Starting phenix.real_space_refine on Sat Aug 23 14:26:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jqs_36578/08_2025/8jqs_36578.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jqs_36578/08_2025/8jqs_36578.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jqs_36578/08_2025/8jqs_36578.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jqs_36578/08_2025/8jqs_36578.map" model { file = "/net/cci-nas-00/data/ceres_data/8jqs_36578/08_2025/8jqs_36578.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jqs_36578/08_2025/8jqs_36578.cif" } resolution = 2.63 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 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 4734 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 58 5.16 5 C 5593 2.51 5 N 1542 2.21 5 O 1697 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8890 Number of models: 1 Model: "" Number of chains: 6 Chain: "a" Number of atoms: 2772 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 352, 2751 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 332} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 69 Planarities with less than four sites: {'GLU:plan': 4, 'TRP:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 53 Conformer: "B" Number of residues, atoms: 352, 2751 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 332} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 69 Planarities with less than four sites: {'GLU:plan': 4, 'TRP:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 53 bond proxies already assigned to first conformer: 2802 Chain: "h" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 888 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 112} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "l" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 761 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 9, 'TRANS': 94} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "H" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 896 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 112} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 797 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 97} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 2776 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 352, 2755 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 332} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 46 Conformer: "B" Number of residues, atoms: 352, 2755 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 332} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 46 bond proxies already assigned to first conformer: 2807 Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N ASER a 62 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER a 62 " occ=0.50 residue: pdb=" N AVAL a 64 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL a 64 " occ=0.50 residue: pdb=" N AMET a 71 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET a 71 " occ=0.50 residue: pdb=" N ASER A 62 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 62 " occ=0.50 residue: pdb=" N AVAL A 64 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL A 64 " occ=0.50 residue: pdb=" N AMET A 71 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET A 71 " occ=0.50 Time building chain proxies: 2.84, per 1000 atoms: 0.32 Number of scatterers: 8890 At special positions: 0 Unit cell: (107.95, 159.8, 107.1, 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 58 16.00 O 1697 8.00 N 1542 7.00 C 5593 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS a 8 " - pdb=" SG CYS a 19 " distance=2.03 Simple disulfide: pdb=" SG CYS a 59 " - pdb=" SG CYS a 147 " distance=2.03 Simple disulfide: pdb=" SG CYS a 183 " - pdb=" SG CYS a 227 " distance=2.04 Simple disulfide: pdb=" SG CYS a 284 " - pdb=" SG CYS a 333 " distance=2.01 Simple disulfide: pdb=" SG CYS a 295 " - pdb=" SG CYS a 316 " distance=2.04 Simple disulfide: pdb=" SG CYS a 317 " - pdb=" SG CYS a 320 " distance=2.03 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 96 " distance=2.03 Simple disulfide: pdb=" SG CYS l 22 " - pdb=" SG CYS l 87 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.04 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 19 " distance=2.14 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 227 " distance=2.03 Simple disulfide: pdb=" SG CYS A 284 " - pdb=" SG CYS A 333 " distance=2.00 Simple disulfide: pdb=" SG CYS A 295 " - pdb=" SG CYS A 316 " distance=2.04 Simple disulfide: pdb=" SG CYS A 317 " - pdb=" SG CYS A 320 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 340.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2114 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 20 sheets defined 13.2% alpha, 30.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'a' and resid 42 through 56 removed outlier: 3.692A pdb=" N ALA a 47 " --> pdb=" O PRO a 43 " (cutoff:3.500A) Processing helix chain 'a' and resid 65 through 82 removed outlier: 3.550A pdb=" N ASN a 69 " --> pdb=" O SER a 65 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLY a 77 " --> pdb=" O ARG a 73 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N GLU a 78 " --> pdb=" O SER a 74 " (cutoff:3.500A) Processing helix chain 'a' and resid 148 through 150 No H-bonds generated for 'chain 'a' and resid 148 through 150' Processing helix chain 'a' and resid 184 through 187 removed outlier: 3.816A pdb=" N VAL a 187 " --> pdb=" O ASP a 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 184 through 187' Processing helix chain 'a' and resid 230 through 234 Processing helix chain 'a' and resid 248 through 252 Processing helix chain 'a' and resid 256 through 260 removed outlier: 3.770A pdb=" N THR a 260 " --> pdb=" O HIS a 257 " (cutoff:3.500A) Processing helix chain 'a' and resid 345 through 349 Processing helix chain 'h' and resid 28 through 32 removed outlier: 4.106A pdb=" N TYR h 32 " --> pdb=" O PHE h 29 " (cutoff:3.500A) Processing helix chain 'h' and resid 87 through 91 removed outlier: 4.117A pdb=" N THR h 91 " --> pdb=" O