Starting phenix.real_space_refine on Sun Jun 22 23:53:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jkf_36371/06_2025/8jkf_36371.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jkf_36371/06_2025/8jkf_36371.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jkf_36371/06_2025/8jkf_36371.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jkf_36371/06_2025/8jkf_36371.map" model { file = "/net/cci-nas-00/data/ceres_data/8jkf_36371/06_2025/8jkf_36371.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jkf_36371/06_2025/8jkf_36371.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 10856 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 11343 2.51 5 N 3201 2.21 5 O 3397 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18049 Number of models: 1 Model: "" Number of chains: 12 Chain: "H" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 889 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain: "L" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Chain: "h" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 889 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain: "l" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Chain: "a" Number of atoms: 2768 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 345, 2762 Classifications: {'peptide': 345} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 325} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 345, 2762 Classifications: {'peptide': 345} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 325} Chain breaks: 2 bond proxies already assigned to first conformer: 2830 Chain: "A" Number of atoms: 2855 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 355, 2848 Classifications: {'peptide': 355} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 335} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 355, 2848 Classifications: {'peptide': 355} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 335} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 2922 Chain: "M" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 889 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain: "N" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Chain: "B" Number of atoms: 2845 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 354, 2838 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 334} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 354, 2838 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 334} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 2911 Chain: "b" Number of atoms: 2769 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 348, 2763 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 16 Conformer: "B" Number of residues, atoms: 348, 2763 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 16 bond proxies already assigned to first conformer: 2829 Chain: "m" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 889 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain: "n" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ASER a 58 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER a 58 " occ=0.50 residue: pdb=" N AVAL A 60 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL A 60 " occ=0.50 residue: pdb=" N AVAL B 60 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL B 60 " occ=0.50 residue: pdb=" N ASER b 58 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER b 58 " occ=0.50 Time building chain proxies: 16.05, per 1000 atoms: 0.89 Number of scatterers: 18049 At special positions: 0 Unit cell: (94.35, 115.6, 170, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 3397 8.00 N 3201 7.00 C 11343 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 95 " distance=2.04 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 88 " distance=2.04 Simple disulfide: pdb=" SG CYS a 4 " - pdb=" SG CYS a 15 " distance=2.04 Simple disulfide: pdb=" SG CYS a 55 " - pdb=" SG CYS a 143 " distance=2.03 Simple disulfide: pdb=" SG CYS a 179 " - pdb=" SG CYS a 223 " distance=2.03 Simple disulfide: pdb=" SG CYS a 280 " - pdb=" SG CYS a 329 " distance=2.03 Simple disulfide: pdb=" SG CYS a 291 " - pdb=" SG CYS a 312 " distance=2.03 Simple disulfide: pdb=" SG CYS a 313 " - pdb=" SG CYS a 316 " distance=2.03 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 15 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 143 " distance=2.03 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 223 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 312 " distance=2.04 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 316 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 95 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 15 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 143 " distance=2.03 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 223 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 329 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 312 " distance=2.04 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 316 " distance=2.03 Simple disulfide: pdb=" SG CYS b 4 " - pdb=" SG CYS b 15 " distance=2.03 Simple disulfide: pdb=" SG CYS b 55 " - pdb=" SG CYS b 143 " distance=2.03 Simple disulfide: pdb=" SG CYS b 179 " - pdb=" SG CYS b 223 " distance=2.03 Simple disulfide: pdb=" SG CYS b 280 " - pdb=" SG CYS b 329 " distance=2.03 Simple disulfide: pdb=" SG CYS b 291 " - pdb=" SG CYS b 312 " distance=2.04 Simple disulfide: pdb=" SG CYS b 313 " - pdb=" SG CYS b 316 " distance=2.03 Simple disulfide: pdb=" SG CYS m 22 " - pdb=" SG CYS m 95 " distance=2.04 Simple disulfide: pdb=" SG CYS n 23 " - pdb=" SG CYS n 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.25 Conformation dependent library (CDL) restraints added in 3.8 seconds 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4190 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 42 sheets defined 13.8% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.00 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.743A pdb=" N ASN H 32 " --> pdb=" O VAL H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'L' and resid 49 through 53 removed outlier: 3.967A pdb=" N SER L 53 " --> pdb=" O ALA L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.081A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'h' and resid 28 through 32 removed outlier: 3.824A pdb=" N ASN h 32 " --> pdb=" O VAL h 29 " (cutoff:3.500A) Processing helix chain 'h' and resid 86 through 90 Processing helix chain 'l' and resid 79 through 83 removed outlier: 4.078A pdb=" N PHE l 83 " --> pdb=" O PRO l 80 " (cutoff:3.500A) Processing helix chain 'a' and resid 38 through 52 Processing helix chain 'a' and resid 61 through 81 removed outlier: 3.699A pdb=" N ASN a 65 " --> pdb=" O SER a 61 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N GLY a 73 " --> pdb=" O ARG a 69 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N GLU a 74 " --> pdb=" O SER a 70 " (cutoff:3.500A) Processing helix chain 'a' and resid 144 through 146 No H-bonds generated for 'chain 'a' and resid 144 through 146' Processing helix chain 'a' and resid 180 through 183 removed outlier: 3.704A pdb=" N VAL a 183 " --> pdb=" O ASP a 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 180 through 183' Processing helix chain 'a' and resid 226 through 230 Processing helix chain 'a' and resid 244 through 248 Processing helix chain 'a' and resid 252 through 256 removed outlier: 3.660A pdb=" N THR a 256 " --> pdb=" O HIS a 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.629A pdb=" N ARG A 31 " --> pdb=" O TRP A 28 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR A 32 " --> pdb=" O ARG A 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 28 through 32' Processing helix chain 'A' and resid 38 through 52 Processing helix chain 'A' and resid 61 through 82 removed outlier: 4.880A pdb=" N GLY A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N GLU A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 180 through 183 removed outlier: 3.854A pdb=" N VAL A 183 " --> pdb=" O ASP A 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 183' Processing helix chain 'A' and resid 237 through 241 removed outlier: 3.870A pdb=" N LEU A 241 " --> pdb=" O GLU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.595A pdb=" N THR A 256 " --> pdb=" O HIS A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 345 removed outlier: 4.099A pdb=" N ASN A 344 " --> pdb=" O PRO A 341 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.630A pdb=" N ASN M 32 " --> pdb=" O VAL M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'M' and resid 86 through 90 Processing helix chain 'B' and resid 38 through 53 Processing helix chain 'B' and resid 61 through 82 removed