Starting phenix.real_space_refine on Sat May 24 23:30:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jkh_36372/05_2025/8jkh_36372.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jkh_36372/05_2025/8jkh_36372.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jkh_36372/05_2025/8jkh_36372.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jkh_36372/05_2025/8jkh_36372.map" model { file = "/net/cci-nas-00/data/ceres_data/8jkh_36372/05_2025/8jkh_36372.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jkh_36372/05_2025/8jkh_36372.cif" } resolution = 2.64 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= 0.001 sd= 0.024 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 10619 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 11084 2.51 5 N 3072 2.21 5 O 3339 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 17603 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2801 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 352, 2794 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 332} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 352, 2794 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 332} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 2865 Chain: "a" Number of atoms: 2693 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 340, 2687 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 320} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Conformer: "B" Number of residues, atoms: 340, 2687 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 320} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 bond proxies already assigned to first conformer: 2751 Chain: "h" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 865 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "l" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 794 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 859 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 112} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 803 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2797 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 352, 2790 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 332} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 352, 2790 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 332} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 2861 Chain: "b" Number of atoms: 2674 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 338, 2668 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 318} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Conformer: "B" Number of residues, atoms: 338, 2668 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 318} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 bond proxies already assigned to first conformer: 2732 Chain: "m" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 861 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "n" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 794 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 859 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 112} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 803 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AVAL A 60 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL A 60 " occ=0.50 residue: pdb=" N ASER a 58 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER a 58 " occ=0.50 residue: pdb=" N AVAL 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: 14.69, per 1000 atoms: 0.83 Number of scatterers: 17603 At special positions: 0 Unit cell: (167.45, 96.9, 139.4, 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 3339 8.00 N 3072 7.00 C 11084 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 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=2.02 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 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 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 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: 3.96 Conformation dependent library (CDL) restraints added in 3.7 seconds 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4144 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 39 sheets defined 13.8% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.61 Creating SS restraints... Processing helix chain 'A' and resid 38 through 53 Processing helix chain 'A' and resid 61 through 81 removed outlier: 3.768A pdb=" N ASN A 65 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N GLY A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 5.524A 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 226 through 230 Processing helix chain 'A' and resid 237 through 241 removed outlier: 4.043A 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: 3.727A pdb=" N THR A 256 " --> pdb=" O HIS A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'a' and resid 41 through 53 Processing helix chain 'a' and resid 61 through 82 removed outlier: 3.555A pdb=" N ASN a 65 " --> pdb=" O SER a 61 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N GLY a 73 " --> pdb=" O ARG a 69 " (cutoff:3.500A) removed outlier: 5.370A 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: 3.900A 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: 3.797A pdb=" N THR a 256 " --> pdb=" O HIS a 253 " (cutoff:3.500A) Processing helix chain 'h' and resid 28 through 32 removed outlier: 3.511A pdb=" N LYS h 32 " --> pdb=" O ILE h 29 " (cutoff:3.500A) Processing helix chain 'h' and resid 61 through 64 removed outlier: 3.678A pdb=" N LYS h 64 " --> pdb=" O ASP h 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 61 through 64' Processing helix chain 'h' and resid 86 through 90 removed outlier: 3.717A pdb=" N THR h 90 " --> pdb=" O ALA h 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.828A pdb=" N LYS H 32 " --> pdb=" O ILE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.916A pdb=" N LYS H 64 " --> pdb=" O ASP H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.734A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 53 Processing helix chain 'B' and resid 61 through 82 removed outlier: 3.643A pdb=" N ASN B 65 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N GLY B 73 " --> pdb=" O ARG B 69 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLU B 74 " --> pdb=" O SER B 70 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN B 82 " --> pdb=" O ILE B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 146 No H-bonds generated for 'chain 'B' and resid 144 through 146' Processing helix chain 'B' and resid 180 through 183 removed outlier: 3.892A 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: 3.689A pdb=" N THR B 256 " --> pdb=" O HIS B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 345 Processing helix chain 'b' and resid 38 through 53 removed outlier: 3.880A pdb=" N ALA b 43 " --> pdb=" O PRO b 39 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA b 44 " --> pdb=" O ARG b 40 " (cutoff:3.500A) Processing helix chain 'b' and resid 61 through 82 removed outlier: 3.504A pdb=" N ASN b 65 " --> pdb=" O SER b 61 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N GLY b 73 " --> pdb=" O ARG b 69 " (cutoff:3.500A) removed outlier: 5.361A 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: 3.890A 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: 3.603A pdb=" N THR b 256 " --> pdb=" O HIS b 253 " (cutoff:3.500A) Processing helix chain 'b' and resid 341 through 345 removed outlier: 4.148A pdb=" N ASN b 344 " --> pdb=" O PRO b 341 " (cutoff:3.500A) Processing helix chain 'm' and resid 28 through 32 Processing helix chain 'm' and resid 61 through 64 removed outlier: 3.685A pdb=" N LYS m 64 " --> pdb=" O ASP m 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 61 through 64' Processing helix chain 'm' and resid 86 through 90 removed outlier: 3.557A pdb=" N THR m 90 " --> pdb=" O ALA m 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 removed outlier: 4.119A pdb=" N LYS M 32 " --> pdb=" O ILE M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 64 removed outlier: 3.811A pdb=" N LYS M 64 " --> pdb=" O ASP M 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 61 through 64' Processing helix chain 'M' and resid 86 through 90 Processing helix chain 'N' and resid 79 through 83 removed outlier: 4.101A pdb=" N PHE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 7 removed outlier: 3.859A pdb=" N ASP A 7 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU A 12 " --> pdb=" O ASP A 7 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N HIS a 2 " --> pdb=" O VAL A 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 35 removed outlier: 6.655A pdb=" N TRP A 168 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 90 removed outlier: 6.452A pdb=" N THR A 87 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N VAL A 135 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL A 89 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLY A 56 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 299 removed outlier: 3.874A pdb=" N LEU A 298 " --> pdb=" O TYR A 331 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N PHE A 277 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N LYS A 213 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU A 212 " --> pdb=" O GLU A 205 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLU A 205 