ALA h 88 " (cutoff:3.500A) Processing helix chain 'l' and resid 26 through 30 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.536A pdb=" N SER H 31 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.880A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 30 Processing helix chain 'A' and resid 42 through 56 removed outlier: 3.747A pdb=" N ALA A 48 " --> pdb=" O ARG A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 84 removed outlier: 3.520A pdb=" N ASN A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLY A 77 " --> pdb=" O ARG A 73 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N GLU A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 184 through 187 removed outlier: 3.855A pdb=" N VAL A 187 " --> pdb=" O ASP A 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 184 through 187' Processing helix chain 'A' and resid 230 through 234 Processing helix chain 'A' and resid 248 through 252 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.666A pdb=" N THR A 260 " --> pdb=" O HIS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 349 Processing sheet with id=AA1, first strand: chain 'a' and resid 2 through 11 removed outlier: 4.539A pdb=" N HIS a 2 " --> pdb=" O VAL A 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 37 through 39 removed outlier: 6.252A pdb=" N LYS a 37 " --> pdb=" O VAL a 171 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N LEU a 173 " --> pdb=" O LYS a 37 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N HIS a 39 " --> pdb=" O LEU a 173 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N VAL a 175 " --> pdb=" O HIS a 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 60 through 61 removed outlier: 7.023A pdb=" N GLY a 60 " --> pdb=" O ALA a 153 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'a' and resid 91 through 94 removed outlier: 6.622A pdb=" N THR a 91 " --> pdb=" O PHE a 137 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL a 139 " --> pdb=" O THR a 91 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL a 93 " --> pdb=" O VAL a 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'a' and resid 333 through 335 removed outlier: 5.756A pdb=" N LEU a 216 " --> pdb=" O GLU a 209 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLU a 209 " --> pdb=" O LEU a 216 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG a 218 " --> pdb=" O GLU a 207 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU a 196 " --> pdb=" O LYS a 193 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU A 196 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG A 218 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N GLU A 209 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N LEU A 216 " --> pdb=" O GLU A 209 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N LYS A 217 " --> pdb=" O PHE A 281 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE A 281 " --> pdb=" O LYS A 217 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 288 through 291 removed outlier: 6.396A pdb=" N LYS a 288 " --> pdb=" O TRP a 315 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N CYS a 317 " --> pdb=" O LYS a 288 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N HIS a 290 " --> pdb=" O CYS a 317 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'h' and resid 3 through 6 removed outlier: 3.584A pdb=" N LEU h 18 " --> pdb=" O TRP h 83 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER h 71 " --> pdb=" O TYR h 80 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'h' and resid 10 through 12 removed outlier: 6.308A pdb=" N ILE h 34 " --> pdb=" O ILE h 50 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE h 50 " --> pdb=" O ILE h 34 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N TRP h 36 " --> pdb=" O MET h 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'h' and resid 10 through 12 removed outlier: 6.981A pdb=" N CYS h 96 " --> pdb=" O TRP h 108 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TRP h 108 " --> pdb=" O CYS h 96 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG h 98 " --> pdb=" O ASP h 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'l' and resid 18 through 23 Processing sheet with id=AB2, first strand: chain 'l' and resid 44 through 47 removed outlier: 6.681A pdb=" N TRP l 34 " --> pdb=" O VAL l 46 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.632A pdb=" N LEU H 18 " --> pdb=" O TRP H 83 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.511A pdb=" N GLU H 10 " --> pdb=" O THR H 115 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ILE H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.511A pdb=" N GLU H 10 " --> pdb=" O THR H 115 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N CYS H 96 " --> pdb=" O TRP H 108 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N TRP H 108 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG H 98 " --> pdb=" O ASP H 106 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.613A pdb=" N TRP L 34 " --> pdb=" O VAL L 46 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AB8, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AB9, first strand: chain 'A' and resid 38 through 39 removed outlier: 6.468A pdb=" N HIS A 39 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL A 175 " --> pdb=" O HIS A 39 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N TRP A 172 " --> pdb=" O GLU A 160 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 92 through 94 removed outlier: 6.983A pdb=" N GLY A 60 " --> pdb=" O ALA A 153 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 288 through 291 removed outlier: 6.250A pdb=" N LYS A 288 " --> pdb=" O TRP A 315 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N CYS A 317 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N HIS A 290 " --> pdb=" O CYS A 317 " (cutoff:3.500A) 284 hydrogen bonds defined for protein. 