outlier: 5.020A pdb=" N GLY B 73 " --> pdb=" O ARG B 69 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N GLU B 74 " --> pdb=" O SER B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 146 No H-bonds generated for 'chain 'B' and resid 144 through 146' Processing helix chain 'B' and resid 180 through 183 removed outlier: 3.793A pdb=" N VAL B 183 " --> pdb=" O ASP B 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 180 through 183' Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.524A pdb=" N THR B 230 " --> pdb=" O LYS B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 241 removed outlier: 3.776A pdb=" N LEU B 241 " --> pdb=" O GLU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 248 Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.772A pdb=" N THR B 256 " --> pdb=" O HIS B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 345 removed outlier: 3.557A pdb=" N ASN B 344 " --> pdb=" O PRO B 341 " (cutoff:3.500A) Processing helix chain 'b' and resid 38 through 52 Processing helix chain 'b' and resid 61 through 82 removed outlier: 3.592A pdb=" N ASN b 65 " --> pdb=" O SER b 61 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N GLY b 73 " --> pdb=" O ARG b 69 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N GLU b 74 " --> pdb=" O SER b 70 " (cutoff:3.500A) Processing helix chain 'b' and resid 144 through 146 No H-bonds generated for 'chain 'b' and resid 144 through 146' Processing helix chain 'b' and resid 180 through 183 removed outlier: 3.797A pdb=" N VAL b 183 " --> pdb=" O ASP b 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 180 through 183' Processing helix chain 'b' and resid 226 through 230 Processing helix chain 'b' and resid 244 through 248 Processing helix chain 'b' and resid 252 through 256 removed outlier: 3.624A pdb=" N THR b 256 " --> pdb=" O HIS b 253 " (cutoff:3.500A) Processing helix chain 'm' and resid 28 through 32 removed outlier: 3.735A pdb=" N ASN m 31 " --> pdb=" O THR m 28 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN m 32 " --> pdb=" O VAL m 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 28 through 32' Processing helix chain 'm' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.193A pdb=" N GLY H 10 " --> pdb=" O THR H 112 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TYR H 33 " --> pdb=" O GLU H 98 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N MET H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.193A pdb=" N GLY H 10 " --> pdb=" O THR H 112 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N TYR H 104 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.504A pdb=" N THR L 72 " --> pdb=" O GLY L 65 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 removed outlier: 7.002A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.751A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'h' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'h' and resid 10 through 12 removed outlier: 6.071A pdb=" N GLY h 10 " --> pdb=" O THR h 112 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR h 33 " --> pdb=" O GLU h 98 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N MET h 34 " --> pdb=" O ILE h 50 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE h 50 " --> pdb=" O MET h 34 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP h 36 " --> pdb=" O VAL h 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'h' and resid 10 through 12 removed outlier: 6.071A pdb=" N GLY h 10 " --> pdb=" O THR h 112 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR h 104 " --> pdb=" O ARG h 97 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'l' and resid 4 through 7 Processing sheet with id=AB2, first strand: chain 'l' and resid 10 through 13 removed outlier: 3.580A pdb=" N ALA l 13 " --> pdb=" O GLU l 105 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU l 33 " --> pdb=" O TYR l 49 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N TYR l 49 " --> pdb=" O LEU l 33 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N TRP l 35 " --> pdb=" O LEU l 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'l' and resid 10 through 13 removed outlier: 3.580A pdb=" N ALA l 13 " --> pdb=" O GLU l 105 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N THR l 97 " --> pdb=" O GLN l 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'a' and resid 1 through 7 removed outlier: 3.795A pdb=" N HIS a 1 " --> pdb=" O GLY a 18 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N HIS A 1 " --> pdb=" O GLY A 18 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N HIS a 2 " --> pdb=" O VAL A 6 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'a' and resid 33 through 36 removed outlier: 6.051A pdb=" N LYS a 33 " --> pdb=" O VAL a 167 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N LEU a 169 " --> pdb=" O LYS a 33 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N HIS a 35 " --> pdb=" O LEU a 169 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N VAL a 171 " --> pdb=" O HIS a 35 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'a' and resid 56 through 57 removed outlier: 7.155A pdb=" N GLY a 56 " --> pdb=" O ALA a 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'a' and resid 87 through 89 removed outlier: 6.535A pdb=" N THR a 87 " --> pdb=" O PHE a 133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'a' and resid 329 through 331 removed outlier: 3.608A pdb=" N GLU a 274 " --> pdb=" O ARG a 324 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N PHE a 277 " --> pdb=" O LYS a 213 " (cutoff:3.500A) removed outlier: 9.214A pdb=" N LYS a 213 " --> pdb=" O PHE a 277 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N LEU a 212 " --> pdb=" O GLU a 205 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N GLU a 205 " --> pdb=" O LEU a 212 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU a 192 " --> pdb=" O LYS a 189 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU A 192 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N GLU A 205 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N LEU A 212 " --> pdb=" O GLU A 205 " (cutoff:3.500A) removed outlier: 9.091A pdb=" N LYS A 213 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N PHE A 277 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'a' and resid 284 through 287 removed outlier: 6.299A pdb=" N LYS a 284 " --> pdb=" O TRP a 311 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N CYS a 313 " --> pdb=" O LYS a 284 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N HIS a 286 " --> pdb=" O CYS a 313 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 33 through 35 removed outlier: 6.383A pdb=" N LYS A 33 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU A 169 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N HIS A 35 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N VAL A 171 " --> pdb=" O HIS A 35 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N SER A 166 " --> pdb=" O HIS A 158 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N HIS A 158 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TRP A 168 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 56 through 57 removed outlier: 7.334A pdb=" N GLY A 56 " --> pdb=" O ALA A 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 87 through 90 removed outlier: 6.316A pdb=" N THR A 87 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL A 135 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL A 89 " --> pdb=" O VAL A 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'A' and resid 284 through 287 Processing sheet with id=AC5, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AC6, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.301A pdb=" N GLY M 10 " --> pdb=" O THR M 112 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TYR M 33 " --> pdb=" O GLU M 98 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N MET M 34 " --> pdb=" O ILE M 50 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILE M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.301A pdb=" N GLY M 10 " --> pdb=" O THR M 112 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N TYR M 104 " --> pdb=" O ARG M 97 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AC9, first strand: chain 'N' and resid 10 through 13 Processing sheet with id=AD1, first strand: chain 'N' and resid 53 through 54 removed outlier: 5.549A pdb=" N LEU N 46 " --> pdb=" O GLN N 37 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N GLN N 37 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR N 97 " --> pdb=" O GLN N 90 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1 through 7 removed outlier: 5.306A pdb=" N HIS B 1 " --> pdb=" O