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG A 214 " --> pdb=" O GLU A 203 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A 192 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU a 192 " --> pdb=" O LYS a 189 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG a 214 " --> pdb=" O GLU a 203 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N GLU a 205 " --> pdb=" O LEU a 212 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N LEU a 212 " --> pdb=" O GLU a 205 " (cutoff:3.500A) removed outlier: 9.297A pdb=" N LYS a 213 " --> pdb=" O PHE a 277 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE a 277 " --> pdb=" O LYS a 213 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 284 through 287 removed outlier: 6.366A pdb=" N LYS A 284 " --> pdb=" O TRP A 311 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N CYS A 313 " --> pdb=" O LYS A 284 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N HIS A 286 " --> pdb=" O CYS A 313 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 56 through 57 removed outlier: 7.237A pdb=" N GLY a 56 " --> pdb=" O ALA a 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'a' and resid 87 through 90 removed outlier: 6.736A pdb=" N THR a 87 " --> pdb=" O PHE a 133 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL a 135 " --> pdb=" O THR a 87 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL a 89 " --> pdb=" O VAL a 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'a' and resid 153 through 155 Processing sheet with id=AA9, first strand: chain 'a' and resid 284 through 287 removed outlier: 6.373A pdb=" N LYS a 284 " --> pdb=" O TRP a 311 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N CYS a 313 " --> pdb=" O LYS a 284 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N HIS a 286 " --> pdb=" O CYS a 313 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'h' and resid 3 through 6 removed outlier: 3.536A pdb=" N SER h 70 " --> pdb=" O TYR h 79 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'h' and resid 11 through 12 removed outlier: 4.693A pdb=" N TYR h 33 " --> pdb=" O LEU h 98 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER h 49 " --> pdb=" O TRP h 36 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ARG h 38 " --> pdb=" O TRP h 47 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N TRP h 47 " --> pdb=" O ARG h 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'l' and resid 4 through 7 removed outlier: 3.500A pdb=" N ASP l 70 " --> pdb=" O SER l 67 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'l' and resid 10 through 12 removed outlier: 6.637A pdb=" N LEU l 33 " --> pdb=" O TYR l 49 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N TYR l 49 " --> pdb=" O LEU l 33 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N TRP l 35 " --> pdb=" O LEU l 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AB6, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.932A pdb=" N MET H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ILE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.811A pdb=" N CYS H 95 " --> pdb=" O TRP H 107 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TRP H 107 " --> pdb=" O CYS H 95 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER H 97 " --> pdb=" O GLY H 105 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA H 103 " --> pdb=" O GLY H 99 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB9, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.644A pdb=" N VAL L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.644A pdb=" N VAL L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 2 through 7 removed outlier: 3.662A pdb=" N ASP B 7 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU B 12 " --> pdb=" O ASP B 7 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N HIS b 2 " --> pdb=" O VAL B 6 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 33 through 36 removed outlier: 6.567A pdb=" N TRP B 168 " --> pdb=" O GLU B 156 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 56 through 57 removed outlier: 6.904A pdb=" N GLY B 56 " --> pdb=" O ALA B 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 87 through 90 removed outlier: 6.711A pdb=" N THR B 87 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N VAL B 135 " --> pdb=" O THR B 87 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL B 89 " --> pdb=" O VAL B 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 329 through 331 removed outlier: 4.887A pdb=" N PHE B 277 " --> pdb=" O LYS B 213 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N LYS B 213 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N LEU B 212 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N GLU B 205 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG B 214 " --> pdb=" O GLU B 203 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU B 192 " --> pdb=" O LYS B 189 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU b 192 " --> pdb=" O LYS b 189 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLU b 205 " --> pdb=" O LEU b 212 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N LEU b 212 " --> pdb=" O GLU b 205 " (cutoff:3.500A) removed outlier: 9.242A pdb=" N LYS b 213 " --> pdb=" O PHE b 277 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE b 277 " --> pdb=" O LYS b 213 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU b 274 " --> pdb=" O ARG b 324 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY b 328 " --> pdb=" O ALA b 325 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 284 through 287 Processing sheet with id=AC8, first strand: chain 'b' and resid 35 through 36 removed outlier: 6.068A pdb=" N HIS b 35 " --> pdb=" O LEU b 169 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL b 171 " --> pdb=" O HIS b 35 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'b' and resid 56 through 57 removed outlier: 7.184A pdb=" N GLY b 56 " --> pdb=" O ALA b 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'b' and resid 87 through 89 removed outlier: 6.741A pdb=" N THR b 87 " --> pdb=" O PHE b 133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'b' and resid 285 through 287 removed outlier: 6.431A pdb=" N HIS b 286 " --> pdb=" O CYS b 313 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'm' and resid 3 through 6 removed outlier: 3.510A pdb=" N SER m 70 " --> pdb=" O TYR m 79 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'm' and resid 11 through 12 removed outlier: 4.732A pdb=" N TYR m 33 " --> pdb=" O LEU m 98 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N MET m 34 " --> pdb=" O ILE m 50 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ILE m 50 " --> pdb=" O MET m 34 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TRP m 36 " --> pdb=" O VAL m 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'm' and resid 11 through 12 Processing sheet with id=AD6, first strand: chain 'n' and resid 5 through 7 Processing sheet with id=AD7, first strand: chain 'n' and resid 10 through 12 removed outlier: 6.899A pdb=" N VAL n 11 " --> pdb=" O GLU n 105 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU n 33 " --> pdb=" O TYR n 49 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TYR n 49 " --> pdb=" O LEU n 33 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TRP n 35 " --> pdb=" O LEU n 47 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'M' and resid 3 through 5 Processing sheet with id=AD9, first strand: chain 'M' and resid 11 through 12 removed outlier: 4.772A pdb=" N TYR M 33 " --> pdb=" O LEU M 98 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N MET M 34 " --> pdb=" O ILE M 50 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILE M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'M' and resid 11 through 12 removed outlier: 6.750A pdb=" N CYS M 95 " --> pdb=" O TRP M 107 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N TRP M 107 " --> pdb=" O CYS M 95 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N SER M 97 " --> pdb=" O GLY M 105 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ALA M 103 " --> pdb=" O GLY M 99 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AE3, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.551A pdb=" N VAL N 11 " --> pdb=" O GLU N 105 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) 568 hydrogen bonds defined for protein. 1389 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: 5.72 Time building geometry restraints manager: 4.