674 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: 1.16 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2872 1.34 - 1.46: 2291 1.46 - 1.59: 3886 1.59 - 1.71: 0 1.71 - 1.84: 84 Bond restraints: 9133 Sorted by residual: bond pdb=" CA GLU a 283 " pdb=" C GLU a 283 " ideal model delta sigma weight residual 1.526 1.480 0.047 1.37e-02 5.33e+03 1.16e+01 bond pdb=" CA CYS a 333 " pdb=" CB CYS a 333 " ideal model delta sigma weight residual 1.530 1.480 0.050 1.55e-02 4.16e+03 1.04e+01 bond pdb=" CA GLU A 85 " pdb=" C GLU A 85 " ideal model delta sigma weight residual 1.523 1.482 0.042 1.34e-02 5.57e+03 9.64e+00 bond pdb=" CA ASP a 331 " pdb=" C ASP a 331 " ideal model delta sigma weight residual 1.522 1.481 0.041 1.37e-02 5.33e+03 8.97e+00 bond pdb=" CA GLU A 84 " pdb=" C GLU A 84 " ideal model delta sigma weight residual 1.523 1.482 0.042 1.62e-02 3.81e+03 6.62e+00 ... (remaining 9128 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 12241 2.45 - 4.89: 173 4.89 - 7.34: 19 7.34 - 9.78: 3 9.78 - 12.23: 3 Bond angle restraints: 12439 Sorted by residual: angle pdb=" N GLY a 332 " pdb=" CA GLY a 332 " pdb=" C GLY a 332 " ideal model delta sigma weight residual 110.45 121.63 -11.18 1.30e+00 5.92e-01 7.40e+01 angle pdb=" N ASN A 86 " pdb=" CA ASN A 86 " pdb=" C ASN A 86 " ideal model delta sigma weight residual 113.61 101.38 12.23 1.50e+00 4.44e-01 6.65e+01 angle pdb=" N CYS A 19 " pdb=" CA CYS A 19 " pdb=" C CYS A 19 " ideal model delta sigma weight residual 107.88 116.07 -8.19 1.41e+00 5.03e-01 3.37e+01 angle pdb=" C GLN L 41 " pdb=" N ALA L 42 " pdb=" CA ALA L 42 " ideal model delta sigma weight residual 120.97 132.62 -11.65 2.84e+00 1.24e-01 1.68e+01 angle pdb=" N GLY a 22 " pdb=" CA GLY a 22 " pdb=" C GLY a 22 " ideal model delta sigma weight residual 110.58 116.00 -5.42 1.35e+00 5.49e-01 1.61e+01 ... (remaining 12434 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 4736 17.42 - 34.83: 505 34.83 - 52.25: 134 52.25 - 69.67: 36 69.67 - 87.08: 11 Dihedral angle restraints: 5422 sinusoidal: 2109 harmonic: 3313 Sorted by residual: dihedral pdb=" CB CYS A 317 " pdb=" SG CYS A 317 " pdb=" SG CYS A 320 " pdb=" CB CYS A 320 " ideal model delta sinusoidal sigma weight residual -86.00 -169.00 83.00 1 1.00e+01 1.00e-02 8.43e+01 dihedral pdb=" CB CYS a 59 " pdb=" SG CYS a 59 " pdb=" SG CYS a 147 " pdb=" CB CYS a 147 " ideal model delta sinusoidal sigma weight residual 93.00 48.49 44.51 1 1.00e+01 1.00e-02 2.75e+01 dihedral pdb=" CA PRO A 40 " pdb=" C PRO A 40 " pdb=" N ASP A 41 " pdb=" CA ASP A 41 " ideal model delta harmonic sigma weight residual 180.00 -154.13 -25.87 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 5419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 936 0.047 - 0.093: 308 0.093 - 0.140: 91 0.140 - 0.186: 2 0.186 - 0.233: 1 Chirality restraints: 1338 Sorted by residual: chirality pdb=" CA CYS A 19 " pdb=" N CYS A 19 " pdb=" C CYS A 19 " pdb=" CB CYS A 19 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA ILE a 82 " pdb=" N ILE a 82 " pdb=" C ILE a 82 " pdb=" CB ILE a 82 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.33e-01 chirality pdb=" CA ILE L 47 " pdb=" N ILE L 47 " pdb=" C ILE L 47 " pdb=" CB ILE L 47 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.04e-01 ... (remaining 1335 not shown) Planarity restraints: 1599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 81 " 0.018 2.00e-02 2.50e+03 3.65e-02 1.34e+01 pdb=" C ALA A 81 " -0.063 2.00e-02 2.50e+03 pdb=" O ALA A 81 " 0.023 2.00e-02 2.50e+03 pdb=" N ILE A 82 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO L 7 " 0.045 5.00e-02 4.00e+02 6.89e-02 7.59e+00 pdb=" N PRO L 8 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU a 282 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.72e+00 pdb=" C GLU a 282 " 0.041 2.00e-02 2.50e+03 pdb=" O GLU a 282 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU a 283 " -0.014 2.00e-02 2.50e+03 ... (remaining 1596 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 272 2.69 - 3.24: 7637 3.24 - 3.80: 12981 3.80 - 4.35: 18334 4.35 - 4.90: 31293 Nonbonded interactions: 70517 Sorted by model distance: nonbonded pdb=" O LEU a 235 " pdb=" OG SER a 256 " model vdw 2.139 3.040 nonbonded pdb=" O PRO A 40 " pdb=" NE1 TRP A 122 " model vdw 2.156 3.120 nonbonded pdb=" OG SER a 301 " pdb=" O TYR a 335 " model vdw 2.168 3.040 nonbonded pdb=" N ASP a 41 " pdb=" OD1 ASP a 41 " model vdw 2.181 3.120 nonbonded pdb=" OG SER A 301 " pdb=" O TYR A 335 " model vdw 2.184 3.040 ... (remaining 70512 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 14 or (resid 15 through 16 and (name N or name C \ A or name C or name O or name CB )) or resid 17 through 29 or (resid 30 through \ 35 and (name N or name CA or name C or name O or name CB )) or resid 36 through \ 61 or resid 63 or resid 65 through 70 or resid 72 through 97 or (resid 98 and (n \ ame N or name CA or name C or name O or name CB )) or resid 99 through 113 or (r \ esid 114 and (name N or name CA or name C or name O or name CB )) or resid 115 t \ hrough 128 or (resid 129 through 132 and (name N or name CA or name C or name O \ or name CB )) or resid 133 through 160 or (resid 161 through 162 and (name N or \ name CA or name C or name O or name CB )) or resid 163 through 358)) selection = (chain 'a' and (resid 1 through 13 or (resid 14 through 16 and (name N or name C \ A or name C or name O or name CB )) or resid 17 through 34 or (resid 35 and (nam \ e N or name CA or name C or name O or name CB )) or resid 36 or (resid 37 and (n \ ame N or name CA or name C or name O or name CB )) or resid 38 through 61 or res \ id 63 or resid 65 through 70 or resid 72 through 145 or (resid 146 and (name N o \ r name CA or name C or name O or name CB )) or resid 147 through 166 or (resid 1 \ 67 through 168 and (name N or name CA or name C or name O or name CB )) or resid \ 169 through 211 or (resid 212 and (name N or name CA or name C or name O or nam \ e CB )) or resid 213 through 292 or (resid 293 and (name N or name CA or name C \ or name O or name CB )) or resid 294 through 329 or (resid 330 and (name N or na \ me CA or name C or name O or name CB )) or resid 331 through 