GLY B 18 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU B 12 " --> pdb=" O ASP B 7 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N HIS b 2 " --> pdb=" O VAL B 6 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 33 through 35 removed outlier: 6.641A pdb=" N LYS B 33 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N LEU B 169 " --> pdb=" O LYS B 33 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N HIS B 35 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N VAL B 171 " --> pdb=" O HIS B 35 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N SER B 166 " --> pdb=" O HIS B 158 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N HIS B 158 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TRP B 168 " --> pdb=" O GLU B 156 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 87 through 89 removed outlier: 6.233A pdb=" N THR B 87 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL B 135 " --> pdb=" O THR B 87 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL B 89 " --> pdb=" O VAL B 135 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 321 through 324 removed outlier: 4.696A pdb=" N PHE B 277 " --> pdb=" O LYS B 213 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N LYS B 213 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N LEU B 212 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N GLU B 205 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG B 214 " --> pdb=" O GLU B 203 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU B 192 " --> pdb=" O LYS B 189 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N GLU b 205 " --> pdb=" O LEU b 212 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LEU b 212 " --> pdb=" O GLU b 205 " (cutoff:3.500A) removed outlier: 9.423A pdb=" N LYS b 213 " --> pdb=" O PHE b 277 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N PHE b 277 " --> pdb=" O LYS b 213 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU b 274 " --> pdb=" O ARG b 324 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY b 328 " --> pdb=" O ALA b 325 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 285 through 287 removed outlier: 6.280A pdb=" N HIS B 286 " --> pdb=" O CYS B 313 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'b' and resid 34 through 36 Processing sheet with id=AD8, first strand: chain 'b' and resid 87 through 89 removed outlier: 6.379A pdb=" N THR b 87 " --> pdb=" O PHE b 133 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL b 135 " --> pdb=" O THR b 87 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL b 89 " --> pdb=" O VAL b 135 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLY b 56 " --> pdb=" O ALA b 149 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'b' and resid 285 through 287 Processing sheet with id=AE1, first strand: chain 'm' and resid 3 through 7 removed outlier: 3.534A pdb=" N THR m 77 " --> pdb=" O ASP m 72 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'm' and resid 10 through 12 removed outlier: 4.049A pdb=" N TYR m 33 " --> pdb=" O GLU m 98 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N MET m 34 " --> pdb=" O ILE m 50 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE m 50 " --> pdb=" O MET m 34 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N TRP m 36 " --> pdb=" O VAL m 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'm' and resid 10 through 12 removed outlier: 4.347A pdb=" N TYR m 104 " --> pdb=" O ARG m 97 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'n' and resid 4 through 7 removed outlier: 3.788A pdb=" N VAL n 19 " --> pdb=" O ILE n 75 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'n' and resid 10 through 13 removed outlier: 3.542A pdb=" N ALA n 13 " --> pdb=" O GLU n 105 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLN n 37 " --> pdb=" O LEU n 46 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU n 46 " --> pdb=" O GLN n 37 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'n' and resid 10 through 13 removed outlier: 3.542A pdb=" N ALA n 13 " --> pdb=" O GLU n 105 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR n 97 " --> pdb=" O GLN n 90 " (cutoff:3.500A) 582 hydrogen bonds defined for protein. 1464 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.89 Time building geometry restraints manager: 5.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5923 1.34 - 1.46: 4569 1.46 - 1.59: 7872 1.59 - 1.71: 0 1.71 - 1.83: 152 Bond restraints: 18516 Sorted by residual: bond pdb=" N VAL L 51 " pdb=" CA VAL L 51 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.25e-02 6.40e+03 1.36e+01 bond pdb=" N VAL N 51 " pdb=" CA VAL N 51 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.25e-02 6.40e+03 1.14e+01 bond pdb=" N VAL l 51 " pdb=" CA VAL l 51 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.10e+01 bond pdb=" N VAL n 51 " pdb=" CA VAL n 51 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.09e+01 bond pdb=" N GLY N 65 " pdb=" CA GLY N 65 " ideal model delta sigma weight residual 1.447 1.477 -0.030 9.30e-03 1.16e+04 1.03e+01 ... (remaining 18511 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 24388 1.64 - 3.28: 639 3.28 - 4.92: 87 4.92 - 6.56: 12 6.56 - 8.19: 2 Bond angle restraints: 25128 Sorted by residual: angle pdb=" CA ALA N 50 " pdb=" C ALA N 50 " pdb=" O ALA N 50 " ideal model delta sigma weight residual 121.84 117.14 4.70 1.16e+00 7.43e-01 1.64e+01 angle pdb=" CA ALA n 50 " pdb=" C ALA n 50 " pdb=" O ALA n 50 " ideal model delta sigma weight residual 121.84 117.16 4.68 1.16e+00 7.43e-01 1.63e+01 angle pdb=" CA GLY N 64 " pdb=" C GLY N 64 " pdb=" O GLY N 64 " ideal model delta sigma weight residual 121.57 118.08 3.49 8.70e-01 1.32e+00 1.61e+01 angle pdb=" CA ALA L 50 " pdb=" C ALA L 50 " pdb=" O ALA L 50 " ideal model delta sigma weight residual 121.54 116.90 4.64 1.16e+00 7.43e-01 1.60e+01 angle pdb=" CA ALA l 50 " pdb=" C ALA l 50 " pdb=" O ALA l 50 " ideal model delta sigma weight residual 121.84 117.26 4.58 1.16e+00 7.43e-01 1.56e+01 ... (remaining 25123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 10088 17.85 - 35.70: 763 35.70 - 53.54: 144 53.54 - 71.39: 23 71.39 - 89.24: 6 Dihedral angle restraints: 11024 sinusoidal: 4477 harmonic: 6547 Sorted by residual: dihedral pdb=" CB CYS a 291 " pdb=" SG CYS a 291 " pdb=" SG CYS a 312 " pdb=" CB CYS a 312 " ideal model delta sinusoidal sigma weight residual -86.00 -147.43 61.43 1 1.00e+01 1.00e-02 5.01e+01 dihedral pdb=" CA SER N 28 " pdb=" C SER N 28 " pdb=" N VAL N 29 " pdb=" CA VAL N 29 " ideal model delta harmonic sigma weight residual 180.00 157.95 22.05 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA SER L 28 " pdb=" C SER L 28 " pdb=" N VAL L 29 " pdb=" CA VAL L 29 " ideal model delta harmonic sigma weight residual 180.00 159.65 20.35 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 11021 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2356 0.068 - 0.135: 314 0.135 - 0.203: 14 0.203 - 0.270: 0 0.270 - 0.338: 1 Chirality restraints: 2685 Sorted by residual: chirality pdb=" CB VAL L 51 " pdb=" CA VAL L 51 " pdb=" CG1 VAL L 51 " pdb=" CG2 VAL L 51 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" CA ILE N 48 " pdb=" N ILE N 48 " pdb=" C ILE N 48 " pdb=" CB ILE N 48 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA ILE n 48 " pdb=" N ILE n 48 " pdb=" C ILE n 48 " pdb=" CB ILE n 48 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.76e-01 ... (remaining 2682 not shown) Planarity restraints: 3216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN n 79 " -0.045 5.00e-02 4.00e+02 6.74e-02 7.27e+00 pdb=" N PRO n 80 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO n 80 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO n 80 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR h 33 " -0.015 2.00e-02 2.50e+03 1.63e-02 5.33e+00 pdb=" CG TYR h 33 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR h 33 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR h 33 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR h 33 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR h 33 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR h 33 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR h 33 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 33 " 0.015 2.00e-02 2.50e+03 1.55e-02 4.81e+00 pdb=" CG TYR H 33 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR H 33 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR H 33 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR H 33 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR H 33 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR H 33 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR H 33 " 0.003 2.00e-02 2.50e+03 ... (remaining 3213 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 133 2.64 - 3.20: 14601 3.20 - 3.77: 25631 3.77 - 4.33: 38965 4.33 - 4.90: 65438 Nonbonded interactions: 144768 Sorted by model distance: nonbonded pdb=" O GLY B 159 " pdb=" OG1 THR B 165 " model vdw 2.069 3.040 nonbonded pdb=" O LEU B 231 " pdb=" OG SER B 252 " model vdw 2.167 3.040 nonbonded pdb=" OG SER B 297 " pdb=" O TYR B 331 " model vdw 2.191 3.040 nonbonded pdb=" OG SER b 297 " pdb=" O TYR b 331 " model vdw 2.200 3.040 nonbonded pdb=" OG SER a 297 " pdb=" O TYR a 331 " model vdw 2.234 3.040 ... (remaining 144763 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 25 or resid 30 through 57 or resid 59 or resid 6 \ 1 through 117 or (resid 118 and (name N or name CA or name C or name O or name C \ B )) or resid 123 through 352)) selection = (chain 'B' and (resid 1 through 25 or resid 30 through 57 or resid 59 or resid 6 \ 1 through 117 or (resid 118 and (name N or name CA or name C or name O or name C \ B )) or resid 123 through 352)) selection = (chain 'a' and (resid 1 through 57 or resid 59 or resid 61 through 117 or (resid \ 118 and (name N or name CA or name C or name O or name CB )) or resid 123 throu \ gh 352)) selection = (chain 'b' and (resid 1 through 57 or resid 59 or resid 61 through 118 or resid \ 123 through 352)) } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'h' selection = chain 'm' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'l' selection = chain 'n' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.020 Extract box with map and model: 0.700 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 53.270 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.140 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: 0.010 Load rotamer database and sin/cos tables:13.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18548 Z= 0.245 Angle : 0.639 8.194 25192 Z= 0.375 Chirality : 0.046 0.338 2685 Planarity : 0.004 0.067 3216 Dihedral : 12.924 89.239 6738 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.26 % Favored : 95.69 % Rotamer: Outliers : 0.96 % Allowed : 0.76 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.18), residues: 2264 helix: 1.69 (0.41), residues: 148 sheet: -0.55 (0.20), residues: 738 loop : -0.58 (0.17), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 115 HIS 0.006 0.001 HIS B 1 PHE 0.009 0.002 PHE n 98 TYR 0.038 0.002 TYR h 33 ARG 0.015 0.000 ARG b 31 Details of bonding type rmsd hydrogen bonds : bond 0.22738 ( 555) hydrogen bonds : angle 9.09504 ( 1464) SS BOND : bond 0.00447 ( 32) SS BOND : angle 1.50277 ( 64) covalent geometry : bond 0.00474 (18516) covalent geometry : angle 0.63556 (25128) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 339 time to evaluate : 1.901 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: h 13 GLN cc_start: 0.8045 (mp10) cc_final: 0.7833 (mm-40) REVERT: l 9 SER cc_start: 0.8266 (m) cc_final: 0.8017 (p) REVERT: N 66 ASP cc_start: 0.6869 (OUTLIER) cc_final: 0.6588 (p0) REVERT: B 0 HIS cc_start: 0.5816 (p-80) cc_final: 0.5364 (p90) REVERT: B 33 LYS cc_start: 0.8348 (ptmt) cc_final: 0.8063 (ptpp) REVERT: B 109 ASN cc_start: 0.7333 (m-40) cc_final: 0.7057 (t0) REVERT: b 31 ARG cc_start: 0.6363 (ttm110) cc_final: 0.6023 (ttt90) REVERT: b 123 PHE cc_start: 0.4408 (OUTLIER) cc_final: 0.3645 (p90) outliers start: 16 outliers final: 3 residues processed: 350 average time/residue: 1.3784 time to fit residues: 534.9055 Evaluate side-chains 239 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 234 time to evaluate : 2.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain A residue 0 HIS Chi-restraints excluded: chain N residue 66 ASP Chi-restraints excluded: chain b residue 110 GLU Chi-restraints excluded: chain b residue 123 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 187 optimal weight: 4.9990 chunk 168 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 201 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 100 GLN l 100 GLN A 1 HIS B 0 HIS B 286 HIS b 2 HIS m 107 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.137661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.101686 restraints weight = 67004.247| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 3.78 r_work: 0.2910 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2903 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2903 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 18548 Z= 0.272 Angle : 0.738 10.274 25192 Z= 0.389 Chirality : 0.049 0.239 2685 Planarity : 0.006 0.053 3216 Dihedral : 5.934 68.955 2521 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.31 % Favored : 95.65 % Rotamer: Outliers : 3.09 % Allowed : 10.29 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.18), residues: 2264 helix: 1.09 (0.39), residues: 153 sheet: -0.37 (0.20), residues: 736 loop : -0.65 (0.17), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP a 168 HIS 0.009 0.002 HIS B 286 PHE 0.016 0.002 PHE A 323 TYR 0.034 0.002 TYR H 33 ARG 0.010 0.001 ARG b 41 Details of bonding type rmsd hydrogen bonds : bond 0.05879 ( 555) hydrogen bonds : angle 6.37214 ( 1464) SS BOND : bond 0.00686 ( 32) SS BOND : angle 1.87018 ( 64) covalent geometry : bond 0.00657 (18516) covalent geometry : angle 0.73301 (25128) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 263 time to evaluate : 2.089 Fit side-chains revert: symmetry clash REVERT: H 29 VAL cc_start: 0.8993 (m) cc_final: 0.8724 (t) REVERT: a 40 ARG cc_start: 0.6822 (mtm-85) cc_final: 0.6533 (ttm110) REVERT: A 12 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7488 (mt-10) REVERT: A 116 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7815 (pttm) REVERT: A 128 LYS cc_start: 0.7988 (ttmm) cc_final: 0.7586 (tttt) REVERT: A 284 LYS cc_start: 0.7962 (mtpp) cc_final: 0.7425 (tttp) REVERT: A 286 HIS cc_start: 0.8072 (m-70) cc_final: 0.7800 (m-70) REVERT: A 309 GLU cc_start: 0.7087 (tm-30) cc_final: 0.6868 (tm-30) REVERT: M 3 GLN cc_start: 0.8356 (tt0) cc_final: 0.8117 (mm110) REVERT: B 63 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.8046 (ttp) REVERT: B 94 LYS cc_start: 0.8292 (mmmm) cc_final: 0.7531 (mtmt) REVERT: B 109 ASN cc_start: 0.7237 (m-40) cc_final: 0.6959 (m-40) REVERT: b 31 ARG cc_start: 0.6439 (ttm110) cc_final: 0.5963 (ttt90) REVERT: b 164 HIS cc_start: 0.6252 (OUTLIER) cc_final: 0.6043 (p90) REVERT: b 261 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8194 (mtt-85) REVERT: b 274 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.7870 (tm-30) outliers start: 58 outliers final: 29 residues processed: 296 average time/residue: 1.3486 time to fit residues: 445.9487 Evaluate side-chains 264 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 230 time to evaluate : 1.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain h residue 54 SER Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 20 THR Chi-restraints excluded: chain l residue 53 SER Chi-restraints excluded: chain l residue 54 LEU Chi-restraints excluded: chain a residue 168 TRP Chi-restraints excluded: chain A residue 0 HIS Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain b residue 110 GLU Chi-restraints excluded: chain b residue 164 HIS Chi-restraints excluded: chain b residue 261 ARG Chi-restraints excluded: chain b residue 274 GLU Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 87 VAL Chi-restraints excluded: chain m residue 112 THR Chi-restraints excluded: chain n residue 5 THR Chi-restraints excluded: chain n residue 9 SER Chi-restraints excluded: chain n residue 63 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 137 optimal weight: 0.8980 chunk 208 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 200 optimal weight: 7.9990 chunk 79 optimal weight: 0.7980 chunk 163 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 107 GLN L 27 GLN L 100 GLN l 100 GLN a 0 HIS a 263 GLN A 113 HIS N 100 GLN B 0 HIS b 131 ASN m 107 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.139023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.104005 restraints weight = 50536.377| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 3.20 r_work: 0.2941 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 18548 Z= 0.155 Angle : 0.607 8.260 25192 Z= 0.321 Chirality : 0.044 0.192 2685 Planarity : 0.005 0.049 3216 Dihedral : 5.378 57.810 2517 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.82 % Favored : 96.14 % Rotamer: Outliers : 2.99 % Allowed : 12.42 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.18), residues: 2264 helix: 1.52 (0.40), residues: 153 sheet: -0.27 (0.20), residues: 713 loop : -0.60 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP a 168 HIS 0.012 0.001 HIS A 113 PHE 0.011 0.002 PHE n 98 TYR 0.013 0.001 TYR H 94 ARG 0.007 0.000 ARG b 41 Details of bonding type rmsd hydrogen bonds : bond 0.04606 ( 555) hydrogen bonds : angle 5.87839 ( 1464) SS BOND : bond 0.00471 ( 32) SS BOND : angle 1.35189 ( 64) covalent geometry : bond 0.00370 (18516) covalent geometry : angle 0.60388 (25128) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 242 time to evaluate : 2.