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3060 1.32 - 1.45: 5123 1.45 - 1.57: 9724 1.57 - 1.70: 0 1.70 - 1.83: 152 Bond restraints: 18059 Sorted by residual: bond pdb=" N GLU A 12 " pdb=" CA GLU A 12 " ideal model delta sigma weight residual 1.460 1.501 -0.041 1.02e-02 9.61e+03 1.60e+01 bond pdb=" CA SER l 30 " pdb=" CB SER l 30 " ideal model delta sigma weight residual 1.531 1.468 0.063 1.65e-02 3.67e+03 1.46e+01 bond pdb=" N PRO b 36 " pdb=" CA PRO b 36 " ideal model delta sigma weight residual 1.469 1.420 0.049 1.28e-02 6.10e+03 1.44e+01 bond pdb=" N LEU m 98 " pdb=" CA LEU m 98 " ideal model delta sigma weight residual 1.454 1.495 -0.040 1.17e-02 7.31e+03 1.20e+01 bond pdb=" N VAL A 6 " pdb=" CA VAL A 6 " ideal model delta sigma weight residual 1.458 1.495 -0.038 1.18e-02 7.18e+03 1.02e+01 ... (remaining 18054 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 23706 1.83 - 3.66: 711 3.66 - 5.49: 93 5.49 - 7.32: 17 7.32 - 9.15: 6 Bond angle restraints: 24533 Sorted by residual: angle pdb=" N ASP b 208 " pdb=" CA ASP b 208 " pdb=" C ASP b 208 " ideal model delta sigma weight residual 113.43 104.97 8.46 1.26e+00 6.30e-01 4.50e+01 angle pdb=" CA ASP A 7 " pdb=" CB ASP A 7 " pdb=" CG ASP A 7 " ideal model delta sigma weight residual 112.60 117.95 -5.35 1.00e+00 1.00e+00 2.86e+01 angle pdb=" N PHE A 123 " pdb=" CA PHE A 123 " pdb=" C PHE A 123 " ideal model delta sigma weight residual 109.07 100.97 8.10 1.52e+00 4.33e-01 2.84e+01 angle pdb=" N GLU A 12 " pdb=" CA GLU A 12 " pdb=" CB GLU A 12 " ideal model delta sigma weight residual 109.51 114.39 -4.88 1.02e+00 9.61e-01 2.28e+01 angle pdb=" CA THR a 165 " pdb=" C THR a 165 " pdb=" O THR a 165 " ideal model delta sigma weight residual 122.27 116.87 5.40 1.16e+00 7.43e-01 2.17e+01 ... (remaining 24528 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 9840 17.35 - 34.70: 684 34.70 - 52.06: 136 52.06 - 69.41: 22 69.41 - 86.76: 13 Dihedral angle restraints: 10695 sinusoidal: 4211 harmonic: 6484 Sorted by residual: dihedral pdb=" CA PRO B 36 " pdb=" C PRO B 36 " pdb=" N ASP B 37 " pdb=" CA ASP B 37 " ideal model delta harmonic sigma weight residual -180.00 -151.73 -28.27 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA GLY M 101 " pdb=" C GLY M 101 " pdb=" N SER M 102 " pdb=" CA SER M 102 " ideal model delta harmonic sigma weight residual 180.00 152.60 27.40 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA SER l 30 " pdb=" C SER l 30 " pdb=" N THR l 31 " pdb=" CA THR l 31 " ideal model delta harmonic sigma weight residual 180.00 152.96 27.04 0 5.00e+00 4.00e-02 2.93e+01 ... (remaining 10692 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2114 0.056 - 0.112: 427 0.112 - 0.168: 88 0.168 - 0.224: 14 0.224 - 0.280: 3 Chirality restraints: 2646 Sorted by residual: chirality pdb=" CA PHE A 8 " pdb=" N PHE A 8 " pdb=" C PHE A 8 " pdb=" CB PHE A 8 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA LEU a 154 " pdb=" N LEU a 154 " pdb=" C LEU a 154 " pdb=" CB LEU a 154 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA ASP A 7 " pdb=" N ASP A 7 " pdb=" C ASP A 7 " pdb=" CB ASP A 7 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 2643 not shown) Planarity restraints: 3142 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR l 74 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.66e+00 pdb=" C THR l 74 " 0.045 2.00e-02 2.50e+03 pdb=" O THR l 74 " -0.017 2.00e-02 2.50e+03 pdb=" N ILE l 75 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 5 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.23e+00 pdb=" C SER A 5 " -0.036 2.00e-02 2.50e+03 pdb=" O SER A 5 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL A 6 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA H 40 " -0.033 5.00e-02 4.00e+02 4.98e-02 3.96e+00 pdb=" N PRO H 41 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO H 41 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 41 " -0.028 5.00e-02 4.00e+02 ... (remaining 3139 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 39 2.38 - 3.01: 9155 3.01 - 3.64: 23785 3.64 - 4.27: 39082 4.27 - 4.90: 68407 Nonbonded interactions: 140468 Sorted by model distance: nonbonded pdb=" CD1 TRP A 28 " pdb=" CD1 TRP B 28 " model vdw 1.753 3.480 nonbonded pdb=" NE1 TRP A 28 " pdb=" CG TRP B 28 " model vdw 1.994 3.340 nonbonded pdb=" NE1 TRP A 28 " pdb=" CB TRP B 28 " model vdw 2.055 3.520 nonbonded pdb=" OH TYR A 122 " pdb=" O SER B 304 " model vdw 2.062 3.040 nonbonded pdb=" CD1 TRP A 28 " pdb=" CG TRP B 28 " model vdw 2.108 3.480 ... (remaining 140463 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 32 or (resid 33 and (name N or name \ CA or name C or name O or name CB )) or resid 34 through 57 or resid 59 or resid \ 61 through 115 or resid 124 or (resid 125 through 128 and (name N or name CA or \ name C or name O or name CB )) or resid 129 through 172 or (resid 173 and (name \ N or name CA or name C or name O or name CB )) or resid 174 through 236 or (res \ id 237 and (name N or name CA or name C or name O or name CB )) or resid 238 thr \ ough 338 or (resid 339 and (name N or name CA or name C or name O or name CB )) \ or resid 340 through 352)) selection = (chain 'B' and (resid 1 through 25 or resid 32 or (resid 33 and (name N or name \ CA or name C or name O or name CB )) or resid 34 through 57 or resid 59 or resid \ 61 through 115 or resid 124 or (resid 125 through 128 and (name N or name CA or \ name C or name O or name CB )) or resid 129 through 236 or (resid 237 and (name \ N or name CA or name C or name O or name CB )) or resid 238 through 338 or (res \ id 339 and (name N or name CA or name C or name O or name CB )) or resid 340 thr \ ough 352)) selection = (chain 'a' and (resid 1 through 9 or (resid 10 through 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 25 or resid 32 through 57 \ or resid 59 or resid 61 through 283 or (resid 284 and (name N or name CA or nam \ e C or name O or name CB )) or resid 285 through 288 or (resid 289 and (name N o \ r name CA or name C or name O or name CB )) or resid 290 through 352)) selection = (chain 'b' and (resid 1 through 9 or (resid 10 through 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 57 or resid 59 or resid 6 \ 1 through 283 or (resid 284 and (name N or name CA or name C or name O or name C \ B )) or resid 285 through 288 or (resid 289 and (name N or name CA or name C or \ name O or name CB )) or resid 290 through 352)) } ncs_group { reference = (chain 'H' and (resid 2 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB )) or resid 44 through 116)) selection = (chain 'M' and (resid 2 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB )) or resid 44 through 116)) selection = (chain 'h' and (resid 2 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 116)) selection = (chain 'm' and resid 2 through 116) } ncs_group { reference = (chain 'L' and (resid 1 through 80 or (resid 81 and (name N or name CA or name C \ or name O or name CB )) or resid 82 through 106)) selection = (chain 'N' and (resid 1 through 80 or (resid 81 and (name N or name CA or name C \ or name O or name CB )) or resid 82 through 106)) selection = (chain 'l' and (resid 1 through 41 or (resid 42 through 43 and (name N or name C \ A or name C or name O or name CB )) or resid 44 through 106)) selection = (chain 'n' and (resid 1 through 41 or (resid 42 through 43 and (name N or name C \ A or name C or name O or name CB )) or resid 44 through 106)) } 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: 4.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.010 Extract box with map and model: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 46.860 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 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 0.063 18091 Z= 0.267 Angle : 0.751 9.152 24597 Z= 0.458 Chirality : 0.050 0.280 2646 Planarity : 0.004 0.050 3142 Dihedral : 12.590 86.758 6455 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.92 % Favored : 94.91 % Rotamer: Outliers : 0.79 % Allowed : 0.58 % Favored : 98.63 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 14.29 % 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: -1.00 (0.18), residues: 2250 helix: 0.48 (0.40), residues: 148 sheet: -1.02 (0.20), residues: 692 loop : -0.53 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP l 32 HIS 0.006 0.001 HIS A 164 PHE 0.019 0.002 PHE A 8 TYR 0.023 0.002 TYR B 122 ARG 0.009 0.001 ARG b 257 Details of bonding type rmsd hydrogen bonds : bond 0.22005 ( 551) hydrogen bonds : angle 8.84604 ( 1389) SS BOND : bond 0.00531 ( 32) SS BOND : angle 1.50954 ( 64) covalent geometry : bond 0.00510 (18059) covalent geometry : angle 0.74780 (24533) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 522 time to evaluate : 1.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 TYR cc_start: 0.8397 (m-80) cc_final: 0.7934 (m-80) REVERT: a 15 CYS cc_start: 0.6005 (m) cc_final: 0.5696 (m) REVERT: a 140 LEU cc_start: 0.8403 (mt) cc_final: 0.7720 (mp) REVERT: a 170 LYS cc_start: 0.7953 (ttpp) cc_final: 0.7751 (ttpp) REVERT: a 224 GLU cc_start: 0.7480 (mt-10) cc_final: 0.7268 (mt-10) REVERT: h 82 MET cc_start: 0.7535 (mtp) cc_final: 0.7330 (mtp) REVERT: l 4 MET cc_start: 0.7568 (mmm) cc_final: 0.7230 (mmm) REVERT: l 63 SER cc_start: 0.7717 (t) cc_final: 0.7495 (p) REVERT: B 4 CYS cc_start: 0.5517 (m) cc_final: 0.5042 (m) REVERT: B 20 PHE cc_start: 0.8508 (m-80) cc_final: 0.8222 (m-80) REVERT: B 170 LYS cc_start: 0.7241 (pttp) cc_final: 0.7032 (pttp) REVERT: B 214 ARG cc_start: 0.7653 (ptm-80) cc_final: 0.7436 (ptt90) REVERT: B 261 ARG cc_start: 0.7088 (mmm160) cc_final: 0.6813 (mmm160) REVERT: B 274 GLU cc_start: 0.6754 (tm-30) cc_final: 0.6245 (tm-30) REVERT: B 276 ARG cc_start: 0.7092 (mtt180) cc_final: 0.6748 (mtm-85) REVERT: b 71 VAL cc_start: 0.8336 (p) cc_final: 0.8004 (m) REVERT: n 63 SER cc_start: 0.8099 (t) cc_final: 0.7880 (p) REVERT: M 109 GLN cc_start: 0.6145 (pp30) cc_final: 0.5874 (pp30) outliers start: 13 outliers final: 7 residues processed: 534 average time/residue: 1.3036 time to fit residues: 775.3853 Evaluate side-chains 448 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 441 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain a residue 