0) cc_final: 0.7249 (tt0) REVERT: b 261 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8331 (mpp-170) REVERT: N 81 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.5878 (pm20) REVERT: a 75 LEU cc_start: 0.7393 (tp) cc_final: 0.7100 (tp) REVERT: a 102 GLN cc_start: 0.8116 (mm-40) cc_final: 0.7697 (mm-40) REVERT: a 157 ASP cc_start: 0.5802 (OUTLIER) cc_final: 0.5464 (t0) REVERT: a 224 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8221 (mt-10) REVERT: a 271 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.8011 (tt0) REVERT: a 279 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7502 (mt-10) REVERT: a 340 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7282 (tp30) outliers start: 37 outliers final: 19 residues processed: 196 average time/residue: 1.4881 time to fit residues: 316.8414 Evaluate side-chains 188 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 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 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 74 THR Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain a residue 129 THR Chi-restraints excluded: chain a residue 134 VAL Chi-restraints excluded: chain a residue 157 ASP Chi-restraints excluded: chain a residue 224 GLU Chi-restraints excluded: chain a residue 236 ILE Chi-restraints excluded: chain a residue 239 SER Chi-restraints excluded: chain a residue 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: 1.9990 chunk 123 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 95 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 L 6 GLN a 147 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.130219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.106793 restraints weight = 86212.186| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 6.14 r_work: 0.2650 rms_B_bonded: 6.07 restraints_weight: 2.0000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2605 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2605 r_free = 0.2605 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2605 r_free = 0.2605 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2605 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 14790 Z= 0.160 Angle : 0.631 11.057 20117 Z= 0.332 Chirality : 0.045 0.152 2151 Planarity : 0.004 0.039 2575 Dihedral : 5.352 25.079 1995 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.25 % Favored : 94.70 % Rotamer: Outliers : 2.98 % Allowed : 12.13 % Favored : 84.89 % 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: -0.28 (0.20), residues: 1824 helix: 1.65 (0.43), residues: 157 sheet: 0.13 (0.25), residues: 479 loop : -0.56 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP b 168 HIS 0.009 0.001 HIS b 2 PHE 0.013 0.002 PHE B 323 TYR 0.015 0.002 TYR M 105 ARG 0.003 0.000 ARG a 99 Details of bonding type rmsd hydrogen bonds : bond 0.04220 ( 419) hydrogen bonds : angle 5.47637 ( 1087) SS BOND : bond 0.00445 ( 28) SS BOND : angle 2.28904 ( 56) covalent geometry : bond 0.00394 (14762) covalent geometry : angle 0.62047 (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 205 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 170 time to evaluate : 1.591 Fit side-chains REVERT: A 347 ARG cc_start: 0.8475 (ptp-110) cc_final: 0.8066 (ptm160) REVERT: B 276 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.7996 (mtp180) REVERT: b 48 GLN cc_start: 0.7627 (tt0) cc_final: 0.7303 (tt0) REVERT: N 81 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.5993 (pm20) REVERT: a 75 LEU cc_start: 0.7350 (tp) cc_final: 0.7072 (tp) REVERT: a 102 GLN cc_start: 0.8153 (mm-40) cc_final: 0.7720 (mm-40) REVERT: a 157 ASP cc_start: 0.5879 (OUTLIER) cc_final: 0.5546 (t0) REVERT: a 224 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8357 (mt-10) REVERT: a 234 ASP cc_start: 0.8357 (p0) cc_final: 0.8142 (p0) REVERT: a 271 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8143 (tt0) REVERT: a 279 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7558 (mt-10) REVERT: a 340 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7319 (tp30) outliers start: 35 outliers final: 22 residues processed: 191 average time/residue: 1.6759 time to fit residues: 347.8749 Evaluate side-chains 195 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain b residue 10 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 178 GLU Chi-restraints excluded: chain b residue 287 VAL Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain a residue 82 ASN Chi-restraints excluded: chain a residue 129 THR Chi-restraints excluded: chain a residue 134 VAL Chi-restraints excluded: chain a residue 157 ASP Chi-restraints excluded: chain a residue 224 GLU Chi-restraints excluded: chain a residue 236 ILE Chi-restraints excluded: chain a residue 239 SER Chi-restraints excluded: chain a residue 271 GLU Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain a residue 287 VAL Chi-restraints excluded: chain a residue 350 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 80 optimal weight: 7.9990 chunk 13 optimal weight: 20.0000 chunk 74 optimal weight: 7.9990 chunk 105 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 140 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 142 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 103 optimal weight: 0.0670 overall best weight: 3.4126 ------------------------------------------------------------------------------- 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 L 6 GLN a 147 