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7595 (mt0) REVERT: H 29 VAL cc_start: 0.8925 (m) cc_final: 0.8632 (t) REVERT: L 14 SER cc_start: 0.8341 (OUTLIER) cc_final: 0.7972 (m) REVERT: L 79 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7191 (mp10) REVERT: h 19 ARG cc_start: 0.8726 (ttt-90) cc_final: 0.8502 (ttt180) REVERT: l 53 SER cc_start: 0.8522 (OUTLIER) cc_final: 0.8316 (m) REVERT: a 40 ARG cc_start: 0.6749 (mtm-85) cc_final: 0.6518 (ttm110) REVERT: a 263 GLN cc_start: 0.8937 (mm-40) cc_final: 0.8726 (mm110) REVERT: A 12 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7401 (mt-10) REVERT: A 116 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7785 (pttm) REVERT: A 128 LYS cc_start: 0.7898 (ttmm) cc_final: 0.7537 (tttt) REVERT: A 220 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.7291 (mmt) REVERT: A 284 LYS cc_start: 0.7914 (mtpp) cc_final: 0.7510 (tttp) REVERT: A 286 HIS cc_start: 0.8012 (m-70) cc_final: 0.7755 (m-70) REVERT: A 309 GLU cc_start: 0.6956 (tm-30) cc_final: 0.6680 (tm-30) REVERT: B 63 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7968 (ttp) REVERT: B 94 LYS cc_start: 0.8274 (mmmm) cc_final: 0.7487 (mtmt) REVERT: B 109 ASN cc_start: 0.7253 (m-40) cc_final: 0.6982 (m-40) REVERT: B 340 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.6604 (mt-10) REVERT: b 31 ARG cc_start: 0.6361 (ttm110) cc_final: 0.5991 (ttt90) REVERT: b 164 HIS cc_start: 0.6303 (OUTLIER) cc_final: 0.6000 (p90) REVERT: b 170 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.6817 (tppt) REVERT: m 76 ASN cc_start: 0.8732 (t0) cc_final: 0.8360 (t0) REVERT: n 103 LYS cc_start: 0.8237 (ttmm) cc_final: 0.7949 (tttp) outliers start: 56 outliers final: 28 residues processed: 273 average time/residue: 1.4192 time to fit residues: 430.7637 Evaluate side-chains 267 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 229 time to evaluate : 2.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 6 GLU Chi-restraints excluded: chain h residue 46 GLU Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 22 THR Chi-restraints excluded: chain l residue 53 SER Chi-restraints excluded: chain l residue 54 LEU Chi-restraints excluded: chain a residue 168 TRP Chi-restraints excluded: chain A residue -2 HIS Chi-restraints excluded: chain A residue 0 HIS Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain b residue 110 GLU Chi-restraints excluded: chain b residue 164 HIS Chi-restraints excluded: chain b residue 170 LYS Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 87 VAL Chi-restraints excluded: chain m residue 112 THR Chi-restraints excluded: chain n residue 5 THR Chi-restraints excluded: chain n residue 9 SER Chi-restraints excluded: chain n residue 63 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 65 optimal weight: 0.9980 chunk 193 optimal weight: 0.6980 chunk 101 optimal weight: 4.9990 chunk 174 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 161 optimal weight: 9.9990 chunk 125 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 107 GLN L 27 GLN l 100 GLN a 0 HIS N 100 GLN B 0 HIS m 107 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.139668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.104631 restraints weight = 52292.446| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 3.25 r_work: 0.2967 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18548 Z= 0.129 Angle : 0.569 7.565 25192 Z= 0.301 Chirality : 0.043 0.185 2685 Planarity : 0.004 0.044 3216 Dihedral : 5.113 51.384 2517 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.69 % Favored : 96.27 % Rotamer: Outliers : 3.09 % Allowed : 13.84 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.18), residues: 2264 helix: 1.72 (0.41), residues: 153 sheet: -0.15 (0.21), residues: 659 loop : -0.54 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP a 168 HIS 0.005 0.001 HIS A 2 PHE 0.010 0.001 PHE b 163 TYR 0.013 0.001 TYR H 94 ARG 0.010 0.000 ARG b 41 Details of bonding type rmsd hydrogen bonds : bond 0.04043 ( 555) hydrogen bonds : angle 5.53427 ( 1464) SS BOND : bond 0.00402 ( 32) SS BOND : angle 1.16756 ( 64) covalent geometry : bond 0.00305 (18516) covalent geometry : angle 0.56620 (25128) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 247 time to evaluate : 2.038 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7595 (mt0) REVERT: H 29 VAL cc_start: 0.8927 (m) cc_final: 0.8624 (t) REVERT: L 14 SER cc_start: 0.8372 (OUTLIER) cc_final: 0.7977 (m) REVERT: L 79 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7182 (mp10) REVERT: h 19 ARG cc_start: 0.8729 (ttt-90) cc_final: 0.8511 (ttt180) REVERT: l 54 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7965 (tp) REVERT: a 40 ARG cc_start: 0.6729 (mtm-85) cc_final: 0.6411 (ttm110) REVERT: a 261 ARG cc_start: 0.8552 (mtt90) cc_final: 0.8220 (mtm110) REVERT: a 263 GLN cc_start: 0.8919 (mm-40) cc_final: 0.8716 (mm110) REVERT: A -2 HIS cc_start: 0.6126 (OUTLIER) cc_final: 0.5783 (t-90) REVERT: A 12 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7375 (mt-10) REVERT: A 85 GLN cc_start: 0.8288 (mp10) cc_final: 0.8042 (mp10) REVERT: A 116 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7834 (pttm) REVERT: A 125 ARG cc_start: 0.6990 (mpp-170) cc_final: 0.6740 (tpp-160) REVERT: A 128 LYS cc_start: 0.7772 (ttmm) cc_final: 0.7414 (tttt) REVERT: A 284 LYS cc_start: 0.7868 (mtpp) cc_final: 0.7429 (tttp) REVERT: A 286 HIS cc_start: 0.7981 (m-70) cc_final: 0.7674 (m-70) REVERT: A 309 GLU cc_start: 0.6942 (tm-30) cc_final: 0.6644 (tm-30) REVERT: B 40 ARG cc_start: 0.6265 (OUTLIER) cc_final: 0.5951 (mtm180) REVERT: B 63 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.7971 (ttp) REVERT: B 94 LYS cc_start: 0.8276 (mmmm) cc_final: 0.7492 (mtmt) REVERT: B 109 ASN cc_start: 0.7215 (m-40) cc_final: 0.6969 (t0) REVERT: B 116 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7829 (ttmm) REVERT: b 31 ARG cc_start: 0.6346 (ttm110) cc_final: 0.6018 (ttt90) REVERT: b 37 ASP cc_start: 0.7204 (OUTLIER) cc_final: 0.6976 (m-30) REVERT: b 67 MET cc_start: 0.8114 (ttt) cc_final: 0.7900 (ttp) REVERT: b 164 HIS cc_start: 0.6282 (OUTLIER) cc_final: 0.5922 (p90) REVERT: b 170 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.6803 (tppt) REVERT: b 261 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.8135 (mtt-85) REVERT: m 76 ASN cc_start: 0.8685 (t0) cc_final: 0.8319 (t0) REVERT: n 75 ILE cc_start: 0.7272 (mm) cc_final: 0.7001 (mm) outliers start: 57 outliers final: 23 residues processed: 276 average time/residue: 1.2740 time to fit residues: 392.3638 Evaluate side-chains 273 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 237 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 6 GLU Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 22 THR Chi-restraints excluded: chain l residue 54 LEU Chi-restraints excluded: chain a residue 168 TRP Chi-restraints excluded: chain A residue -2 HIS Chi-restraints excluded: chain A residue 0 HIS Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain b residue 37 ASP Chi-restraints excluded: chain b residue 110 GLU Chi-restraints excluded: chain b residue 164 HIS Chi-restraints excluded: chain b residue 170 LYS Chi-restraints excluded: chain b residue 261 ARG Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 112 THR Chi-restraints excluded: chain n residue 5 THR Chi-restraints excluded: chain n residue 9 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 102 optimal weight: 5.9990 chunk 135 optimal weight: 0.7980 chunk 67 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 163 optimal weight: 9.9990 chunk 193 optimal weight: 2.9990 chunk 178 optimal weight: 0.0030 chunk 107 optimal weight: 3.9990 overall best weight: 2.