Starting phenix.real_space_refine on Wed Jul 30 18:55:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jqs_36578/07_2025/8jqs_36578.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jqs_36578/07_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_36578/07_2025/8jqs_36578.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jqs_36578/07_2025/8jqs_36578.map" model { file = "/net/cci-nas-00/data/ceres_data/8jqs_36578/07_2025/8jqs_36578.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jqs_36578/07_2025/8jqs_36578.cif" } resolution = 2.63 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'ASP:plan': 2, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} 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: {'ASP:plan': 2, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} 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: {'GLN:plan1': 1, 'GLU:plan': 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: {'GLU:plan': 3, 'ARG:plan': 1} 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: {'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG: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: {'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG: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: 9.62, per 1000 atoms: 1.08 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: 2.04 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.27 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: 2.80 Time building geometry restraints manager: 2.45 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: 4.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 28.670 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.640 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (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 TRP 0.024 0.002 TRP a 334 HIS 0.009 0.002 HIS a 2 PHE 0.013 0.002 PHE A 281 TYR 0.015 0.002 TYR A 179 ARG 0.006 0.001 ARG H 74 Details of bonding type rmsd hydrogen bonds : bond 0.25520 ( 268) hydrogen bonds : angle 8.93255 ( 674) SS BOND : bond 0.02842 ( 16) SS BOND : angle 2.56611 ( 32) covalent geometry : bond 0.00676 ( 9133) covalent geometry : angle 0.77158 (12439) *********************** 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 : 0.989 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: 0.6989 (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: 0.7685 (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: 1.2373 time to fit residues: 303.7014 Evaluate side-chains 198 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 186 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 94 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 87 optimal weight: 0.3980 chunk 33 optimal weight: 0.1980 chunk 53 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 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 = 0.3737 r_free = 0.3737 target = 0.121921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.103497 restraints weight = 63971.608| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 5.15 r_work: 0.3228 rms_B_bonded: 5.15 restraints_weight: 2.0000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3221 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 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 = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9149 Z= 0.174 Angle : 0.650 11.162 12471 Z= 0.341 Chirality : 0.046 0.230 1338 Planarity : 0.006 0.060 1599 Dihedral : 6.287 55.503 1281 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.62 % Allowed : 21.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.25), residues: 1153 helix: -0.61 (0.50), residues: 86 sheet: -0.36 (0.29), residues: 380 loop : -0.96 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP a 122 HIS 0.007 0.001 HIS a 2 PHE 0.010 0.001 PHE l 61 TYR 0.023 0.002 TYR L 48 ARG 0.006 0.001 ARG a 18 Details of bonding type rmsd hydrogen bonds : bond 0.04210 ( 268) hydrogen bonds : angle 5.68095 ( 674) SS BOND : bond 0.00638 ( 16) SS BOND : angle 2.25651 ( 32) covalent geometry : bond 0.00425 ( 9133) covalent geometry : angle 0.64115 (12439) *********************** 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 210 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 0.906 Fit side-chains REVERT: a 10 VAL cc_start: 0.8531 (p) cc_final: 0.8236 (t) REVERT: a 259 ASN cc_start: 0.8425 (t0) cc_final: 0.8026 (t160) REVERT: a 343 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8547 (tttt) REVERT: h 28 SER cc_start: 0.8355 (t) cc_final: 0.8138 (p) REVERT: h 80 TYR cc_start: 0.8380 (m-80) cc_final: 0.8150 (m-80) REVERT: l 62 SER cc_start: 0.8281 (m) cc_final: 0.7920 (t) REVERT: L 68 THR cc_start: 0.8889 (p) cc_final: 0.8618 (m) REVERT: A 18 ARG cc_start: 0.7414 (tmt-80) cc_final: 0.7062 (tpt170) REVERT: A 78 GLU cc_start: 0.8155 (tt0) cc_final: 0.7908 (tm-30) REVERT: A 83 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7739 (mt) REVERT: A 150 LYS cc_start: 0.8693 (ptpt) cc_final: 0.8344 (ptmm) REVERT: A 182 GLU cc_start: 0.8379 (pt0) cc_final: 0.8148 (pt0) REVERT: A 228 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7467 (mt-10) REVERT: A 249 LYS cc_start: 0.8472 (tttp) cc_final: 0.8176 (tttp) outliers start: 23 outliers final: 10 residues processed: 199 average time/residue: 1.3832 time to fit residues: 291.1794 Evaluate side-chains 