156 GLU Chi-restraints excluded: chain a residue 164 HIS Chi-restraints excluded: chain a residue 174 ASP Chi-restraints excluded: chain a residue 176 SER Chi-restraints excluded: chain l residue 31 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 0.6980 chunk 167 optimal weight: 0.2980 chunk 92 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 173 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 105 optimal weight: 0.4980 chunk 128 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 1 HIS A 2 HIS A 82 ASN ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 76 ASN h 76 ASN H 76 ASN H 81 GLN B 109 ASN b 76 ASN b 263 GLN M 81 GLN ** M 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.121177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.099389 restraints weight = 67440.494| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 3.61 r_work: 0.3083 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 18091 Z= 0.163 Angle : 0.645 9.979 24597 Z= 0.343 Chirality : 0.046 0.162 2646 Planarity : 0.005 0.045 3142 Dihedral : 5.589 58.586 2482 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.87 % Favored : 95.08 % Rotamer: Outliers : 2.63 % Allowed : 12.61 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -0.60 (0.17), residues: 2250 helix: 1.12 (0.41), residues: 147 sheet: -0.43 (0.21), residues: 670 loop : -0.50 (0.16), residues: 1433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP a 168 HIS 0.012 0.001 HIS a 35 PHE 0.015 0.001 PHE B 277 TYR 0.025 0.002 TYR B 122 ARG 0.006 0.001 ARG a 276 Details of bonding type rmsd hydrogen bonds : bond 0.04082 ( 551) hydrogen bonds : angle 6.01999 ( 1389) SS BOND : bond 0.00720 ( 32) SS BOND : angle 2.28936 ( 64) covalent geometry : bond 0.00387 (18059) covalent geometry : angle 0.63546 (24533) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 480 time to evaluate : 2.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 LEU cc_start: 0.8601 (mt) cc_final: 0.8247 (mt) REVERT: A 156 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7783 (mp0) REVERT: A 272 GLU cc_start: 0.8187 (tt0) cc_final: 0.7926 (tm-30) REVERT: A 276 ARG cc_start: 0.8153 (ptp-170) cc_final: 0.7948 (ptp90) REVERT: a 15 CYS cc_start: 0.7605 (m) cc_final: 0.7336 (m) REVERT: a 55 CYS cc_start: 0.7594 (p) cc_final: 0.7228 (p) REVERT: a 62 ARG cc_start: 0.7946 (mtt-85) cc_final: 0.7657 (mtt-85) REVERT: a 255 ASN cc_start: 0.8732 (t0) cc_final: 0.8490 (t0) REVERT: a 261 ARG cc_start: 0.8241 (mtt-85) cc_final: 0.7990 (mtt-85) REVERT: a 276 ARG cc_start: 0.8265 (ptp90) cc_final: 0.7903 (ptp90) REVERT: a 294 ARG cc_start: 0.8514 (ptm160) cc_final: 0.8072 (ptm-80) REVERT: a 317 THR cc_start: 0.8333 (m) cc_final: 0.7759 (p) REVERT: a 329 CYS cc_start: 0.7370 (t) cc_final: 0.7097 (t) REVERT: h 53 SER cc_start: 0.8698 (t) cc_final: 0.8462 (m) REVERT: h 90 THR cc_start: 0.8521 (t) cc_final: 0.8295 (m) REVERT: l 63 SER cc_start: 0.8094 (t) cc_final: 0.7795 (p) REVERT: L 60 SER cc_start: 0.8239 (p) cc_final: 0.7958 (t) REVERT: B 5 SER cc_start: 0.8361 (m) cc_final: 0.8141 (p) REVERT: B 20 PHE cc_start: 0.8722 (m-80) cc_final: 0.8393 (m-80) REVERT: B 154 LEU cc_start: 0.8658 (mt) cc_final: 0.8275 (mt) REVERT: B 170 LYS cc_start: 0.8065 (pttp) cc_final: 0.7641 (pttp) REVERT: B 261 ARG cc_start: 0.8418 (mmm160) cc_final: 0.8072 (mmm160) REVERT: B 274 GLU cc_start: 0.7625 (tm-30) cc_final: 0.7402 (tm-30) REVERT: B 314 ARG cc_start: 0.8049 (mtp85) cc_final: 0.7825 (mtt90) REVERT: b 221 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8361 (ptpt) REVERT: m 20 LEU cc_start: 0.8455 (mt) cc_final: 0.8253 (mp) REVERT: n 37 GLN cc_start: 0.8833 (tt0) cc_final: 0.8512 (tt0) REVERT: M 109 GLN cc_start: 0.7081 (pp30) cc_final: 0.6812 (pp30) REVERT: N 9 SER cc_start: 0.7770 (p) cc_final: 0.7493 (t) outliers start: 49 outliers final: 18 residues processed: 496 average time/residue: 1.3286 time to fit residues: 730.1714 Evaluate side-chains 464 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 445 time to evaluate : 1.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain a residue 70 SER Chi-restraints excluded: chain h residue 5 VAL Chi-restraints excluded: chain h residue 11 LEU Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 112 LEU Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain l residue 9 SER Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain b residue 221 LYS Chi-restraints excluded: chain b residue 246 SER Chi-restraints excluded: chain b residue 307 VAL Chi-restraints excluded: chain b residue 310 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 80 optimal weight: 0.4980 chunk 187 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 177 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 128 optimal weight: 0.5980 chunk 194 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 1 HIS A 2 HIS A 82 ASN A 95 ASN ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 GLN A 344 ASN a 35 HIS a 164 HIS h 76 ASN H 76 ASN H 81 GLN B 76 ASN B 344 ASN b 76 ASN b 82 ASN b 263 GLN m 83 ASN N 55 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.119448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.098186 restraints weight = 63301.604| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 3.33 r_work: 0.3080 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 18091 Z= 0.156 Angle : 0.638 16.108 24597 Z= 0.334 Chirality : 0.045 0.159 2646 Planarity : 0.005 0.054 3142 Dihedral : 5.068 28.626 2472 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.33 % Favored : 95.62 % Rotamer: Outliers : 3.05 % Allowed : 15.49 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 (0.17), residues: 2250 helix: 1.55 (0.40), residues: 149 sheet: -0.34 (0.20), residues: 705 loop : -0.49 (0.16), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 28 HIS 0.005 0.001 HIS A 35 PHE 0.015 0.001 PHE H 27 TYR 0.021 0.002 TYR a 34 ARG 0.005 0.001 ARG A 40 Details of bonding type rmsd hydrogen bonds : bond 0.04157 ( 551) hydrogen bonds : angle 5.67287 ( 1389) SS BOND : bond 0.00580 ( 32) SS BOND : angle 2.38074 ( 64) covalent geometry : bond 0.00379 (18059) covalent geometry : angle 0.62672 (24533) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 470 time to evaluate : 2.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8130 (tt) REVERT: A 71 VAL cc_start: 0.8379 (t) cc_final: 0.8146 (p) REVERT: A 154 LEU cc_start: 0.8599 (mt) cc_final: 0.8291 (mt) REVERT: A 156 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7719 (mp0) REVERT: A 237 GLU cc_start: 0.7671 (tp30) cc_final: 0.7424 (tp30) REVERT: A 272 GLU cc_start: 0.8198 (tt0) cc_final: 0.7963 (tm-30) REVERT: A 288 GLU cc_start: 0.7436 (mt-10) cc_final: 0.6794 (mt-10) REVERT: A 333 MET cc_start: 0.8604 (mtp) cc_final: 0.8370 (mtp) REVERT: A 338 ARG cc_start: 0.7526 (tpp80) cc_final: 0.7257 (ttm-80) REVERT: a 15 CYS cc_start: 0.7540 (m) cc_final: 0.7230 (m) REVERT: a 55 CYS cc_start: 0.7389 (p) cc_final: 0.6988 (p) REVERT: a 97 MET cc_start: 0.8803 (mtt) cc_final: 0.8494 (mtp) REVERT: a 276 ARG cc_start: 0.8320 (ptp90) cc_final: 0.8014 (ptp90) REVERT: l 4 MET cc_start: 0.8619 (mmm) cc_final: 0.7905 (mmm) REVERT: l 63 SER cc_start: 0.8040 (t) cc_final: 0.7715 (p) REVERT: L 11 VAL cc_start: 0.8326 (OUTLIER) cc_final: 0.8086 (m) REVERT: L 60 SER cc_start: 0.8175 (p) cc_final: 0.7900 (t) REVERT: B 20 PHE cc_start: 0.8742 (m-80) cc_final: 0.8462 (m-80) REVERT: B 263 GLN cc_start: 0.8538 (mm-40) cc_final: 0.8314 (mm110) REVERT: B 274 GLU cc_start: 0.7619 (tm-30) cc_final: 0.7370 (tm-30) REVERT: B 314 ARG cc_start: 0.8115 (mtp85) cc_final: 0.7907 (mtt90) REVERT: b 170 LYS cc_start: 0.8275 (ptmm) cc_final: 0.8007 (ttpp) REVERT: b 221 LYS cc_start: 0.8586 (ptpt) cc_final: 0.8376 (pttp) REVERT: b 314 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7886 (ttt180) REVERT: M 109 GLN cc_start: 0.7255 (pp30) cc_final: 0.7008 (pp30) outliers start: 56 outliers final: 25 residues processed: 489 average time/residue: 1.4194 time to fit residues: 764.4157 Evaluate side-chains 467 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 439 time to evaluate : 2.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain a residue 82 ASN Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 251 LEU Chi-restraints excluded: chain h residue 11 LEU Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 62 SER Chi-restraints excluded: chain h residue 112 LEU Chi-restraints excluded: chain l residue 11 VAL Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain b residue 219 GLU Chi-restraints excluded: chain b residue 246 SER Chi-restraints excluded: chain b residue 307 VAL Chi-restraints excluded: chain b residue 310 GLU Chi-restraints excluded: chain b residue 314 ARG Chi-restraints excluded: chain n residue 54 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 64 optimal weight: 0.0570 chunk 39 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 156 optimal weight: 0.6980 chunk 131 optimal weight: 0.7980 chunk 10 optimal weight: 0.4980 chunk 200 optimal weight: 0.7980 chunk 199 optimal weight: 0.9990 chunk 213 optimal weight: 2.