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 ASN L 27 GLN L 100 GLN a 0 HIS N 100 GLN B 0 HIS m 31 ASN m 107 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.138188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.115189 restraints weight = 55244.262| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 4.79 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3308 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3308 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18548 Z= 0.182 Angle : 0.624 8.382 25192 Z= 0.328 Chirality : 0.045 0.213 2685 Planarity : 0.005 0.047 3216 Dihedral : 5.331 57.263 2517 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.09 % Favored : 95.87 % Rotamer: Outliers : 3.60 % Allowed : 14.30 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.18), residues: 2264 helix: 1.62 (0.40), residues: 153 sheet: -0.24 (0.20), residues: 718 loop : -0.56 (0.17), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP a 168 HIS 0.006 0.001 HIS b 158 PHE 0.012 0.002 PHE b 163 TYR 0.015 0.002 TYR H 94 ARG 0.009 0.000 ARG b 41 Details of bonding type rmsd hydrogen bonds : bond 0.04618 ( 555) hydrogen bonds : angle 5.64165 ( 1464) SS BOND : bond 0.00507 ( 32) SS BOND : angle 1.38831 ( 64) covalent geometry : bond 0.00439 (18516) covalent geometry : angle 0.62091 (25128) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 239 time to evaluate : 1.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7339 (mt0) REVERT: H 29 VAL cc_start: 0.8909 (m) cc_final: 0.8668 (t) REVERT: L 14 SER cc_start: 0.8186 (OUTLIER) cc_final: 0.7799 (m) REVERT: L 79 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7294 (mp10) REVERT: h 19 ARG cc_start: 0.8275 (ttt-90) cc_final: 0.8056 (ttt180) REVERT: a 286 HIS cc_start: 0.7881 (m-70) cc_final: 0.7650 (m-70) REVERT: A -2 HIS cc_start: 0.6072 (OUTLIER) cc_final: 0.5698 (t-90) REVERT: A 12 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7197 (mt-10) REVERT: A 85 GLN cc_start: 0.8025 (mp10) cc_final: 0.7716 (mp10) REVERT: A 116 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7677 (pttm) REVERT: A 125 ARG cc_start: 0.7038 (mpp-170) cc_final: 0.6835 (tpp-160) REVERT: A 284 LYS cc_start: 0.7814 (mtpp) cc_final: 0.7489 (tttp) REVERT: A 286 HIS cc_start: 0.8116 (m-70) cc_final: 0.7870 (m-70) REVERT: A 309 GLU cc_start: 0.6662 (tm-30) cc_final: 0.6438 (tm-30) REVERT: N 54 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8590 (mp) REVERT: N 55 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7894 (mm110) REVERT: B 40 ARG cc_start: 0.6265 (OUTLIER) cc_final: 0.5811 (mtm180) REVERT: B 63 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7645 (ttp) REVERT: B 94 LYS cc_start: 0.8244 (mmmm) cc_final: 0.7497 (mtmt) REVERT: B 116 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7640 (ttmm) REVERT: B 272 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7597 (tm-30) REVERT: B 340 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6608 (mt-10) REVERT: b 31 ARG cc_start: 0.6298 (ttm110) cc_final: 0.5995 (ttt90) REVERT: b 164 HIS cc_start: 0.6248 (OUTLIER) cc_final: 0.6029 (p90) REVERT: b 170 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7719 (ttpp) REVERT: b 261 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7452 (mtt-85) outliers start: 67 outliers final: 36 residues processed: 275 average time/residue: 1.3933 time to fit residues: 428.8501 Evaluate side-chains 285 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 234 time to evaluate : 2.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 6 GLU Chi-restraints excluded: chain h residue 46 GLU Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 22 THR Chi-restraints excluded: chain a residue 168 TRP Chi-restraints excluded: chain A residue -2 HIS Chi-restraints excluded: chain A residue 0 HIS Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 55 GLN Chi-restraints excluded: chain B residue 0 HIS Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain b residue 164 HIS Chi-restraints excluded: chain b residue 170 LYS Chi-restraints excluded: chain b residue 261 ARG Chi-restraints excluded: chain b residue 346 VAL Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 87 VAL Chi-restraints excluded: chain m residue 112 THR Chi-restraints excluded: chain n residue 5 THR Chi-restraints excluded: chain n residue 9 SER Chi-restraints excluded: chain n residue 10 SER Chi-restraints excluded: chain n residue 63 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 102 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 216 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN L 100 GLN l 100 GLN a 0 HIS a 263 GLN A 164 HIS B 0 HIS m 107 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.137669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.114919 restraints weight = 56472.875| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 4.86 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3311 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3311 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 18548 Z= 0.194 Angle : 0.635 8.571 25192 Z= 0.333 Chirality : 0.045 0.222 2685 Planarity : 0.005 0.048 3216 Dihedral : 5.223 40.684 2514 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.09 % Favored : 95.87 % Rotamer: Outliers : 3.80 % Allowed : 14.86 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.56 (0.18), residues: 2264 helix: 1.52 (0.39), residues: 153 sheet: -0.27 (0.20), residues: 718 loop : -0.61 (0.17), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP a 168 HIS 0.011 0.001 HIS A 164 PHE 0.012 0.002 PHE b 163 TYR 0.015 0.002 TYR N 49 ARG 0.008 0.000 ARG b 41 Details of bonding type rmsd hydrogen bonds : bond 0.04688 ( 555) hydrogen bonds : angle 5.63063 ( 1464) SS BOND : bond 0.00526 ( 32) SS BOND : angle 1.44560 ( 64) covalent geometry : bond 0.00470 (18516) covalent geometry : angle 0.63159 (25128) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 235 time to evaluate : 1.997 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7294 (mt0) REVERT: H 29 VAL cc_start: 0.8919 (m) cc_final: 0.8691 (t) REVERT: H 98 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7913 (tt0) REVERT: L 14 SER cc_start: 0.8235 (OUTLIER) cc_final: 0.7838 (m) REVERT: L 79 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7275 (mp10) REVERT: a 286 HIS cc_start: 0.7886 (m-70) cc_final: 0.7679 (m-70) REVERT: A -2 HIS cc_start: 0.6061 (OUTLIER) cc_final: 0.5767 (t-90) REVERT: A 12 GLU cc_start: 0.7429 (mm-30) cc_final: 0.7177 (mt-10) REVERT: A 85 GLN cc_start: 0.8130 (mp10) cc_final: 0.7788 (mp10) REVERT: A 116 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7694 (pttm) REVERT: A 284 LYS cc_start: 0.7883 (mtpp) cc_final: 0.7538 (tttp) REVERT: A 286 HIS cc_start: 0.8080 (m-70) cc_final: 0.7838 (m-70) REVERT: A 309 GLU cc_start: 0.6685 (tm-30) cc_final: 0.6480 (tm-30) REVERT: N 54 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8629 (mp) REVERT: N 55 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7896 (mm110) REVERT: B 63 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7686 (ttp) REVERT: B 94 LYS cc_start: 0.8211 (mmmm) cc_final: 0.7487 (mtmt) REVERT: B 116 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7643 (ttmm) REVERT: B 272 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7634 (tm-30) REVERT: B 340 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.6592 (mt-10) REVERT: b 31 ARG cc_start: 0.6366 (ttm110) cc_final: 0.6039 (ttt90) REVERT: b 33 LYS cc_start: 0.5785 (tmtt) cc_final: 0.4856 (tmmt) REVERT: b 170 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7741 (ttpp) REVERT: b 261 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7457 (mtt-85) REVERT: n 103 LYS cc_start: 0.8298 (ttpm) cc_final: 0.8021 (tttp) outliers start: 71 outliers final: 36 residues processed: 275 average time/residue: 1.4553 time to fit residues: 446.4760 Evaluate side-chains 281 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 231 time to evaluate : 2.