358)) } ncs_group { reference = (chain 'H' and (resid 2 through 9 or (resid 10 and (name N or name CA or name C \ or name O or name CB )) or resid 11 through 12 or (resid 13 and (name N or name \ CA or name C or name O or name CB )) or resid 14 through 66 or (resid 67 and (na \ me N or name CA or name C or name O or name CB )) or resid 68 through 118)) selection = (chain 'h' and (resid 2 through 86 or (resid 87 through 88 and (name N or name C \ A or name C or name O or name CB )) or resid 89 through 118)) } ncs_group { reference = (chain 'L' and (resid 4 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 79 or (resid 80 and (name N or name \ CA or name C or name O or name CB )) or resid 81 or (resid 82 through 83 and (n \ ame N or name CA or name C or name O or name CB )) or resid 84 through 105 or (r \ esid 106 and (name N or name CA or name C or name O or name CB )) or resid 107)) \ selection = (chain 'l' and (resid 4 through 28 or (resid 29 and (name N or name CA or name C \ or name O or name CB )) or resid 30 through 107)) } 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: 5.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.110 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 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 : 0.007 0.107 9149 Z= 0.308 Angle : 0.781 12.229 12471 Z= 0.439 Chirality : 0.048 0.233 1338 Planarity : 0.006 0.069 1599 Dihedral : 16.248 87.083 3260 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.41 % Allowed : 17.09 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.25), residues: 1153 helix: -1.50 (0.47), residues: 85 sheet: -0.77 (0.28), residues: 376 loop : -0.98 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 74 TYR 0.015 0.002 TYR A 179 PHE 0.013 0.002 PHE A 281 TRP 0.024 0.002 TRP a 334 HIS 0.009 0.002 HIS a 2 Details of bonding type rmsd covalent geometry : bond 0.00676 ( 9133) covalent geometry : angle 0.77158 (12439) SS BOND : bond 0.02842 ( 16) SS BOND : angle 2.56611 ( 32) hydrogen bonds : bond 0.25520 ( 268) hydrogen bonds : angle 8.93255 ( 674) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 218 time to evaluate : 0.211 Fit side-chains REVERT: a 195 LYS cc_start: 0.7882 (mttt) cc_final: 0.7614 (mttm) REVERT: a 249 LYS cc_start: 0.8471 (tttt) cc_final: 0.8263 (tttp) REVERT: h 80 TYR cc_start: 0.7589 (m-80) cc_final: 0.7158 (m-80) REVERT: L 68 THR cc_start: 0.8712 (p) cc_final: 0.8400 (m) REVERT: A 18 ARG cc_start: 0.7236 (tmt-80) cc_final: 0.6990 (tmt-80) REVERT: A 145 LYS cc_start: 0.8338 (mtmm) cc_final: 0.8091 (mtmm) REVERT: A 150 LYS cc_start: 0.8275 (ptpt) cc_final: 0.7889 (ptmm) REVERT: A 182 GLU cc_start: 0.7902 (pt0) cc_final: 0.7684 (pt0) REVERT: A 228 GLU cc_start: 0.7007 (mt-10) cc_final: 0.6797 (mt-10) REVERT: A 242 GLU cc_start: 0.7299 (mm-30) cc_final: 0.6899 (mm-30) REVERT: A 249 LYS cc_start: 0.8147 (tttp) cc_final: 0.7825 (tttp) outliers start: 21 outliers final: 12 residues processed: 231 average time/residue: 0.5167 time to fit residues: 126.2597 Evaluate side-chains 197 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 185 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 14 LYS Chi-restraints excluded: chain a residue 41 ASP Chi-restraints excluded: chain a residue 240 ILE Chi-restraints excluded: chain a residue 326 SER Chi-restraints excluded: chain a residue 333 CYS Chi-restraints excluded: chain l residue 10 VAL Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 301 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 1 HIS ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.121902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.103548 restraints weight = 62669.900| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 5.11 r_work: 0.3232 rms_B_bonded: 5.09 restraints_weight: 2.0000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3224 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3224 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9149 Z= 0.173 Angle : 0.651 11.648 12471 Z= 0.342 Chirality : 0.046 0.205 1338 Planarity : 0.006 0.060 1599 Dihedral : 6.292 54.667 1281 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.83 % Allowed : 21.17 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.25), residues: 1153 helix: -0.61 (0.50), residues: 86 sheet: -0.31 (0.29), residues: 380 loop : -0.95 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG a 18 TYR 0.023 0.002 TYR L 48 PHE 0.011 0.001 PHE l 61 TRP 0.017 0.002 TRP a 122 HIS 0.007 0.001 HIS a 2 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 9133) covalent geometry : angle 0.64336 (12439) SS BOND : bond 0.00756 ( 16) SS BOND : angle 2.12149 ( 32) hydrogen bonds : bond 0.03989 ( 268) hydrogen bonds : angle 5.64697 ( 674) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 187 time to evaluate : 0.203 Fit side-chains REVERT: a 10 VAL cc_start: 0.8540 (p) cc_final: 0.8237 (t) REVERT: a 16 GLU cc_start: 0.7485 (tt0) cc_final: 0.7276 (mt-10) REVERT: a 259 ASN cc_start: 0.8423 (t0) cc_final: 0.8028 (t160) REVERT: a 343 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8529 (tttt) REVERT: h 28 SER cc_start: 0.8353 (t) cc_final: 0.8131 (p) REVERT: h 80 TYR cc_start: 0.8370 (m-80) cc_final: 0.8143 (m-80) REVERT: l 62 SER cc_start: 0.8289 (m) cc_final: 0.7927 (t) REVERT: L 68 THR cc_start: 0.8895 (p) cc_final: 0.8623 (m) REVERT: A 18 ARG cc_start: 0.7402 (tmt-80) cc_final: 0.7049 (tpt170) REVERT: A 78 GLU cc_start: 0.8158 (tt0) cc_final: 0.7878 (tm-30) REVERT: A 83 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7730 (mt) REVERT: A 150 LYS cc_start: 0.8694 (ptpt) cc_final: 0.8345 (ptmm) REVERT: A 182 GLU cc_start: 0.8345 (pt0) cc_final: 0.8112 (pt0) REVERT: A 228 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7446 (mt-10) REVERT: A 249 LYS cc_start: 0.8471 (tttp) cc_final: 0.8173 (tttp) outliers start: 25 outliers final: 12 residues processed: 201 average time/residue: 0.5794 time to fit residues: 123.3461 Evaluate side-chains 197 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 183 