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 1 HIS A 76 ASN A 82 ASN ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 255 ASN h 76 ASN H 76 ASN H 81 GLN L 38 GLN b 76 ASN b 82 ASN b 95 ASN b 263 GLN m 83 ASN n 92 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.119430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.098773 restraints weight = 50532.990| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.89 r_work: 0.3137 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 18091 Z= 0.133 Angle : 0.606 14.978 24597 Z= 0.318 Chirality : 0.044 0.215 2646 Planarity : 0.004 0.053 3142 Dihedral : 4.895 27.494 2471 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.47 % Favored : 95.49 % Rotamer: Outliers : 2.94 % Allowed : 16.75 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 (0.17), residues: 2250 helix: 1.71 (0.41), residues: 149 sheet: -0.27 (0.20), residues: 685 loop : -0.47 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 28 HIS 0.004 0.001 HIS A 286 PHE 0.016 0.001 PHE H 27 TYR 0.017 0.001 TYR B 122 ARG 0.005 0.000 ARG A 40 Details of bonding type rmsd hydrogen bonds : bond 0.03573 ( 551) hydrogen bonds : angle 5.42503 ( 1389) SS BOND : bond 0.00619 ( 32) SS BOND : angle 2.07562 ( 64) covalent geometry : bond 0.00319 (18059) covalent geometry : angle 0.59707 (24533) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 459 time to evaluate : 2.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ARG cc_start: 0.5908 (mmt180) cc_final: 0.5584 (mmt180) REVERT: A 40 ARG cc_start: 0.7969 (mtm-85) cc_final: 0.7702 (mtm-85) REVERT: A 66 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8099 (tt) REVERT: A 71 VAL cc_start: 0.8345 (t) cc_final: 0.8091 (p) REVERT: A 110 GLU cc_start: 0.7001 (pt0) cc_final: 0.6787 (pt0) REVERT: A 237 GLU cc_start: 0.7539 (tp30) cc_final: 0.7306 (tp30) REVERT: A 288 GLU cc_start: 0.7347 (mt-10) cc_final: 0.6727 (mt-10) REVERT: A 338 ARG cc_start: 0.7470 (tpp80) cc_final: 0.7248 (ttm-80) REVERT: a 55 CYS cc_start: 0.7203 (p) cc_final: 0.6812 (p) REVERT: a 69 ARG cc_start: 0.8119 (ttm170) cc_final: 0.7902 (ttm170) REVERT: a 261 ARG cc_start: 0.8070 (mtt-85) cc_final: 0.7844 (mtt-85) REVERT: a 276 ARG cc_start: 0.8203 (ptp90) cc_final: 0.7885 (ptp90) REVERT: a 288 GLU cc_start: 0.7375 (tp30) cc_final: 0.7051 (tp30) REVERT: l 4 MET cc_start: 0.8578 (mmm) cc_final: 0.7777 (mmm) REVERT: l 63 SER cc_start: 0.7995 (t) cc_final: 0.7682 (p) REVERT: L 11 VAL cc_start: 0.8277 (OUTLIER) cc_final: 0.8041 (m) REVERT: L 60 SER cc_start: 0.8118 (p) cc_final: 0.7840 (t) REVERT: B 20 PHE cc_start: 0.8722 (m-80) cc_final: 0.8435 (m-80) REVERT: B 263 GLN cc_start: 0.8497 (mm-40) cc_final: 0.8289 (mm110) REVERT: B 274 GLU cc_start: 0.7474 (tm-30) cc_final: 0.7206 (tm-30) REVERT: B 314 ARG cc_start: 0.8056 (mtp85) cc_final: 0.7852 (mtt90) REVERT: b 51 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7247 (mt-10) REVERT: b 69 ARG cc_start: 0.7993 (ttm110) cc_final: 0.7584 (ttm-80) REVERT: b 76 ASN cc_start: 0.8683 (m-40) cc_final: 0.8455 (m-40) REVERT: b 170 LYS cc_start: 0.8199 (ptmm) cc_final: 0.7969 (ttpp) REVERT: b 255 ASN cc_start: 0.8478 (t0) cc_final: 0.8164 (t160) REVERT: b 310 GLU cc_start: 0.6730 (OUTLIER) cc_final: 0.6474 (mm-30) REVERT: n 38 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.6782 (tp40) REVERT: M 109 GLN cc_start: 0.7215 (pp30) cc_final: 0.6976 (pp30) outliers start: 55 outliers final: 31 residues processed: 480 average time/residue: 1.4070 time to fit residues: 747.9018 Evaluate side-chains 482 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 446 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain a residue 52 ASP Chi-restraints excluded: chain a residue 70 SER Chi-restraints excluded: chain a residue 82 ASN Chi-restraints excluded: chain a residue 251 LEU Chi-restraints excluded: chain a residue 315 GLU Chi-restraints excluded: chain h residue 11 LEU Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 62 SER Chi-restraints excluded: chain h residue 90 THR Chi-restraints excluded: chain h residue 112 LEU Chi-restraints excluded: chain l residue 11 VAL Chi-restraints excluded: chain l residue 60 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain b residue 51 GLU Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 219 GLU Chi-restraints excluded: chain b residue 246 SER Chi-restraints excluded: chain b residue 307 VAL Chi-restraints excluded: chain b residue 310 GLU Chi-restraints excluded: chain n residue 38 GLN Chi-restraints excluded: chain n residue 77 SER Chi-restraints excluded: chain n residue 103 LYS Chi-restraints excluded: chain M residue 95 CYS Chi-restraints excluded: chain N residue 89 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 105 optimal weight: 0.2980 chunk 58 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 169 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 1 HIS A 76 ASN A 82 ASN a 255 ASN h 76 ASN H 76 ASN H 81 GLN b 82 ASN b 95 ASN b 263 GLN m 83 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.118657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.097103 restraints weight = 58157.515| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 3.20 r_work: 0.3096 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 18091 Z= 0.164 Angle : 0.635 14.218 24597 Z= 0.333 Chirality : 0.044 0.217 2646 Planarity : 0.005 0.055 3142 Dihedral : 5.059 29.265 2471 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.52 % Allowed : 16.91 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 (0.17), residues: 2250 helix: 1.61 (0.40), residues: 149 sheet: -0.25 (0.20), residues: 685 loop : -0.56 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 330 HIS 0.005 0.001 HIS A 35 PHE 0.018 0.001 PHE H 27 TYR 0.018 0.002 TYR H 94 ARG 0.009 0.001 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.03912 ( 551) hydrogen bonds : angle 5.45626 ( 1389) SS BOND : bond 0.00749 ( 32) SS BOND : angle 2.19259 ( 64) covalent geometry : bond 0.00401 (18059) covalent geometry : angle 0.62636 (24533) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 450 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.6442 (tpt-90) REVERT: A 31 ARG cc_start: 0.6024 (mmt180) cc_final: 0.5701 (mmt180) REVERT: A 237 GLU cc_start: 0.7595 (tp30) cc_final: 0.7363 (tp30) REVERT: A 288 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7254 (mt-10) REVERT: A 338 ARG cc_start: 0.7528 (tpp80) cc_final: 0.7290 (ttm-80) REVERT: a 15 CYS cc_start: 0.7455 (m) cc_final: 0.7129 (m) REVERT: a 48 GLN cc_start: 0.8649 (tt0) cc_final: 0.8322 (tt0) REVERT: a 55 CYS cc_start: 0.7232 (p) cc_final: 0.6834 (p) REVERT: a 69 ARG cc_start: 0.8150 (ttm170) cc_final: 0.7816 (ttm170) REVERT: a 261 ARG cc_start: 0.8136 (mtt-85) cc_final: 0.7915 (mtt-85) REVERT: a 276 ARG cc_start: 0.8236 (ptp90) cc_final: 0.7926 (ptp90) REVERT: a 288 GLU cc_start: 0.7438 (tp30) cc_final: 0.7106 (tp30) REVERT: l 4 MET cc_start: 0.8622 (mmm) cc_final: 0.7654 (mmm) REVERT: l 63 SER cc_start: 0.7983 (t) cc_final: 0.7648 (p) REVERT: L 11 VAL cc_start: 0.8340 (OUTLIER) cc_final: 0.8103 (m) REVERT: L 60 SER cc_start: 0.8125 (p) cc_final: 0.7828 (t) REVERT: B 20 PHE cc_start: 0.8742 (m-80) cc_final: 0.8389 (m-80) REVERT: B 156 GLU cc_start: 0.7281 (mp0) cc_final: 0.7028 (mp0) REVERT: B 263 GLN cc_start: 0.8514 (mm-40) cc_final: 0.8261 (mm110) REVERT: B 314 ARG cc_start: 0.8049 (mtp85) cc_final: 0.7805 (mtt90) REVERT: b 51 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7308 (mt-10) REVERT: b 69 ARG cc_start: 0.8034 (ttm110) cc_final: 0.7628 (ttm-80) REVERT: b 76 ASN cc_start: 0.8728 (m-40) cc_final: 0.8475 (m-40) REVERT: b 141 LYS cc_start: 0.8362 (mppt) cc_final: 0.8117 (mppt) REVERT: b 221 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8261 (ptpt) REVERT: b 255 ASN cc_start: 0.8492 (t0) cc_final: 0.8194 (t160) REVERT: b 310 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6597 (mm-30) REVERT: n 38 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.6983 (tp40) REVERT: M 109 GLN cc_start: 0.7252 (pp30) cc_final: 0.7018 (pp30) outliers start: 66 outliers final: 38 residues processed: 478 average time/residue: 1.4020 time to fit residues: 738.9768 Evaluate side-chains 478 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 434 time to evaluate : 2.