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 6 GLU Chi-restraints excluded: chain h residue 46 GLU Chi-restraints excluded: chain h residue 54 SER Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 22 THR Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 100 GLN Chi-restraints excluded: chain a residue 168 TRP Chi-restraints excluded: chain A residue -2 HIS Chi-restraints excluded: chain A residue 0 HIS Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 55 GLN Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain b residue 170 LYS Chi-restraints excluded: chain b residue 261 ARG Chi-restraints excluded: chain b residue 346 VAL Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 87 VAL Chi-restraints excluded: chain m residue 112 THR Chi-restraints excluded: chain n residue 5 THR Chi-restraints excluded: chain n residue 9 SER Chi-restraints excluded: chain n residue 10 SER Chi-restraints excluded: chain n residue 63 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 6 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 137 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 chunk 134 optimal weight: 1.9990 chunk 140 optimal weight: 0.7980 chunk 161 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 75 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 107 GLN L 27 GLN L 100 GLN l 100 GLN a 0 HIS a 147 HIS a 263 GLN A 164 HIS N 100 GLN B 0 HIS m 107 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.141093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.117731 restraints weight = 54586.797| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 4.89 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3351 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3351 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18548 Z= 0.118 Angle : 0.550 8.059 25192 Z= 0.291 Chirality : 0.042 0.185 2685 Planarity : 0.004 0.043 3216 Dihedral : 4.833 38.641 2514 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.64 % Favored : 96.31 % Rotamer: Outliers : 2.64 % Allowed : 16.13 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.43 (0.18), residues: 2264 helix: 1.80 (0.41), residues: 153 sheet: -0.24 (0.20), residues: 701 loop : -0.50 (0.17), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP a 168 HIS 0.009 0.001 HIS A 164 PHE 0.015 0.001 PHE l 98 TYR 0.012 0.001 TYR A 175 ARG 0.008 0.000 ARG b 41 Details of bonding type rmsd hydrogen bonds : bond 0.03770 ( 555) hydrogen bonds : angle 5.32039 ( 1464) SS BOND : bond 0.00362 ( 32) SS BOND : angle 1.09517 ( 64) covalent geometry : bond 0.00278 (18516) covalent geometry : angle 0.54811 (25128) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 239 time to evaluate : 1.991 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.7322 (mt0) REVERT: H 29 VAL cc_start: 0.8916 (m) cc_final: 0.8693 (t) REVERT: L 14 SER cc_start: 0.8131 (OUTLIER) cc_final: 0.7733 (m) REVERT: A -2 HIS cc_start: 0.6033 (OUTLIER) cc_final: 0.5788 (t-90) REVERT: A 12 GLU cc_start: 0.7354 (mm-30) cc_final: 0.7154 (mt-10) REVERT: A 85 GLN cc_start: 0.8182 (mp10) cc_final: 0.7839 (mp10) REVERT: A 116 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7698 (pttm) REVERT: A 284 LYS cc_start: 0.7813 (mtpp) cc_final: 0.7519 (tttp) REVERT: A 286 HIS cc_start: 0.8091 (m-70) cc_final: 0.7835 (m-70) REVERT: B 63 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7553 (ttp) REVERT: B 94 LYS cc_start: 0.8249 (mmmm) cc_final: 0.7579 (mtmt) REVERT: b 31 ARG cc_start: 0.6310 (ttm110) cc_final: 0.6101 (ttt90) REVERT: b 170 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7719 (ttpp) REVERT: b 274 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7455 (tm-30) REVERT: b 309 GLU cc_start: 0.7121 (mm-30) cc_final: 0.6678 (tp30) REVERT: n 103 LYS cc_start: 0.8259 (ttpm) cc_final: 0.8032 (tttp) outliers start: 48 outliers final: 23 residues processed: 263 average time/residue: 1.3433 time to fit residues: 394.6623 Evaluate side-chains 260 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 230 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain h residue 6 GLU Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 22 THR Chi-restraints excluded: chain a residue 168 TRP Chi-restraints excluded: chain A residue -2 HIS Chi-restraints excluded: chain A residue 0 HIS Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain b residue 170 LYS Chi-restraints excluded: chain b residue 274 GLU Chi-restraints excluded: chain b residue 346 VAL Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 112 THR Chi-restraints excluded: chain n residue 5 THR Chi-restraints excluded: chain n residue 9 SER Chi-restraints excluded: chain n residue 10 SER Chi-restraints excluded: chain n residue 74 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 165 optimal weight: 0.9990 chunk 210 optimal weight: 10.0000 chunk 176 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 156 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 27 optimal weight: 0.6980 chunk 21 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 182 optimal weight: 8.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 107 GLN L 27 GLN L 100 GLN a 0 HIS a 263 GLN A 164 HIS N 100 GLN B 0 HIS m 76 ASN m 107 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.139389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.104884 restraints weight = 64428.830| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 3.53 r_work: 0.2918 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2895 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18548 Z= 0.176 Angle : 0.623 8.203 25192 Z= 0.326 Chirality : 0.045 0.215 2685 Planarity : 0.004 0.046 3216 Dihedral : 5.067 38.553 2514 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.91 % Favored : 96.05 % Rotamer: Outliers : 2.94 % Allowed : 16.38 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.18), residues: 2264 helix: 1.63 (0.40), residues: 153 sheet: -0.25 (0.20), residues: 726 loop : -0.56 (0.17), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP a 168 HIS 0.009 0.001 HIS A 164 PHE 0.016 0.002 PHE L 98 TYR 0.015 0.002 TYR H 94 ARG 0.008 0.000 ARG b 41 Details of bonding type rmsd hydrogen bonds : bond 0.04463 ( 555) hydrogen bonds : angle 5.50491 ( 1464) SS BOND : bond 0.00494 ( 32) SS BOND : angle 1.38354 ( 64) covalent geometry : bond 0.00426 (18516) covalent geometry : angle 0.61985 (25128) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 232 time to evaluate : 3.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7651 (mt0) REVERT: H 29 VAL cc_start: 0.9003 (m) cc_final: 0.8700 (t) REVERT: L 14 SER cc_start: 0.8430 (OUTLIER) cc_final: 0.7971 (m) REVERT: L 79 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7544 (tp40) REVERT: A -2 HIS cc_start: 0.6131 (OUTLIER) cc_final: 0.5814 (t-90) REVERT: A 12 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7447 (mt-10) REVERT: A 85 GLN cc_start: 0.8415 (mp10) cc_final: 0.8093 (mp10) REVERT: A 116 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7850 (pttm) REVERT: A 284 LYS cc_start: 0.7874 (mtpp) cc_final: 0.7517 (tttp) REVERT: A 286 HIS cc_start: 0.8056 (m-70) cc_final: 0.7781 (m-70) REVERT: N 54 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8841 (mp) REVERT: N 55 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.8112 (mm110) REVERT: B 63 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.8183 (ttp) REVERT: B 94 LYS cc_start: 0.8184 (mmmm) cc_final: 0.7482 (mtmt) REVERT: B 128 LYS cc_start: 0.7572 (tmmt) cc_final: 0.6740 (tmtt) REVERT: B 340 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.6443 (mt-10) REVERT: b 31 ARG cc_start: 0.6380 (ttm110) cc_final: 0.6061 (ttt90) REVERT: b 33 LYS cc_start: 0.5800 (tmtt) cc_final: 0.5575 (tmmm) REVERT: b 170 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7854 (ttpp) REVERT: b 261 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.8209 (mtt-85) REVERT: n 103 LYS cc_start: 0.8099 (ttpm) cc_final: 0.7803 (tttp) outliers start: 54 outliers final: 29 residues processed: 265 average time/residue: 1.6522 time to fit residues: 496.6459 Evaluate side-chains 268 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 228 time to evaluate : 2.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 6 GLU Chi-restraints excluded: chain h residue 46 GLU Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 22 THR Chi-restraints excluded: chain a residue 168 TRP Chi-restraints excluded: chain A residue -2 HIS Chi-restraints excluded: chain A residue 0 HIS Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 55 GLN Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain b residue 170 LYS Chi-restraints excluded: chain b residue 261 ARG Chi-restraints excluded: chain b residue 346 VAL Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 112 THR Chi-restraints excluded: chain n residue 5 THR Chi-restraints excluded: chain n residue 9 SER Chi-restraints excluded: chain n residue 10 SER Chi-restraints excluded: chain n residue 74 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 135 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 162 optimal weight: 8.9990 chunk 179 optimal weight: 0.0000 chunk 192 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 125 optimal weight: 0.8980 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 107 GLN L 27 GLN L 100 GLN a 0 HIS a 263 GLN A 164 HIS m 107 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.141901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.106927 restraints weight = 43180.022| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.93 r_work: 0.3056 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18548 Z= 0.107 Angle : 0.542 8.672 25192 Z= 0.286 Chirality : 0.042 0.176 2685 Planarity : 0.004 0.042 3216 Dihedral : 4.690 35.850 2514 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.60 % Favored : 96.36 % Rotamer: Outliers : 2.23 % Allowed : 17.55 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.18), residues: 2264 helix: 1.88 (0.41), residues: 153 sheet: -0.18 (0.20), residues: 701 loop : -0.46 (0.17), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP a 168 HIS 0.008 0.001 HIS A 164 PHE 0.009 0.001 PHE L 98 TYR 0.013 0.001 TYR A 175 ARG 0.007 0.000 ARG b 41 Details of bonding type rmsd hydrogen bonds : bond 0.03553 ( 555) hydrogen bonds : angle 5.20231 ( 1464) SS BOND : bond 0.00343 ( 32) SS BOND : angle 1.03017 ( 64) covalent geometry : bond 0.00250 (18516) covalent geometry : angle 0.54007 (25128) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 229 time to evaluate : 2.