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 41 ASP Chi-restraints excluded: chain a residue 212 ASP Chi-restraints excluded: chain a residue 240 ILE Chi-restraints excluded: chain a residue 343 LYS Chi-restraints excluded: chain a residue 355 MET Chi-restraints excluded: chain l residue 10 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 171 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 50 optimal weight: 0.0070 chunk 28 optimal weight: 0.9980 chunk 77 optimal weight: 0.2980 chunk 13 optimal weight: 0.0970 chunk 29 optimal weight: 0.9980 chunk 34 optimal weight: 0.0070 chunk 57 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.2214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 80 ASN a 99 ASN h 6 GLN H 6 GLN H 100 ASN ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.123931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.105866 restraints weight = 58048.516| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 4.91 r_work: 0.3280 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3271 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9149 Z= 0.104 Angle : 0.557 7.630 12471 Z= 0.291 Chirality : 0.043 0.171 1338 Planarity : 0.005 0.051 1599 Dihedral : 5.260 47.543 1266 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.83 % Allowed : 22.22 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.26), residues: 1153 helix: 1.00 (0.56), residues: 79 sheet: -0.01 (0.29), residues: 398 loop : -0.66 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG a 18 TYR 0.021 0.001 TYR L 48 PHE 0.008 0.001 PHE a 327 TRP 0.015 0.001 TRP a 122 HIS 0.003 0.001 HIS a 257 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 9133) covalent geometry : angle 0.54926 (12439) SS BOND : bond 0.00441 ( 16) SS BOND : angle 1.94121 ( 32) hydrogen bonds : bond 0.03185 ( 268) hydrogen bonds : angle 5.17868 ( 674) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 209 time to evaluate : 0.200 Fit side-chains REVERT: a 259 ASN cc_start: 0.8376 (t0) cc_final: 0.7951 (t160) REVERT: a 265 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8277 (mtt-85) REVERT: h 28 SER cc_start: 0.8276 (t) cc_final: 0.8028 (p) REVERT: L 68 THR cc_start: 0.8866 (p) cc_final: 0.8598 (m) REVERT: A 18 ARG cc_start: 0.7406 (tmt-80) cc_final: 0.6947 (tpt170) REVERT: A 83 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7655 (mt) REVERT: A 129 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7781 (ttt-90) REVERT: A 150 LYS cc_start: 0.8629 (ptpt) cc_final: 0.8278 (ptmm) REVERT: A 182 GLU cc_start: 0.8323 (pt0) cc_final: 0.8075 (pt0) REVERT: A 242 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7532 (mm-30) outliers start: 25 outliers final: 13 residues processed: 223 average time/residue: 0.5258 time to fit residues: 123.9117 Evaluate side-chains 209 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 193 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 41 ASP Chi-restraints excluded: chain a residue 212 ASP Chi-restraints excluded: chain a residue 242 GLU Chi-restraints excluded: chain a residue 265 ARG Chi-restraints excluded: chain a residue 355 MET Chi-restraints excluded: chain h residue 34 ILE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 171 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 85 optimal weight: 0.9980 chunk 87 optimal weight: 0.0270 chunk 79 optimal weight: 0.2980 chunk 42 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 99 ASN H 6 GLN A 27 ASN ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.121994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.103632 restraints weight = 74674.304| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 5.46 r_work: 0.3220 rms_B_bonded: 5.20 restraints_weight: 2.0000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9149 Z= 0.170 Angle : 0.620 12.762 12471 Z= 0.322 Chirality : 0.046 0.240 1338 Planarity : 0.005 0.049 1599 Dihedral : 5.384 48.736 1263 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.83 % Allowed : 22.75 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.25), residues: 1153 helix: 1.32 (0.56), residues: 79 sheet: 0.02 (0.29), residues: 394 loop : -0.72 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG a 18 TYR 0.024 0.001 TYR L 48 PHE 0.011 0.001 PHE A 137 TRP 0.010 0.001 TRP a 334 HIS 0.006 0.001 HIS a 2 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 9133) covalent geometry : angle 0.61016 (12439) SS BOND : bond 0.00655 ( 16) SS BOND : angle 2.23497 ( 32) hydrogen bonds : bond 0.03724 ( 268) hydrogen bonds : angle 5.18149 ( 674) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: a 10 VAL cc_start: 0.8516 (OUTLIER) cc_final: 0.8240 (t) REVERT: a 259 ASN cc_start: 0.8448 (t0) cc_final: 0.8046 (t160) REVERT: a 265 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8269 (mtt-85) REVERT: h 28 SER cc_start: 0.8224 (t) cc_final: 0.7995 (p) REVERT: L 68 THR cc_start: 0.8862 (p) cc_final: 0.8601 (m) REVERT: A 18 ARG cc_start: 0.7450 (tmt-80) cc_final: 0.7238 (tmt-80) REVERT: A 83 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7706 (mt) REVERT: A 143 THR cc_start: 0.8224 (p) cc_final: 0.7929 (p) REVERT: A 150 LYS cc_start: 0.8680 (ptpt) cc_final: 0.8325 (ptmm) REVERT: A 182 GLU cc_start: 0.8320 (pt0) cc_final: 0.8078 (pt0) REVERT: A 242 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7581 (mm-30) REVERT: A 280 ARG cc_start: 0.8100 (mmm-85) cc_final: 0.7559 (mtt180) outliers start: 25 outliers final: 14 residues processed: 206 average time/residue: 0.4850 time to fit residues: 106.1512 Evaluate side-chains 207 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 190 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 10 VAL Chi-restraints excluded: chain a residue 41 ASP Chi-restraints excluded: chain a residue 212 ASP Chi-restraints excluded: chain a residue 240 ILE Chi-restraints excluded: chain a residue 265 ARG Chi-restraints excluded: chain h residue 34 ILE Chi-restraints excluded: chain l residue 25 ASP Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 171 