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ARG Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain a residue 70 SER Chi-restraints excluded: chain a residue 82 ASN Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 315 GLU Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 62 SER Chi-restraints excluded: chain h residue 90 THR Chi-restraints excluded: chain h residue 112 LEU Chi-restraints excluded: chain l residue 11 VAL Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain l residue 89 GLN Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain b residue 51 GLU Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain b residue 204 SER Chi-restraints excluded: chain b residue 219 GLU Chi-restraints excluded: chain b residue 221 LYS Chi-restraints excluded: chain b residue 246 SER Chi-restraints excluded: chain b residue 293 THR Chi-restraints excluded: chain b residue 301 THR Chi-restraints excluded: chain b residue 307 VAL Chi-restraints excluded: chain b residue 310 GLU Chi-restraints excluded: chain m residue 90 THR Chi-restraints excluded: chain n residue 38 GLN Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 77 SER Chi-restraints excluded: chain n residue 103 LYS Chi-restraints excluded: chain N residue 89 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 104 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 123 optimal weight: 0.8980 chunk 188 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 166 optimal weight: 0.7980 chunk 183 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 1 HIS A 76 ASN a 255 ASN h 76 ASN H 76 ASN H 81 GLN L 38 GLN b 82 ASN b 95 ASN b 263 GLN m 83 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.119056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.097210 restraints weight = 71559.411| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 3.79 r_work: 0.3021 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 18091 Z= 0.156 Angle : 0.635 13.462 24597 Z= 0.332 Chirality : 0.044 0.210 2646 Planarity : 0.004 0.052 3142 Dihedral : 5.035 28.455 2471 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.15 % Allowed : 18.28 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.17), residues: 2250 helix: 1.67 (0.40), residues: 149 sheet: -0.24 (0.20), residues: 702 loop : -0.54 (0.16), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 330 HIS 0.005 0.001 HIS B 35 PHE 0.019 0.001 PHE H 27 TYR 0.017 0.002 TYR B 122 ARG 0.011 0.001 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.03756 ( 551) hydrogen bonds : angle 5.39053 ( 1389) SS BOND : bond 0.00717 ( 32) SS BOND : angle 2.17885 ( 64) covalent geometry : bond 0.00382 (18059) covalent geometry : angle 0.62571 (24533) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 444 time to evaluate : 1.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8462 (p) cc_final: 0.8221 (m) REVERT: A 31 ARG cc_start: 0.6277 (mmt180) cc_final: 0.6032 (mmt180) REVERT: A 40 ARG cc_start: 0.8058 (mtm-85) cc_final: 0.7836 (mtm-85) REVERT: A 66 ILE cc_start: 0.8605 (mt) cc_final: 0.8235 (tt) REVERT: A 71 VAL cc_start: 0.8443 (t) cc_final: 0.8217 (p) REVERT: A 110 GLU cc_start: 0.7097 (pt0) cc_final: 0.6888 (pt0) REVERT: A 237 GLU cc_start: 0.7789 (tp30) cc_final: 0.7565 (tp30) REVERT: A 288 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7424 (mt-10) REVERT: A 338 ARG cc_start: 0.7667 (tpp80) cc_final: 0.7437 (ttm-80) REVERT: a 15 CYS cc_start: 0.7729 (m) cc_final: 0.7429 (m) REVERT: a 48 GLN cc_start: 0.8733 (tt0) cc_final: 0.8424 (tt0) REVERT: a 55 CYS cc_start: 0.7479 (p) cc_final: 0.7121 (p) REVERT: a 69 ARG cc_start: 0.8237 (ttm170) cc_final: 0.7916 (ttm170) REVERT: a 255 ASN cc_start: 0.8788 (t0) cc_final: 0.8440 (t0) REVERT: a 261 ARG cc_start: 0.8317 (mtt-85) cc_final: 0.8095 (mtt-85) REVERT: a 276 ARG cc_start: 0.8385 (ptp90) cc_final: 0.8105 (ptp90) REVERT: a 288 GLU cc_start: 0.7564 (tp30) cc_final: 0.7233 (tp30) REVERT: l 4 MET cc_start: 0.8698 (mmm) cc_final: 0.7862 (mmm) REVERT: l 60 SER cc_start: 0.8436 (OUTLIER) cc_final: 0.8225 (t) REVERT: l 63 SER cc_start: 0.8045 (t) cc_final: 0.7713 (p) REVERT: L 11 VAL cc_start: 0.8379 (OUTLIER) cc_final: 0.8136 (m) REVERT: L 60 SER cc_start: 0.8184 (p) cc_final: 0.7872 (t) REVERT: B 20 PHE cc_start: 0.8779 (m-80) cc_final: 0.8408 (m-80) REVERT: B 156 GLU cc_start: 0.7477 (mp0) cc_final: 0.7210 (mp0) REVERT: B 263 GLN cc_start: 0.8639 (mm-40) cc_final: 0.8434 (mm110) REVERT: b 51 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7470 (mt-10) REVERT: b 69 ARG cc_start: 0.8120 (ttm110) cc_final: 0.7710 (ttm-80) REVERT: b 76 ASN cc_start: 0.8821 (m-40) cc_final: 0.8562 (m-40) REVERT: b 141 LYS cc_start: 0.8434 (mppt) cc_final: 0.8171 (mppt) REVERT: b 221 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8326 (ptpt) REVERT: b 255 ASN cc_start: 0.8533 (t0) cc_final: 0.8170 (t160) REVERT: b 284 LYS cc_start: 0.8198 (tptp) cc_final: 0.7750 (tptp) REVERT: b 287 VAL cc_start: 0.8513 (m) cc_final: 0.8308 (t) REVERT: b 310 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6804 (mm-30) REVERT: n 38 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.6984 (tp40) REVERT: M 109 GLN cc_start: 0.7373 (pp30) cc_final: 0.7135 (pp30) outliers start: 59 outliers final: 34 residues processed: 472 average time/residue: 1.3881 time to fit residues: 722.7652 Evaluate side-chains 479 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 439 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain a residue 52 ASP Chi-restraints excluded: chain a residue 70 SER Chi-restraints excluded: chain a residue 82 ASN Chi-restraints excluded: chain a residue 315 GLU Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 90 THR Chi-restraints excluded: chain h residue 112 LEU Chi-restraints excluded: chain l residue 11 VAL Chi-restraints excluded: chain l residue 60 SER Chi-restraints excluded: chain l residue 89 GLN Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain b residue 51 GLU Chi-restraints excluded: chain b residue 204 SER Chi-restraints excluded: chain b residue 221 LYS Chi-restraints excluded: chain b residue 246 SER Chi-restraints excluded: chain b residue 293 THR Chi-restraints excluded: chain b residue 297 SER Chi-restraints excluded: chain b residue 301 THR Chi-restraints excluded: chain b residue 310 GLU Chi-restraints excluded: chain m residue 90 THR Chi-restraints excluded: chain n residue 38 GLN Chi-restraints excluded: chain n residue 77 SER Chi-restraints excluded: chain n residue 103 LYS Chi-restraints excluded: chain N residue 89 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 213 optimal weight: 2.9990 chunk 155 optimal weight: 0.0970 chunk 134 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 220 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 43 optimal weight: 0.0470 chunk 82 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 34 optimal weight: 0.2980 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 1 HIS A 76 ASN a 263 GLN h 76 ASN H 76 ASN H 81 GLN b 82 ASN b 95 ASN b 263 GLN m 83 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.120326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.098271 restraints weight = 74628.828| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 3.95 r_work: 0.3038 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 18091 Z= 0.118 Angle : 0.589 12.562 24597 Z= 0.308 Chirality : 0.043 0.187 2646 Planarity : 0.004 0.044 3142 Dihedral : 4.771 26.432 2471 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.94 % Allowed : 18.75 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.18), residues: 2250 helix: 1.84 (0.41), residues: 149 sheet: -0.09 (0.20), residues: 725 loop : -0.46 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 330 HIS 0.004 0.001 HIS a 195 PHE 0.021 0.001 PHE H 27 TYR 0.014 0.001 TYR B 122 ARG 0.008 0.000 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.03300 ( 551) hydrogen bonds : angle 5.21400 ( 1389) SS BOND : bond 0.00609 ( 32) SS BOND : angle 2.22369 ( 64) covalent geometry : bond 0.00283 (18059) covalent geometry : angle 0.57871 (24533) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 464 time to evaluate : 1.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8421 (p) cc_final: 0.8188 (m) REVERT: A 31 ARG cc_start: 0.6280 (mmt180) cc_final: 0.5898 (mmt180) REVERT: A 40 ARG cc_start: 0.7961 (mtm-85) cc_final: 0.7651 (mtm-85) REVERT: A 66 ILE cc_start: 0.8568 (mt) cc_final: 0.8188 (tt) REVERT: A 71 VAL cc_start: 0.8381 (t) cc_final: 0.8134 (p) REVERT: A 110 GLU cc_start: 0.7074 (pt0) cc_final: 0.6785 (pt0) REVERT: A 237 GLU cc_start: 0.7772 (tp30) cc_final: 0.7520 (tp30) REVERT: a 48 GLN cc_start: 0.8712 (tt0) cc_final: 0.8414 (tt0) REVERT: a 55 CYS cc_start: 0.7452 (p) cc_final: 0.7089 (p) REVERT: a 69 ARG cc_start: 0.8210 (ttm170) cc_final: 0.7905 (ttm170) REVERT: a 255 ASN cc_start: 0.8735 (t0) cc_final: 0.8472 (t0) REVERT: a 276 ARG cc_start: 0.8374 (ptp90) cc_final: 0.8079 (ptp90) REVERT: a 288 GLU cc_start: 0.7581 (tp30) cc_final: 0.7244 (tp30) REVERT: h 6 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7437 (pm20) REVERT: l 4 MET cc_start: 0.8690 (mmm) cc_final: 0.7838 (mmm) REVERT: l 60 SER cc_start: 0.8451 (t) cc_final: 0.8239 (t) REVERT: l 63 SER cc_start: 0.8026 (t) cc_final: 0.7667 (p) REVERT: L 11 VAL cc_start: 0.8368 (OUTLIER) cc_final: 0.8118 (m) REVERT: L 60 SER cc_start: 0.8185 (p) cc_final: 0.7863 (t) REVERT: B 20 PHE cc_start: 0.8777 (m-80) cc_final: 0.8407 (m-80) REVERT: B 156 GLU cc_start: 0.7477 (mp0) cc_final: 0.7186 (mp0) REVERT: B 274 GLU cc_start: 0.7568 (tm-30) cc_final: 0.7104 (tm-30) REVERT: B 276 ARG cc_start: 0.8021 (mtm-85) cc_final: 0.7564 (mtt-85) REVERT: b 51 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7473 (mt-10) REVERT: b 69 ARG cc_start: 0.8115 (ttm110) cc_final: 0.7833 (ttm-80) REVERT: b 141 LYS cc_start: 0.8436 (mppt) cc_final: 0.8155 (mppt) REVERT: b 255 ASN cc_start: 0.8517 (t0) cc_final: 0.8115 (t160) REVERT: b 284 LYS cc_start: 0.8178 (tptp) cc_final: 0.7699 (tptp) REVERT: b 287 VAL cc_start: 0.8495 (m) cc_final: 0.8293 (t) REVERT: b 293 THR cc_start: 0.8172 (OUTLIER) cc_final: 0.7903 (p) REVERT: b 310 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6769 (mm-30) REVERT: M 109 GLN cc_start: 0.7380 (pp30) cc_final: 0.7142 (pp30) outliers start: 55 outliers final: 37 residues processed: 489 average time/residue: 1.4009 time to fit residues: 756.9035 Evaluate side-chains 489 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 447 time to evaluate : 1.