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7694 (mt0) REVERT: H 29 VAL cc_start: 0.9008 (m) cc_final: 0.8696 (t) REVERT: H 43 LYS cc_start: 0.8408 (mmtp) cc_final: 0.8190 (mmtp) REVERT: L 14 SER cc_start: 0.8413 (OUTLIER) cc_final: 0.7945 (m) REVERT: L 79 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7561 (tp40) REVERT: h 19 ARG cc_start: 0.8853 (ttt-90) cc_final: 0.8589 (ttt180) REVERT: a 263 GLN cc_start: 0.8690 (mm-40) cc_final: 0.8388 (mm110) REVERT: A -2 HIS cc_start: 0.6186 (OUTLIER) cc_final: 0.5907 (t-90) REVERT: A 12 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7499 (mt-10) REVERT: A 85 GLN cc_start: 0.8469 (mp10) cc_final: 0.8164 (mp10) REVERT: A 116 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7910 (pttm) REVERT: A 284 LYS cc_start: 0.7864 (mtpp) cc_final: 0.7503 (tttp) REVERT: A 286 HIS cc_start: 0.8075 (m-70) cc_final: 0.7809 (m-70) REVERT: B 63 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8277 (ttp) REVERT: B 94 LYS cc_start: 0.8226 (mmmm) cc_final: 0.7487 (mtmt) REVERT: B 128 LYS cc_start: 0.7521 (tmmt) cc_final: 0.6723 (tmtt) REVERT: b 31 ARG cc_start: 0.6434 (ttm110) cc_final: 0.6178 (ttt90) REVERT: b 170 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7941 (ttpp) REVERT: b 309 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7400 (tp30) REVERT: m 76 ASN cc_start: 0.8642 (t0) cc_final: 0.8316 (t0) REVERT: n 103 LYS cc_start: 0.8074 (ttpm) cc_final: 0.7833 (tttp) outliers start: 40 outliers final: 28 residues processed: 255 average time/residue: 1.2859 time to fit residues: 367.7880 Evaluate side-chains 261 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 226 time to evaluate : 2.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 6 GLU Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 22 THR Chi-restraints excluded: chain a residue 168 TRP Chi-restraints excluded: chain A residue -2 HIS Chi-restraints excluded: chain A residue 0 HIS Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain b residue 170 LYS Chi-restraints excluded: chain b residue 346 VAL Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 112 THR Chi-restraints excluded: chain n residue 5 THR Chi-restraints excluded: chain n residue 9 SER Chi-restraints excluded: chain n residue 10 SER Chi-restraints excluded: chain n residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 194 optimal weight: 0.3980 chunk 73 optimal weight: 0.0470 chunk 116 optimal weight: 1.9990 chunk 150 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 49 optimal weight: 0.5980 chunk 94 optimal weight: 0.0370 chunk 108 optimal weight: 5.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN L 100 GLN l 100 GLN A 164 HIS m 107 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.143064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.108722 restraints weight = 51213.452| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 3.31 r_work: 0.3016 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3027 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3027 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 18548 Z= 0.095 Angle : 0.529 9.213 25192 Z= 0.278 Chirality : 0.041 0.174 2685 Planarity : 0.004 0.040 3216 Dihedral : 4.509 34.548 2514 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.33 % Favored : 96.63 % Rotamer: Outliers : 2.13 % Allowed : 17.90 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.18), residues: 2264 helix: 1.98 (0.41), residues: 153 sheet: -0.08 (0.20), residues: 704 loop : -0.40 (0.17), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 115 HIS 0.007 0.001 HIS A 164 PHE 0.009 0.001 PHE a 163 TYR 0.013 0.001 TYR A 175 ARG 0.007 0.000 ARG b 41 Details of bonding type rmsd hydrogen bonds : bond 0.03321 ( 555) hydrogen bonds : angle 5.06272 ( 1464) SS BOND : bond 0.00297 ( 32) SS BOND : angle 0.92534 ( 64) covalent geometry : bond 0.00218 (18516) covalent geometry : angle 0.52789 (25128) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 236 time to evaluate : 2.088 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7582 (mt0) REVERT: H 29 VAL cc_start: 0.8927 (m) cc_final: 0.8638 (t) REVERT: H 43 LYS cc_start: 0.8369 (mmtp) cc_final: 0.8157 (mmtp) REVERT: L 14 SER cc_start: 0.8335 (OUTLIER) cc_final: 0.7831 (m) REVERT: L 79 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7452 (tp40) REVERT: h 19 ARG cc_start: 0.8725 (ttt-90) cc_final: 0.8454 (ttt180) REVERT: A -2 HIS cc_start: 0.6218 (OUTLIER) cc_final: 0.5962 (t-90) REVERT: A 12 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7351 (mt-10) REVERT: A 85 GLN cc_start: 0.8370 (mp10) cc_final: 0.8067 (mp10) REVERT: A 116 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7863 (pttm) REVERT: A 284 LYS cc_start: 0.7791 (mtpp) cc_final: 0.7445 (tttp) REVERT: A 286 HIS cc_start: 0.8008 (m-70) cc_final: 0.7772 (m-70) REVERT: N 107 LYS cc_start: 0.6952 (mtmt) cc_final: 0.6687 (mtpp) REVERT: B 63 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.8038 (ttp) REVERT: B 94 LYS cc_start: 0.8167 (mmmm) cc_final: 0.7440 (mtmt) REVERT: B 128 LYS cc_start: 0.7498 (tmmt) cc_final: 0.6709 (tmtt) REVERT: b 170 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7871 (ttpp) REVERT: b 309 GLU cc_start: 0.7519 (mm-30) cc_final: 0.7282 (tp30) REVERT: m 76 ASN cc_start: 0.8556 (t0) cc_final: 0.8221 (t0) REVERT: n 103 LYS cc_start: 0.8045 (ttpm) cc_final: 0.7783 (tttp) outliers start: 38 outliers final: 26 residues processed: 259 average time/residue: 1.3320 time to fit residues: 384.7916 Evaluate side-chains 260 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 227 time to evaluate : 2.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 6 GLU Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 22 THR Chi-restraints excluded: chain l residue 100 GLN Chi-restraints excluded: chain a residue 168 TRP Chi-restraints excluded: chain A residue -2 HIS Chi-restraints excluded: chain A residue 0 HIS Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain B residue 0 HIS Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain b residue 170 LYS Chi-restraints excluded: chain b residue 346 VAL Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 112 THR Chi-restraints excluded: chain n residue 5 THR Chi-restraints excluded: chain n residue 10 SER Chi-restraints excluded: chain n residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 206 optimal weight: 0.4980 chunk 157 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 169 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 168 optimal weight: 6.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN L 100 GLN l 100 GLN a 0 HIS a 263 GLN A 164 HIS m 107 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.139998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.117056 restraints weight = 51996.106| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 4.55 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3354 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3354 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18548 Z= 0.165 Angle : 0.612 9.192 25192 Z= 0.319 Chirality : 0.044 0.206 2685 Planarity : 0.004 0.043 3216 Dihedral : 4.826 35.057 2514 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.82 % Favored : 96.14 % Rotamer: Outliers : 2.54 % Allowed : 17.60 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.18), residues: 2264 helix: 1.79 (0.40), residues: 153 sheet: -0.19 (0.20), residues: 709 loop : -0.45 (0.17), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP a 168 HIS 0.007 0.001 HIS A 164 PHE 0.014 0.002 PHE l 98 TYR 0.015 0.002 TYR H 94 ARG 0.007 0.000 ARG b 41 Details of bonding type rmsd hydrogen bonds : bond 0.04223 ( 555) hydrogen bonds : angle 5.31926 ( 1464) SS BOND : bond 0.00463 ( 32) SS BOND : angle 1.29312 ( 64) covalent geometry : bond 0.00400 (18516) covalent geometry : angle 0.60896 (25128) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12654.40 seconds wall clock time: 218 minutes 26.54 seconds (13106.54 seconds total)