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.127867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.104012 restraints weight = 78368.756| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 5.81 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3104 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 14790 Z= 0.226 Angle : 0.710 12.768 20117 Z= 0.373 Chirality : 0.047 0.159 2151 Planarity : 0.005 0.039 2575 Dihedral : 5.678 26.277 1995 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.47 % Favored : 94.48 % Rotamer: Outliers : 3.05 % Allowed : 12.44 % Favored : 84.51 % 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: -0.41 (0.20), residues: 1824 helix: 1.45 (0.42), residues: 157 sheet: 0.01 (0.25), residues: 478 loop : -0.63 (0.18), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP b 168 HIS 0.012 0.001 HIS b 2 PHE 0.017 0.002 PHE B 323 TYR 0.022 0.002 TYR M 105 ARG 0.005 0.001 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.04965 ( 419) hydrogen bonds : angle 5.67217 ( 1087) SS BOND : bond 0.00599 ( 28) SS BOND : angle 2.60303 ( 56) covalent geometry : bond 0.00559 (14762) covalent geometry : angle 0.69797 (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 205 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 1.592 Fit side-chains REVERT: H 112 GLN cc_start: 0.7303 (OUTLIER) cc_final: 0.6997 (mt0) REVERT: L 79 ARG cc_start: 0.7113 (mmm-85) cc_final: 0.6751 (mtp-110) REVERT: A 29 ARG cc_start: 0.6982 (OUTLIER) cc_final: 0.5981 (ptm-80) REVERT: B 192 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7335 (mm-30) REVERT: B 276 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7300 (mtp180) REVERT: b 48 GLN cc_start: 0.7325 (tt0) cc_final: 0.7071 (tt0) REVERT: b 343 SER cc_start: 0.8433 (m) cc_final: 0.8154 (p) REVERT: N 81 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.5635 (pm20) REVERT: a 102 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7759 (mm-40) REVERT: a 224 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7400 (mt-10) REVERT: a 271 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7561 (tt0) REVERT: a 279 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7045 (mt-10) REVERT: a 340 GLU cc_start: 0.7423 (mm-30) cc_final: 0.7104 (mm-30) outliers start: 36 outliers final: 22 residues processed: 192 average time/residue: 1.5529 time to fit residues: 322.3900 Evaluate side-chains 193 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 1.848 ------------------------------------------------------------------------------- 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 29 ARG 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 276 ARG Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain b residue 10 LYS Chi-restraints excluded: chain b residue 55 CYS Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 78 ILE Chi-restraints excluded: chain b residue 132 SER Chi-restraints excluded: chain b residue 178 GLU Chi-restraints excluded: chain b residue 287 VAL Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain a residue 129 THR Chi-restraints excluded: chain a residue 134 VAL Chi-restraints excluded: chain a residue 224 GLU Chi-restraints excluded: chain a residue 236 ILE Chi-restraints excluded: chain a residue 239 SER Chi-restraints excluded: chain a residue 271 GLU Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain a residue 287 VAL Chi-restraints excluded: chain a residue 350 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 28 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 142 optimal weight: 2.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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 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 = 0.131190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.108099 restraints weight = 91115.002| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 5.65 r_work: 0.2644 rms_B_bonded: 5.60 restraints_weight: 2.0000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2632 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2632 r_free = 0.2632 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.40 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 = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2631 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 14790 Z= 0.139 Angle : 0.611 11.333 20117 Z= 0.321 Chirality : 0.044 0.153 2151 Planarity : 0.004 0.038 2575 Dihedral : 5.327 23.720 1995 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.91 % Favored : 95.03 % Rotamer: Outliers : 3.05 % Allowed : 12.76 % Favored : 84.19 % 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: -0.26 (0.20), residues: 1824 helix: 1.65 (0.43), residues: 157 sheet: 0.14 (0.25), residues: 481 loop : -0.55 (0.18), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP b 168 HIS 0.008 0.001 HIS b 2 PHE 0.012 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 0.03958 ( 419) hydrogen bonds : angle 5.44337 ( 1087) SS BOND : bond 0.00389 ( 28) SS BOND : angle 1.99120 ( 56) covalent geometry : bond 0.00338 (14762) covalent geometry : angle 0.60297 (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 207 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 171 time to evaluate : 1.589 Fit side-chains REVERT: H 112 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.7251 (mt0) REVERT: A 29 ARG cc_start: 0.7119 (OUTLIER) cc_final: 0.6150 (ptm-80) REVERT: B 192 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8339 (mm-30) REVERT: B 276 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7977 (mtp180) REVERT: b 48 GLN cc_start: 0.7587 (tt0) cc_final: 0.7283 (tt0) REVERT: N 81 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6000 (pm20) REVERT: a 75 LEU cc_start: 0.7212 (tp) cc_final: 0.6975 (tp) REVERT: a 102 GLN cc_start: 0.8137 (mm-40) cc_final: 0.7681 (mm-40) REVERT: a 157 ASP cc_start: 0.5848 (OUTLIER) cc_final: 0.5522 (t0) REVERT: a 224 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8404 (mt-10) REVERT: a 271 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8167 (tt0) REVERT: a 279 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7530 (mt-10) REVERT: a 340 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7229 (mm-30) outliers start: 36 outliers final: 21 residues processed: 194 average time/residue: 1.4847 time to fit residues: 311.5293 Evaluate side-chains 192 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 1.561 ------------------------------------------------------------------------------- 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 29 ARG 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 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 178 GLU Chi-restraints excluded: chain b residue 287 VAL Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain a residue 129 THR Chi-restraints excluded: chain a residue 134 VAL Chi-restraints excluded: chain a residue 157 ASP Chi-restraints excluded: chain a residue 224 GLU Chi-restraints excluded: chain a residue 236 ILE Chi-restraints excluded: chain a residue 239 SER Chi-restraints excluded: chain a residue 271 GLU Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain a residue 287 VAL Chi-restraints excluded: chain a residue 350 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 148 optimal weight: 7.9990 chunk 168 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 147 optimal weight: 0.9990 chunk 96 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.130942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.107289 restraints weight = 87837.530| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 5.86 r_work: 0.2652 rms_B_bonded: 5.84 restraints_weight: 2.0000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 14790 Z= 0.135 Angle : 0.603 10.864 20117 Z= 0.317 Chirality : 0.044 0.150 2151 Planarity : 0.004 0.040 2575 Dihedral : 5.217 22.780 1995 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.13 % Favored : 94.81 % Rotamer: Outliers : 2.86 % Allowed : 13.14 % 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: -0.19 (0.20), residues: 1824 helix: 1.70 (0.43), residues: 157 sheet: 0.13 (0.24), residues: 494 loop : -0.47 (0.18), residues: 1173 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 0.016 0.002 PHE L 83 TYR 0.014 0.002 TYR M 35 ARG 0.003 0.000 ARG L 61 Details of bonding type rmsd hydrogen bonds : bond 0.03879 ( 419) hydrogen bonds : angle 5.36337 ( 1087) SS BOND : bond 0.00386 ( 28) SS BOND : angle 1.92461 ( 56) covalent geometry : bond 0.00327 (14762) covalent geometry : angle 0.59526 (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 202 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 169 time to evaluate : 1.794 Fit side-chains REVERT: H 112 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.7281 (mt0) REVERT: A 29 ARG cc_start: 0.7150 (OUTLIER) cc_final: 0.6185 (ptm-80) REVERT: B 276 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8012 (mtp180) REVERT: B 340 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7704 (mm-30) REVERT: b 48 GLN cc_start: 0.7601 (tt0) cc_final: 0.7308 (tt0) REVERT: b 309 GLU cc_start: 0.8095 (tp30) cc_final: 0.7311 (pm20) REVERT: b 343 SER cc_start: 0.8394 (m) cc_final: 0.8148 (p) REVERT: N 81 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6004 (pm20) REVERT: a 51 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7798 (mm-30) REVERT: a 75 LEU cc_start: 0.7297 (tp) cc_final: 0.7047 (tp) REVERT: a 102 GLN cc_start: 0.8173 (mm-40) cc_final: 0.7730 (mm-40) REVERT: a 157 ASP cc_start: 0.5916 (OUTLIER) cc_final: 0.5599 (t0) REVERT: a 224 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8443 (mt-10) REVERT: a 234 ASP cc_start: 0.8379 (p0) cc_final: 0.8116 (p0) REVERT: a 271 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8200 (tt0) REVERT: a 279 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7509 (mt-10) REVERT: a 340 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7230 (mm-30) outliers start: 33 outliers final: 20 residues processed: 190 average time/residue: 1.5797 time to fit residues: 324.9218 Evaluate side-chains 191 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 1.559 ------------------------------------------------------------------------------- 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 29 ARG 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 276 ARG Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain b residue 55 CYS Chi-restraints excluded: chain b residue 78 ILE Chi-restraints excluded: chain b residue 132 SER Chi-restraints excluded: chain b residue 178 GLU Chi-restraints excluded: chain b residue 287 VAL Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain a residue 51 GLU Chi-restraints excluded: chain a residue 129 THR Chi-restraints excluded: chain a residue 134 VAL Chi-restraints excluded: chain a residue 157 ASP Chi-restraints excluded: chain a residue 224 GLU Chi-restraints excluded: chain a residue 236 ILE Chi-restraints excluded: chain a residue 239 SER Chi-restraints excluded: chain a residue 271 GLU Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain a residue 287 VAL Chi-restraints excluded: chain a residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 149 optimal weight: 0.8980 chunk 18 optimal weight: 20.0000 chunk 126 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 175 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 174 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 46 optimal weight: 0.0020 chunk 160 optimal weight: 7.