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain a residue 52 ASP Chi-restraints excluded: chain a residue 70 SER Chi-restraints excluded: chain a residue 82 ASN Chi-restraints excluded: chain a residue 315 GLU Chi-restraints excluded: chain h residue 6 GLU Chi-restraints excluded: chain h residue 11 LEU Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 88 GLU Chi-restraints excluded: chain h residue 90 THR Chi-restraints excluded: chain h residue 112 LEU Chi-restraints excluded: chain l residue 11 VAL Chi-restraints excluded: chain l residue 89 GLN Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain b residue 51 GLU Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain b residue 204 SER Chi-restraints excluded: chain b residue 246 SER Chi-restraints excluded: chain b residue 293 THR Chi-restraints excluded: chain b residue 301 THR Chi-restraints excluded: chain b residue 310 GLU Chi-restraints excluded: chain m residue 21 SER Chi-restraints excluded: chain m residue 90 THR Chi-restraints excluded: chain n residue 31 THR Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 89 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 7 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 61 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 87 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 184 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 1 HIS A 76 ASN a 151 ASN a 263 GLN a 286 HIS h 76 ASN H 76 ASN H 81 GLN ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN b 82 ASN b 95 ASN b 263 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.118834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.097473 restraints weight = 63401.932| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 3.35 r_work: 0.3089 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 18091 Z= 0.167 Angle : 0.646 12.472 24597 Z= 0.336 Chirality : 0.044 0.202 2646 Planarity : 0.004 0.057 3142 Dihedral : 4.993 28.477 2471 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.26 % Allowed : 18.64 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 (0.17), residues: 2250 helix: 1.76 (0.40), residues: 147 sheet: -0.12 (0.20), residues: 704 loop : -0.56 (0.16), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 330 HIS 0.005 0.001 HIS A 35 PHE 0.022 0.001 PHE H 27 TYR 0.017 0.002 TYR H 94 ARG 0.008 0.001 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.03799 ( 551) hydrogen bonds : angle 5.34810 ( 1389) SS BOND : bond 0.00743 ( 32) SS BOND : angle 2.47142 ( 64) covalent geometry : bond 0.00411 (18059) covalent geometry : angle 0.63422 (24533) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 458 time to evaluate : 1.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8435 (p) cc_final: 0.8192 (m) REVERT: A 31 ARG cc_start: 0.6119 (mmt180) cc_final: 0.5834 (mmt90) REVERT: A 40 ARG cc_start: 0.7981 (mtm-85) cc_final: 0.7629 (mtm-85) REVERT: A 66 ILE cc_start: 0.8587 (mt) cc_final: 0.8192 (tt) REVERT: A 71 VAL cc_start: 0.8393 (t) cc_final: 0.8150 (p) REVERT: A 110 GLU cc_start: 0.6979 (pt0) cc_final: 0.6686 (pt0) REVERT: A 237 GLU cc_start: 0.7663 (tp30) cc_final: 0.7457 (tp30) REVERT: a 15 CYS cc_start: 0.7487 (m) cc_final: 0.7155 (m) REVERT: a 48 GLN cc_start: 0.8672 (tt0) cc_final: 0.8345 (tt0) REVERT: a 55 CYS cc_start: 0.7237 (p) cc_final: 0.6844 (p) REVERT: a 69 ARG cc_start: 0.8159 (ttm170) cc_final: 0.7830 (ttm170) REVERT: a 261 ARG cc_start: 0.8170 (mtt-85) cc_final: 0.7962 (mtt-85) REVERT: a 276 ARG cc_start: 0.8295 (ptp90) cc_final: 0.7995 (ptp90) REVERT: a 288 GLU cc_start: 0.7516 (tp30) cc_final: 0.7174 (tp30) REVERT: l 60 SER cc_start: 0.8431 (OUTLIER) cc_final: 0.8211 (t) REVERT: l 63 SER cc_start: 0.7994 (t) cc_final: 0.7649 (p) REVERT: L 11 VAL cc_start: 0.8335 (OUTLIER) cc_final: 0.8096 (m) REVERT: L 60 SER cc_start: 0.8157 (p) cc_final: 0.7840 (t) REVERT: B 20 PHE cc_start: 0.8761 (m-80) cc_final: 0.8400 (m-80) REVERT: B 156 GLU cc_start: 0.7387 (mp0) cc_final: 0.7114 (mp0) REVERT: B 274 GLU cc_start: 0.7455 (tm-30) cc_final: 0.7165 (tm-30) REVERT: B 276 ARG cc_start: 0.7930 (mtm-85) cc_final: 0.7588 (mtm-85) REVERT: b 51 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7356 (mt-10) REVERT: b 69 ARG cc_start: 0.8061 (ttm110) cc_final: 0.7657 (ttm-80) REVERT: b 141 LYS cc_start: 0.8402 (mppt) cc_final: 0.8161 (mppt) REVERT: b 221 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8273 (ptpt) REVERT: b 255 ASN cc_start: 0.8504 (t0) cc_final: 0.8190 (t160) REVERT: b 284 LYS cc_start: 0.8152 (tptp) cc_final: 0.7676 (tptp) REVERT: b 293 THR cc_start: 0.8163 (OUTLIER) cc_final: 0.7905 (p) REVERT: n 38 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.6625 (tp40) REVERT: M 109 GLN cc_start: 0.7296 (pp30) cc_final: 0.7047 (pp30) outliers start: 61 outliers final: 46 residues processed: 486 average time/residue: 1.3793 time to fit residues: 739.7434 Evaluate side-chains 500 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 448 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain a residue 52 ASP Chi-restraints excluded: chain a residue 70 SER Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 82 ASN Chi-restraints excluded: chain a residue 315 GLU Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 62 SER Chi-restraints excluded: chain h residue 88 GLU Chi-restraints excluded: chain h residue 90 THR Chi-restraints excluded: chain h residue 112 LEU Chi-restraints excluded: chain l residue 9 SER Chi-restraints excluded: chain l residue 11 VAL Chi-restraints excluded: chain l residue 60 SER Chi-restraints excluded: chain l residue 89 GLN Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain b residue 51 GLU Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain b residue 204 SER Chi-restraints excluded: chain b residue 219 GLU Chi-restraints excluded: chain b residue 221 LYS Chi-restraints excluded: chain b residue 246 SER Chi-restraints excluded: chain b residue 293 THR Chi-restraints excluded: chain b residue 297 SER Chi-restraints excluded: chain b residue 301 THR Chi-restraints excluded: chain m residue 21 SER Chi-restraints excluded: chain m residue 90 THR Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain n residue 31 THR Chi-restraints excluded: chain n residue 38 GLN Chi-restraints excluded: chain n residue 103 LYS Chi-restraints excluded: chain M residue 17 SER Chi-restraints excluded: chain N residue 89 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 56 optimal weight: 0.9980 chunk 138 optimal weight: 0.6980 chunk 76 optimal weight: 0.4980 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 203 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 1 HIS A 76 ASN a 151 ASN a 255 ASN a 263 GLN h 76 ASN H 76 ASN H 81 GLN L 38 GLN B 76 ASN B 95 ASN B 263 GLN b 82 ASN b 95 ASN b 263 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.119273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.097677 restraints weight = 65340.130| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 3.55 r_work: 0.3062 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 18091 Z= 0.160 Angle : 0.645 13.794 24597 Z= 0.335 Chirality : 0.044 0.200 2646 Planarity : 0.004 0.054 3142 Dihedral : 4.999 27.858 2471 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.15 % Allowed : 19.07 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.17), residues: 2250 helix: 1.69 (0.40), residues: 147 sheet: -0.13 (0.20), residues: 712 loop : -0.53 (0.16), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 330 HIS 0.005 0.001 HIS A 35 PHE 0.022 0.001 PHE H 27 TYR 0.017 0.002 TYR m 94 ARG 0.007 0.001 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.03746 ( 551) hydrogen bonds : angle 5.34805 ( 1389) SS BOND : bond 0.00732 ( 32) SS BOND : angle 2.39502 ( 64) covalent geometry : bond 0.00394 (18059) covalent geometry : angle 0.63381 (24533) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 454 time to evaluate : 1.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8425 (p) cc_final: 0.8203 (m) REVERT: A 31 ARG cc_start: 0.6214 (mmt180) cc_final: 0.5825 (mmt180) REVERT: A 40 ARG cc_start: 0.7999 (mtm-85) cc_final: 0.7706 (mtm-85) REVERT: A 51 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7804 (mp0) REVERT: A 71 VAL cc_start: 0.8435 (t) cc_final: 0.8206 (p) REVERT: A 110 GLU cc_start: 0.7035 (pt0) cc_final: 0.6770 (pt0) REVERT: A 237 GLU cc_start: 0.7767 (tp30) cc_final: 0.7559 (tp30) REVERT: a 15 CYS cc_start: 0.7538 (m) cc_final: 0.7219 (m) REVERT: a 47 LYS cc_start: 0.8573 (tttt) cc_final: 0.8342 (tttp) REVERT: a 48 GLN cc_start: 0.8679 (tt0) cc_final: 0.8400 (tt0) REVERT: a 55 CYS cc_start: 0.7347 (p) cc_final: 0.6959 (p) REVERT: a 69 ARG cc_start: 0.8200 (ttm170) cc_final: 0.7879 (ttm170) REVERT: a 261 ARG cc_start: 0.8203 (mtt-85) cc_final: 0.7997 (mtt-85) REVERT: a 276 ARG cc_start: 0.8348 (ptp90) cc_final: 0.8040 (ptp90) REVERT: a 288 GLU cc_start: 0.7550 (tp30) cc_final: 0.7205 (tp30) REVERT: h 6 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7387 (pm20) REVERT: l 63 SER cc_start: 0.8020 (t) cc_final: 0.7668 (p) REVERT: L 11 VAL cc_start: 0.8357 (OUTLIER) cc_final: 0.8113 (m) REVERT: L 60 SER cc_start: 0.8202 (p) cc_final: 0.7870 (t) REVERT: B 20 PHE cc_start: 0.8772 (m-80) cc_final: 0.8400 (m-80) REVERT: B 156 GLU cc_start: 0.7463 (mp0) cc_final: 0.6970 (mp0) REVERT: B 276 ARG cc_start: 0.8016 (mtm-85) cc_final: 0.7771 (mtt-85) REVERT: B 340 GLU cc_start: 0.7892 (tt0) cc_final: 0.7688 (tt0) REVERT: b 51 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7475 (mt-10) REVERT: b 69 ARG cc_start: 0.8116 (ttm110) cc_final: 0.7709 (ttm-80) REVERT: b 141 LYS cc_start: 0.8426 (mppt) cc_final: 0.8160 (mppt) REVERT: b 221 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8302 (ptpt) REVERT: b 255 ASN cc_start: 0.8525 (t0) cc_final: 0.8188 (t160) REVERT: b 284 LYS cc_start: 0.8150 (tptp) cc_final: 0.7639 (tptp) REVERT: b 293 THR cc_start: 0.8191 (OUTLIER) cc_final: 0.7945 (p) REVERT: b 310 GLU cc_start: 0.6942 (mm-30) cc_final: 0.6545 (tm-30) REVERT: b 315 GLU cc_start: 0.7618 (pt0) cc_final: 0.7352 (pt0) REVERT: n 38 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.6663 (tp40) REVERT: M 109 GLN cc_start: 0.7367 (pp30) cc_final: 0.7162 (pp30) outliers start: 59 outliers final: 44 residues processed: 485 average time/residue: 1.3836 time to fit residues: 740.4615 Evaluate side-chains 500 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 449 time to evaluate : 1.