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 60 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 57 optimal weight: 0.0170 chunk 38 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 99 ASN ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.121809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.103215 restraints weight = 61092.163| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 5.07 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3477 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3477 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 9149 Z= 0.191 Angle : 0.654 12.249 12471 Z= 0.339 Chirality : 0.046 0.254 1338 Planarity : 0.005 0.045 1599 Dihedral : 5.488 48.042 1263 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.25 % Allowed : 23.17 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.25), residues: 1153 helix: 1.30 (0.56), residues: 79 sheet: -0.12 (0.29), residues: 379 loop : -0.76 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 129 TYR 0.022 0.002 TYR L 48 PHE 0.010 0.001 PHE A 137 TRP 0.013 0.001 TRP a 122 HIS 0.006 0.001 HIS a 2 Details of bonding type rmsd covalent geometry : bond 0.00481 ( 9133) covalent geometry : angle 0.63684 (12439) SS BOND : bond 0.00778 ( 16) SS BOND : angle 3.03822 ( 32) hydrogen bonds : bond 0.03845 ( 268) hydrogen bonds : angle 5.17531 ( 674) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 192 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: a 10 VAL cc_start: 0.8457 (OUTLIER) cc_final: 0.8140 (t) REVERT: a 265 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.7178 (mtt-85) REVERT: L 68 THR cc_start: 0.8715 (p) cc_final: 0.8479 (m) REVERT: A 83 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7366 (mt) REVERT: A 143 THR cc_start: 0.8276 (p) cc_final: 0.7968 (p) REVERT: A 150 LYS cc_start: 0.8275 (ptpt) cc_final: 0.7978 (ptmm) REVERT: A 182 GLU cc_start: 0.7814 (pt0) cc_final: 0.7505 (pt0) REVERT: A 242 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6793 (mm-30) REVERT: A 265 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.7251 (mtp85) REVERT: A 280 ARG cc_start: 0.7052 (mmm-85) cc_final: 0.6469 (mtt180) outliers start: 29 outliers final: 17 residues processed: 206 average time/residue: 0.4923 time to fit residues: 107.8611 Evaluate side-chains 212 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 191 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 10 VAL Chi-restraints excluded: chain a residue 41 ASP Chi-restraints excluded: chain a residue 212 ASP Chi-restraints excluded: chain a residue 240 ILE Chi-restraints excluded: chain a residue 265 ARG Chi-restraints excluded: chain a residue 355 MET Chi-restraints excluded: chain h residue 34 ILE Chi-restraints excluded: chain l residue 25 ASP Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 265 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 18 optimal weight: 0.9990 chunk 11 optimal weight: 0.1980 chunk 37 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 99 ASN a 259 ASN ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.121142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.102042 restraints weight = 68747.028| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 4.77 r_work: 0.3236 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 9149 Z= 0.221 Angle : 0.687 14.956 12471 Z= 0.355 Chirality : 0.047 0.254 1338 Planarity : 0.005 0.045 1599 Dihedral : 5.702 49.771 1263 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.56 % Allowed : 22.96 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.25), residues: 1153 helix: 1.08 (0.57), residues: 79 sheet: -0.18 (0.29), residues: 379 loop : -0.84 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 129 TYR 0.022 0.002 TYR L 48 PHE 0.011 0.002 PHE A 137 TRP 0.014 0.002 TRP h 33 HIS 0.006 0.001 HIS a 2 Details of bonding type rmsd covalent geometry : bond 0.00550 ( 9133) covalent geometry : angle 0.66896 (12439) SS BOND : bond 0.00890 ( 16) SS BOND : angle 3.17088 ( 32) hydrogen bonds : bond 0.04072 ( 268) hydrogen bonds : angle 5.21354 ( 674) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 187 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: a 10 VAL cc_start: 0.8554 (OUTLIER) cc_final: 0.8262 (t) REVERT: a 265 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8223 (mtt-85) REVERT: L 68 THR cc_start: 0.8858 (p) cc_final: 0.8608 (m) REVERT: A 83 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7656 (mt) REVERT: A 143 THR cc_start: 0.8351 (p) cc_final: 0.8042 (p) REVERT: A 150 LYS cc_start: 0.8704 (ptpt) cc_final: 0.8365 (ptmm) REVERT: A 182 GLU cc_start: 0.8289 (pt0) cc_final: 0.8047 (pt0) REVERT: A 242 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7564 (mm-30) REVERT: A 265 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8249 (mtp85) outliers start: 32 outliers final: 21 residues processed: 202 average time/residue: 0.5013 time to fit residues: 107.6934 Evaluate side-chains 212 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 187 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 10 VAL Chi-restraints excluded: chain a residue 41 ASP Chi-restraints excluded: chain a residue 117 HIS Chi-restraints excluded: chain a residue 212 ASP Chi-restraints excluded: chain a residue 240 ILE Chi-restraints excluded: chain a residue 241 GLU Chi-restraints excluded: chain a residue 265 ARG Chi-restraints excluded: chain a residue 355 MET Chi-restraints excluded: chain h residue 34 ILE Chi-restraints excluded: chain l residue 10 VAL Chi-restraints excluded: chain l residue 25 ASP Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 265 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 49 optimal weight: 0.1980 chunk 84 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 91 optimal weight: 0.0040 chunk 24 optimal weight: 0.0980 chunk 54 optimal weight: 0.3980 chunk 93 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 overall best weight: 0.2792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 80 ASN a 99 ASN ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.123497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.104744 restraints weight = 63627.423| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 5.29 r_work: 0.3248 rms_B_bonded: 5.25 restraints_weight: 2.0000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 9149 Z= 0.121 Angle : 0.607 13.225 12471 Z= 0.314 Chirality : 0.044 0.222 1338 Planarity : 0.005 0.040 1599 Dihedral : 5.277 48.401 1263 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.94 % Allowed : 23.69 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.26), residues: 1153 helix: 1.43 (0.59), residues: 80 sheet: -0.03 (0.30), residues: 376 loop : -0.63 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 129 TYR 0.022 0.001 TYR L 48 PHE 0.006 0.001 PHE A 327 TRP 0.016 0.001 TRP a 122 HIS 0.003 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 9133) covalent geometry : angle 0.58965 (12439) SS BOND : bond 0.00835 ( 16) SS BOND : angle 2.89480 ( 32) hydrogen bonds : bond 0.03168 ( 268) hydrogen bonds : angle 4.94917 ( 674) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: a 265 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8223 (mtt-85) REVERT: L 68 THR cc_start: 0.8849 (p) cc_final: 0.8580 (m) REVERT: A 83 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7558 (mt) REVERT: A 150 LYS cc_start: 0.8703 (ptpt) cc_final: 0.8332 (ptmm) REVERT: A 182 GLU cc_start: 0.8346 (pt0) cc_final: 0.8101 (pt0) REVERT: A 242 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7574 (mm-30) REVERT: A 265 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8298 (mtp85) REVERT: A 278 GLU cc_start: 0.8461 (tt0) cc_final: 0.8054 (tt0) REVERT: A 280 ARG cc_start: 0.8099 (mmm-85) cc_final: 0.7681 (mtt90) outliers start: 26 outliers final: 15 residues processed: 205 average time/residue: 0.4897 time to fit residues: 106.9615 Evaluate side-chains 202 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 184 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 10 VAL Chi-restraints excluded: chain a residue 41 ASP Chi-restraints excluded: chain a residue 136 SER Chi-restraints excluded: chain a residue 240 ILE Chi-restraints excluded: chain a residue 241 GLU Chi-restraints excluded: chain a residue 242 GLU Chi-restraints excluded: chain a residue 265 ARG Chi-restraints excluded: chain a residue 355 MET Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 357 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 20 optimal weight: 0.2980 chunk 59 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 26 optimal weight: 0.0980 chunk 7 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.122244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.104212 restraints weight = 48571.574| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 4.01 r_work: 0.3295 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3292 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3292 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 9149 Z= 0.172 Angle : 0.664 13.910 12471 Z= 0.342 Chirality : 0.046 0.238 1338 Planarity : 0.005 0.044 1599 Dihedral : 5.428 46.536 1263 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.52 % Allowed : 24.63 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.25), residues: 1153 helix: 1.31 (0.58), residues: 80 sheet: -0.09 (0.29), residues: 384 loop : -0.60 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 342 TYR 0.020 0.001 TYR L 48 PHE 0.008 0.001 PHE A 137 TRP 0.010 0.001 TRP h 33 HIS 0.004 0.001 HIS a 2 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 9133) covalent geometry : angle 0.64186 (12439) SS BOND : bond 0.00936 ( 16) SS BOND : angle 3.44825 ( 32) hydrogen bonds : bond 0.03609 ( 268) hydrogen bonds : angle 5.01502 ( 674) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 182 time to evaluate : 0.338 Fit side-chains REVERT: a 265 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.8087 (mtt-85) REVERT: L 68 THR cc_start: 0.8827 (p) cc_final: 0.8572 (m) REVERT: A 83 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7531 (mt) REVERT: A 150 LYS cc_start: 0.8679 (ptpt) cc_final: 0.8332 (ptmm) REVERT: A 242 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7461 (mm-30) REVERT: A 265 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.8133 (mtp85) REVERT: A 278 GLU cc_start: 0.8325 (tt0) cc_final: 0.7873 (tt0) REVERT: A 280 ARG cc_start: 0.7949 (mmm-85) cc_final: 0.7550 (mtt90) outliers start: 22 outliers final: 17 residues processed: 192 average time/residue: 0.5112 time to fit residues: 104.2184 Evaluate side-chains 203 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 10 VAL Chi-restraints excluded: chain a residue 41 ASP Chi-restraints excluded: chain a residue 136 SER Chi-restraints excluded: chain a residue 240 ILE Chi-restraints excluded: chain a residue 242 GLU Chi-restraints excluded: chain a residue 265 ARG Chi-restraints excluded: chain a residue 355 MET Chi-restraints excluded: chain l residue 10 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 265 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 101 optimal weight: 0.0970 chunk 30 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 103 optimal weight: 0.3980 chunk 75 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 99 ASN H 6 GLN ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.122072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.103612 restraints weight = 60646.766| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 5.04 r_work: 0.3240 rms_B_bonded: 5.04 restraints_weight: 2.0000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3232 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 9149 Z= 0.175 Angle : 0.678 14.721 12471 Z= 0.349 Chirality : 0.046 0.247 1338 Planarity : 0.005 0.043 1599 Dihedral : 5.478 46.697 1263 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.52 % Allowed : 25.16 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.25), residues: 1153 helix: 1.27 (0.58), residues: 80 sheet: -0.08 (0.29), residues: 