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- 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 6 GLN 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 = 0.132815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.109552 restraints weight = 89481.965| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 6.21 r_work: 0.2664 rms_B_bonded: 6.16 restraints_weight: 2.0000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 14790 Z= 0.101 Angle : 0.553 10.417 20117 Z= 0.291 Chirality : 0.042 0.151 2151 Planarity : 0.004 0.039 2575 Dihedral : 4.926 21.310 1995 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.80 % Favored : 95.15 % Rotamer: Outliers : 2.54 % Allowed : 13.71 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.24 (0.43), residues: 149 sheet: 0.28 (0.25), residues: 486 loop : -0.33 (0.19), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 118 HIS 0.005 0.001 HIS b 2 PHE 0.011 0.001 PHE H 80 TYR 0.013 0.001 TYR M 35 ARG 0.002 0.000 ARG b 69 Details of bonding type rmsd hydrogen bonds : bond 0.03298 ( 419) hydrogen bonds : angle 5.18105 ( 1087) SS BOND : bond 0.00301 ( 28) SS BOND : angle 1.52653 ( 56) covalent geometry : bond 0.00237 (14762) covalent geometry : angle 0.54826 (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 199 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 1.562 Fit side-chains REVERT: H 112 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.7236 (mt0) REVERT: b 48 GLN cc_start: 0.7566 (tt0) cc_final: 0.7311 (tt0) REVERT: b 309 GLU cc_start: 0.8093 (tp30) cc_final: 0.7309 (pm20) REVERT: a 75 LEU cc_start: 0.7144 (tp) cc_final: 0.6907 (tp) REVERT: a 102 GLN cc_start: 0.8148 (mm-40) cc_final: 0.7672 (mm-40) REVERT: a 157 ASP cc_start: 0.5887 (OUTLIER) cc_final: 0.5595 (t0) REVERT: a 224 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8438 (mt-10) REVERT: a 234 ASP cc_start: 0.8301 (p0) cc_final: 0.8044 (p0) REVERT: a 271 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8139 (tt0) REVERT: a 279 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7323 (mt-10) REVERT: a 340 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7338 (tp30) outliers start: 28 outliers final: 17 residues processed: 187 average time/residue: 1.5260 time to fit residues: 309.5528 Evaluate side-chains 189 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 1.567 ------------------------------------------------------------------------------- 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 37 ASP Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain B residue 140 LEU 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 b residue 280 CYS Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain a residue 129 THR Chi-restraints excluded: chain a residue 134 VAL Chi-restraints excluded: chain a residue 157 ASP Chi-restraints excluded: chain a residue 224 GLU Chi-restraints excluded: chain a residue 236 ILE Chi-restraints excluded: chain a residue 239 SER Chi-restraints excluded: chain a residue 271 GLU 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: 7.9990 chunk 38 optimal weight: 0.0170 chunk 169 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 176 optimal weight: 0.6980 chunk 89 optimal weight: 7.9990 chunk 67 optimal weight: 0.0470 chunk 70 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.4316 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.135579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.112773 restraints weight = 95443.485| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 6.31 r_work: 0.2712 rms_B_bonded: 6.29 restraints_weight: 2.0000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2689 r_free = 0.2689 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2689 r_free = 0.2689 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2689 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14790 Z= 0.085 Angle : 0.516 9.944 20117 Z= 0.270 Chirality : 0.042 0.140 2151 Planarity : 0.004 0.039 2575 Dihedral : 4.560 20.191 1995 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.41 % Favored : 95.48 % Rotamer: Outliers : 2.03 % Allowed : 14.48 % Favored : 83.49 % 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: 0.27 (0.21), residues: 1824 helix: 2.30 (0.43), residues: 151 sheet: 0.39 (0.25), residues: 470 loop : -0.14 (0.19), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 118 HIS 0.003 0.001 HIS b 2 PHE 0.012 0.001 PHE L 98 TYR 0.013 0.001 TYR M 35 ARG 0.003 0.000 ARG A 214 Details of bonding type rmsd hydrogen bonds : bond 0.02824 ( 419) hydrogen bonds : angle 4.94284 ( 1087) SS BOND : bond 0.00244 ( 28) SS BOND : angle 1.17458 ( 56) covalent geometry : bond 0.00195 (14762) covalent geometry : angle 0.51343 (20061) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11439.09 seconds wall clock time: 196 minutes 56.39 seconds (11816.39 seconds total)