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain a residue 70 SER Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 251 LEU Chi-restraints excluded: chain a residue 315 GLU Chi-restraints excluded: chain h residue 6 GLU Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 62 SER Chi-restraints excluded: chain h residue 88 GLU Chi-restraints excluded: chain h residue 90 THR Chi-restraints excluded: chain h residue 112 LEU Chi-restraints excluded: chain l residue 9 SER Chi-restraints excluded: chain l residue 89 GLN Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain b residue 51 GLU Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain b residue 204 SER Chi-restraints excluded: chain b residue 221 LYS Chi-restraints excluded: chain b residue 246 SER Chi-restraints excluded: chain b residue 293 THR Chi-restraints excluded: chain b residue 297 SER Chi-restraints excluded: chain b residue 301 THR Chi-restraints excluded: chain m residue 90 THR Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain n residue 31 THR Chi-restraints excluded: chain n residue 38 GLN Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 77 SER Chi-restraints excluded: chain n residue 103 LYS Chi-restraints excluded: chain M residue 17 SER Chi-restraints excluded: chain M residue 114 THR Chi-restraints excluded: chain N residue 89 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 63 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 217 optimal weight: 3.9990 chunk 211 optimal weight: 0.7980 chunk 152 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 105 optimal weight: 0.1980 chunk 93 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 1 HIS A 76 ASN A 158 HIS a 82 ASN a 151 ASN a 255 ASN a 263 GLN h 76 ASN H 76 ASN H 81 GLN B 76 ASN B 95 ASN B 263 GLN b 82 ASN b 95 ASN b 263 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.119659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.097615 restraints weight = 74802.453| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 3.95 r_work: 0.3012 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 18091 Z= 0.151 Angle : 0.648 13.755 24597 Z= 0.336 Chirality : 0.044 0.196 2646 Planarity : 0.004 0.043 3142 Dihedral : 4.952 27.521 2471 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.84 % Allowed : 19.96 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -0.39 (0.18), residues: 2250 helix: 1.78 (0.40), residues: 147 sheet: -0.17 (0.20), residues: 724 loop : -0.49 (0.16), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP a 168 HIS 0.004 0.001 HIS A 35 PHE 0.024 0.001 PHE H 27 TYR 0.017 0.001 TYR B 175 ARG 0.007 0.000 ARG a 336 Details of bonding type rmsd hydrogen bonds : bond 0.03655 ( 551) hydrogen bonds : angle 5.31475 ( 1389) SS BOND : bond 0.00710 ( 32) SS BOND : angle 2.34758 ( 64) covalent geometry : bond 0.00371 (18059) covalent geometry : angle 0.63723 (24533) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 455 time to evaluate : 1.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8459 (p) cc_final: 0.8248 (m) REVERT: A 37 ASP cc_start: 0.6773 (p0) cc_final: 0.6497 (p0) REVERT: A 40 ARG cc_start: 0.8037 (mtm-85) cc_final: 0.7757 (mtm-85) REVERT: A 51 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7885 (mp0) REVERT: A 71 VAL cc_start: 0.8437 (t) cc_final: 0.8213 (p) REVERT: A 110 GLU cc_start: 0.7118 (pt0) cc_final: 0.6853 (pt0) REVERT: A 237 GLU cc_start: 0.7820 (tp30) cc_final: 0.7618 (tp30) REVERT: a 15 CYS cc_start: 0.7720 (m) cc_final: 0.7411 (m) REVERT: a 48 GLN cc_start: 0.8743 (tt0) cc_final: 0.8456 (tt0) REVERT: a 55 CYS cc_start: 0.7481 (p) cc_final: 0.7102 (p) REVERT: a 69 ARG cc_start: 0.8243 (ttm170) cc_final: 0.7927 (ttm170) REVERT: a 255 ASN cc_start: 0.8803 (t0) cc_final: 0.8595 (t0) REVERT: a 261 ARG cc_start: 0.8337 (mtt-85) cc_final: 0.8130 (mtt-85) REVERT: a 276 ARG cc_start: 0.8427 (ptp90) cc_final: 0.8125 (ptp90) REVERT: a 288 GLU cc_start: 0.7605 (tp30) cc_final: 0.7245 (tp30) REVERT: l 63 SER cc_start: 0.8041 (t) cc_final: 0.7713 (p) REVERT: L 11 VAL cc_start: 0.8366 (OUTLIER) cc_final: 0.8121 (m) REVERT: L 60 SER cc_start: 0.8238 (p) cc_final: 0.7914 (t) REVERT: B 20 PHE cc_start: 0.8781 (m-80) cc_final: 0.8415 (m-80) REVERT: B 156 GLU cc_start: 0.7304 (mp0) cc_final: 0.7014 (mp0) REVERT: B 170 LYS cc_start: 0.8305 (pttp) cc_final: 0.8087 (pttp) REVERT: B 274 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7136 (tm-30) REVERT: B 276 ARG cc_start: 0.8103 (mtm-85) cc_final: 0.7671 (mtt-85) REVERT: B 340 GLU cc_start: 0.7910 (tt0) cc_final: 0.7700 (tt0) REVERT: b 51 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7563 (mt-10) REVERT: b 69 ARG cc_start: 0.8174 (ttm110) cc_final: 0.7774 (ttm-80) REVERT: b 141 LYS cc_start: 0.8442 (mppt) cc_final: 0.8193 (mppt) REVERT: b 255 ASN cc_start: 0.8536 (t0) cc_final: 0.8168 (t160) REVERT: b 284 LYS cc_start: 0.8219 (tptp) cc_final: 0.7721 (tptp) REVERT: b 293 THR cc_start: 0.8211 (OUTLIER) cc_final: 0.7978 (p) REVERT: b 310 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6671 (tm-30) REVERT: b 315 GLU cc_start: 0.7667 (pt0) cc_final: 0.7399 (pt0) REVERT: n 38 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.6707 (tp40) outliers start: 53 outliers final: 45 residues processed: 483 average time/residue: 1.4352 time to fit residues: 768.2986 Evaluate side-chains 497 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 447 time to evaluate : 2.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain a residue 70 SER Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 82 ASN Chi-restraints excluded: chain a residue 315 GLU Chi-restraints excluded: chain h residue 28 THR Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 62 SER Chi-restraints excluded: chain h residue 88 GLU Chi-restraints excluded: chain h residue 90 THR Chi-restraints excluded: chain h residue 112 LEU Chi-restraints excluded: chain l residue 9 SER Chi-restraints excluded: chain l residue 89 GLN Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain b residue 51 GLU Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain b residue 204 SER Chi-restraints excluded: chain b residue 246 SER Chi-restraints excluded: chain b residue 293 THR Chi-restraints excluded: chain b residue 297 SER Chi-restraints excluded: chain b residue 301 THR Chi-restraints excluded: chain m residue 21 SER Chi-restraints excluded: chain m residue 90 THR Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain n residue 31 THR Chi-restraints excluded: chain n residue 38 GLN Chi-restraints excluded: chain n residue 77 SER Chi-restraints excluded: chain n residue 103 LYS Chi-restraints excluded: chain M residue 17 SER Chi-restraints excluded: chain M residue 114 THR Chi-restraints excluded: chain N residue 89 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 203 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 168 optimal weight: 0.3980 chunk 219 optimal weight: 1.9990 chunk 74 optimal weight: 0.0000 chunk 98 optimal weight: 1.9990 chunk 134 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 1 HIS A 76 ASN A 158 HIS a 82 ASN a 151 ASN a 263 GLN h 76 ASN H 76 ASN H 81 GLN B 76 ASN B 95 ASN B 263 GLN b 82 ASN b 95 ASN b 263 GLN M 109 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.120109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.098643 restraints weight = 65988.242| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 3.53 r_work: 0.3054 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 18091 Z= 0.130 Angle : 0.631 13.483 24597 Z= 0.326 Chirality : 0.043 0.188 2646 Planarity : 0.004 0.043 3142 Dihedral : 4.899 27.239 2471 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.15 % Allowed : 19.64 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 2250 helix: 1.86 (0.40), residues: 147 sheet: -0.16 (0.20), residues: 724 loop : -0.47 (0.16), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP a 168 HIS 0.004 0.001 HIS B 195 PHE 0.026 0.001 PHE H 27 TYR 0.015 0.001 TYR B 122 ARG 0.008 0.000 ARG A 41 Details of bonding type rmsd hydrogen bonds : bond 0.03515 ( 551) hydrogen bonds : angle 5.27073 ( 1389) SS BOND : bond 0.00674 ( 32) SS BOND : angle 2.28322 ( 64) covalent geometry : bond 0.00318 (18059) covalent geometry : angle 0.62071 (24533) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16625.14 seconds wall clock time: 285 minutes 26.84 seconds (17126.84 seconds total)