379 loop : -0.60 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 342 TYR 0.020 0.001 TYR L 48 PHE 0.008 0.001 PHE A 327 TRP 0.011 0.001 TRP a 122 HIS 0.004 0.001 HIS a 2 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 9133) covalent geometry : angle 0.65433 (12439) SS BOND : bond 0.00950 ( 16) SS BOND : angle 3.59068 ( 32) hydrogen bonds : bond 0.03658 ( 268) hydrogen bonds : angle 5.03108 ( 674) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 180 time to evaluate : 0.325 Fit side-chains REVERT: a 265 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8211 (mtt-85) REVERT: L 68 THR cc_start: 0.8834 (p) cc_final: 0.8578 (m) REVERT: A 83 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7584 (mt) REVERT: A 150 LYS cc_start: 0.8725 (ptpt) cc_final: 0.8468 (ptmm) REVERT: A 242 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7574 (mm-30) REVERT: A 265 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8258 (mtp85) REVERT: A 278 GLU cc_start: 0.8431 (tt0) cc_final: 0.7907 (tt0) REVERT: A 280 ARG cc_start: 0.8098 (mmm-85) cc_final: 0.7605 (mtt90) outliers start: 22 outliers final: 17 residues processed: 192 average time/residue: 0.5361 time to fit residues: 109.1753 Evaluate side-chains 199 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 179 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 10 VAL Chi-restraints excluded: chain a residue 41 ASP Chi-restraints excluded: chain a residue 117 HIS Chi-restraints excluded: chain a residue 136 SER Chi-restraints excluded: chain a residue 240 ILE Chi-restraints excluded: chain a residue 242 GLU Chi-restraints excluded: chain a residue 265 ARG Chi-restraints excluded: chain a residue 355 MET Chi-restraints excluded: chain h residue 34 ILE Chi-restraints excluded: chain l residue 10 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 265 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 73 optimal weight: 0.8980 chunk 0 optimal weight: 0.0870 chunk 97 optimal weight: 0.5980 chunk 23 optimal weight: 0.0570 chunk 24 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 99 ASN ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.123073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.104190 restraints weight = 67843.321| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 5.49 r_work: 0.3233 rms_B_bonded: 5.36 restraints_weight: 2.0000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 9149 Z= 0.141 Angle : 0.649 14.194 12471 Z= 0.334 Chirality : 0.045 0.235 1338 Planarity : 0.005 0.044 1599 Dihedral : 5.332 47.708 1263 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.31 % Allowed : 25.37 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.26), residues: 1153 helix: 1.39 (0.58), residues: 80 sheet: -0.03 (0.29), residues: 383 loop : -0.49 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 342 TYR 0.020 0.001 TYR L 48 PHE 0.007 0.001 PHE a 327 TRP 0.013 0.001 TRP a 122 HIS 0.004 0.001 HIS a 2 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 9133) covalent geometry : angle 0.62685 (12439) SS BOND : bond 0.00891 ( 16) SS BOND : angle 3.39682 ( 32) hydrogen bonds : bond 0.03348 ( 268) hydrogen bonds : angle 4.94468 ( 674) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 0.307 Fit side-chains REVERT: a 265 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8243 (mtt-85) REVERT: L 68 THR cc_start: 0.8846 (p) cc_final: 0.8610 (m) REVERT: A 83 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7550 (mt) REVERT: A 150 LYS cc_start: 0.8737 (ptpt) cc_final: 0.8482 (ptmm) REVERT: A 242 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7592 (mm-30) REVERT: A 265 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8302 (mtp85) REVERT: A 278 GLU cc_start: 0.8477 (tt0) cc_final: 0.8074 (tt0) REVERT: A 280 ARG cc_start: 0.8129 (mmm-85) cc_final: 0.7732 (mtt90) outliers start: 20 outliers final: 16 residues processed: 188 average time/residue: 0.5441 time to fit residues: 108.2015 Evaluate side-chains 197 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 178 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 10 VAL Chi-restraints excluded: chain a residue 41 ASP Chi-restraints excluded: chain a residue 117 HIS Chi-restraints excluded: chain a residue 136 SER Chi-restraints excluded: chain a residue 240 ILE Chi-restraints excluded: chain a residue 242 GLU Chi-restraints excluded: chain a residue 265 ARG Chi-restraints excluded: chain a residue 355 MET Chi-restraints excluded: chain l residue 10 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 265 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 63 optimal weight: 1.9990 chunk 111 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 5 optimal weight: 0.4980 chunk 74 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.121448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.102140 restraints weight = 72586.719| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 4.90 r_work: 0.3236 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3228 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3228 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 9149 Z= 0.197 Angle : 0.695 14.123 12471 Z= 0.357 Chirality : 0.047 0.253 1338 Planarity : 0.005 0.044 1599 Dihedral : 5.546 46.754 1263 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.62 % Allowed : 25.26 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.25), residues: 1153 helix: 1.18 (0.57), residues: 80 sheet: -0.08 (0.29), residues: 379 loop : -0.60 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 342 TYR 0.020 0.002 TYR L 48 PHE 0.010 0.001 PHE A 137 TRP 0.012 0.001 TRP h 33 HIS 0.005 0.001 HIS a 2 Details of bonding type rmsd covalent geometry : bond 0.00492 ( 9133) covalent geometry : angle 0.67208 (12439) SS BOND : bond 0.01004 ( 16) SS BOND : angle 3.57389 ( 32) hydrogen bonds : bond 0.03869 ( 268) hydrogen bonds : angle 5.07722 ( 674) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3697.69 seconds wall clock time: 63 minutes 20.47 seconds (3800.47 seconds total)