187 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 175 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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 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 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 42 optimal weight: 0.0770 chunk 107 optimal weight: 0.0010 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 72 optimal weight: 0.0980 chunk 95 optimal weight: 0.3980 chunk 58 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.3144 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 ASN ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.123101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.104944 restraints weight = 72589.145| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 5.26 r_work: 0.3252 rms_B_bonded: 5.12 restraints_weight: 2.0000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3244 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3244 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9149 Z= 0.118 Angle : 0.572 7.910 12471 Z= 0.299 Chirality : 0.044 0.190 1338 Planarity : 0.005 0.052 1599 Dihedral : 5.361 48.831 1266 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.52 % Allowed : 22.33 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.25), residues: 1153 helix: 0.95 (0.56), residues: 79 sheet: -0.07 (0.29), residues: 398 loop : -0.71 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 122 HIS 0.004 0.001 HIS a 2 PHE 0.008 0.001 PHE a 327 TYR 0.020 0.001 TYR L 48 ARG 0.006 0.000 ARG a 18 Details of bonding type rmsd hydrogen bonds : bond 0.03462 ( 268) hydrogen bonds : angle 5.22307 ( 674) SS BOND : bond 0.00483 ( 16) SS BOND : angle 1.99281 ( 32) covalent geometry : bond 0.00292 ( 9133) covalent geometry : angle 0.56366 (12439) *********************** 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 215 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 193 time to evaluate : 1.128 Fit side-chains REVERT: a 140 ASP cc_start: 0.7239 (t0) cc_final: 0.6965 (t0) REVERT: a 259 ASN cc_start: 0.8390 (t0) cc_final: 0.7965 (t160) REVERT: a 265 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8283 (mtt-85) REVERT: h 28 SER cc_start: 0.8274 (t) cc_final: 0.8032 (p) REVERT: L 68 THR cc_start: 0.8873 (p) cc_final: 0.8619 (m) REVERT: A 18 ARG cc_start: 0.7446 (tmt-80) cc_final: 0.7083 (tmt-80) REVERT: A 78 GLU cc_start: 0.8162 (tt0) cc_final: 0.7947 (tm-30) REVERT: A 83 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7696 (mt) REVERT: A 150 LYS cc_start: 0.8649 (ptpt) cc_final: 0.8304 (ptmm) REVERT: A 182 GLU cc_start: 0.8345 (pt0) cc_final: 0.8114 (pt0) REVERT: A 228 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7372 (mt-10) REVERT: A 242 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7556 (mm-30) REVERT: A 249 LYS cc_start: 0.8428 (tttp) cc_final: 0.8036 (tttp) outliers start: 22 outliers final: 12 residues processed: 205 average time/residue: 1.5836 time to fit residues: 346.0529 Evaluate side-chains 202 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 188 time to evaluate : 1.535 ------------------------------------------------------------------------------- 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 265 ARG 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 A residue 61 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 44 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 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 = 0.3728 r_free = 0.3728 target = 0.121199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.102749 restraints weight = 74912.970| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 5.46 r_work: 0.3208 rms_B_bonded: 5.21 restraints_weight: 2.0000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3200 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3200 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9149 Z= 0.201 Angle : 0.644 12.718 12471 Z= 0.335 Chirality : 0.046 0.246 1338 Planarity : 0.005 0.050 1599 Dihedral : 5.625 50.388 1265 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.94 % Allowed : 22.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.25), residues: 1153 helix: 1.12 (0.55), residues: 80 sheet: -0.18 (0.29), residues: 389 loop : -0.79 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP h 33 HIS 0.007 0.001 HIS a 2 PHE 0.012 0.002 PHE A 137 TYR 0.017 0.002 TYR L 48 ARG 0.004 0.001 ARG a 18 Details of bonding type rmsd hydrogen bonds : bond 0.04024 ( 268) hydrogen bonds : angle 5.27629 ( 674) SS BOND : bond 0.00699 ( 16) SS BOND : angle 2.40272 ( 32) covalent geometry : bond 0.00496 ( 9133) covalent geometry : angle 0.63338 (12439) *********************** 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 221 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 195 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: a 259 ASN cc_start: 0.8473 (t0) cc_final: 0.8254 (t160) REVERT: a 265 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8272 (mtt-85) REVERT: h 28 SER cc_start: 0.8218 (t) cc_final: 0.7989 (p) REVERT: L 68 THR cc_start: 0.8864 (p) cc_final: 0.8606 (m) REVERT: A 18 ARG cc_start: 0.7506 (tmt-80) cc_final: 0.7292 (tmt-80) REVERT: A 78 GLU cc_start: 0.8241 (tt0) cc_final: 0.8022 (tm-30) REVERT: A 83 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7731 (mt) REVERT: A 143 THR cc_start: 0.8316 (p) cc_final: 0.8018 (p) REVERT: A 150 LYS cc_start: 0.8701 (ptpt) cc_final: 0.8357 (ptmm) REVERT: A 228 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7362 (mt-10) REVERT: A 242 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7584 (mm-30) REVERT: A 249 LYS cc_start: 0.8423 (tttp) cc_final: 0.8029 (tttp) REVERT: A 280 ARG cc_start: 0.8079 (mmm-85) cc_final: 0.7545 (mtt90) outliers start: 26 outliers final: 17 residues processed: 208 average time/residue: 1.2485 time to fit residues: 276.7096 Evaluate side-chains 209 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 190 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 10 VAL Chi-restraints excluded: chain H residue 11 VAL 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 14 optimal weight: 0.1980 chunk 38 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3736 r_free = 0.3736 target = 0.121753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.102863 restraints weight = 61254.495| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 4.50 r_work: 0.3258 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3251 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3251 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9149 Z= 0.176 Angle : 0.635 14.898 12471 Z= 0.329 Chirality : 0.046 0.229 1338 Planarity : 0.005 0.044 1599 Dihedral : 5.547 48.501 1265 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.94 % Allowed : 22.75 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.25), residues: 1153 helix: 1.18 (0.56), residues: 80 sheet: -0.14 (0.28), residues: 401 loop : -0.77 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 122 HIS 0.005 0.001 HIS a 2 PHE 0.009 0.001 PHE A 137 TYR 0.016 0.001 TYR L 48 ARG 0.005 0.000 ARG a 18 Details of bonding type rmsd hydrogen bonds : bond 0.03768 ( 268) hydrogen bonds : angle 5.17996 ( 674) SS BOND : bond 0.00759 ( 16) SS BOND : angle 2.47744 ( 32) covalent geometry : bond 0.00433 ( 9133) covalent geometry : angle 0.62352 (12439) *********************** 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: 26 poor density : 195 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 259 ASN cc_start: 0.8470 (t0) cc_final: 0.8253 (t160) REVERT: a 265 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8167 (mtt-85) REVERT: L 68 THR cc_start: 0.8850 (p) cc_final: 0.8585 (m) REVERT: A 83 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7644 (mt) REVERT: A 143 THR cc_start: 0.8368 (p) cc_final: 0.8076 (p) REVERT: A 150 LYS cc_start: 0.8688 (ptpt) cc_final: 0.8352 (ptmm) REVERT: A 228 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7380 (mt-10) REVERT: A 242 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7509 (mm-30) REVERT: A 280 ARG cc_start: 0.7985 (mmm-85) cc_final: 0.7317 (mtt180) outliers start: 26 outliers final: 18 residues processed: 206 average time/residue: 1.3862 time to fit residues: 303.5752 Evaluate side-chains 211 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 191 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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 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 25 ASP Chi-restraints excluded: chain H residue 11 VAL 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 171 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3736 r_free = 0.3736 target = 0.121648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.102620 restraints weight = 67355.943| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 4.68 r_work: 0.3246 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 9149 Z= 0.191 Angle : 0.662 14.302 12471 Z= 0.342 Chirality : 0.046 0.261 1338 Planarity : 0.005 0.044 1599 Dihedral : 5.598 48.774 1265 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.35 % Allowed : 22.85 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.25), residues: 1153 helix: 1.18 (0.57), residues: 80 sheet: -0.18 (0.29), residues: 389 loop : -0.79 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP a 122 HIS 0.005 0.001 HIS a 2 PHE 0.010 0.001 PHE A 137 TYR 0.016 0.001 TYR L 48 ARG 0.004 0.001 ARG a 18 Details of bonding type rmsd hydrogen bonds : bond 0.03836 ( 268) hydrogen bonds : angle 5.15563 ( 674) SS BOND : bond 0.00904 ( 16) SS BOND : angle 3.27827 ( 32) covalent geometry : bond 0.00476 ( 9133) covalent geometry : angle 0.64193 (12439) *********************** 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 215 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 185 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: a 10 VAL cc_start: 0.8518 (OUTLIER) cc_final: 0.8211 (t) REVERT: a 265 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8173 (mtt-85) REVERT: L 68 THR cc_start: 0.8843 (p) cc_final: 0.8585 (m) REVERT: A 82 ILE cc_start: 0.8486 (mm) cc_final: 0.8246 (tt) REVERT: A 83 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7646 (mt) REVERT: A 143 THR cc_start: 0.8369 (p) cc_final: 0.8073 (p) REVERT: A 150 LYS cc_start: 0.8707 (ptpt) cc_final: 0.8367 (ptmm) REVERT: A 228 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7392 (mt-10) REVERT: A 242 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7540 (mm-30) REVERT: A 280 ARG cc_start: 0.8014 (mmm-85) cc_final: 0.7534 (mtt90) outliers start: 30 outliers final: 20 residues processed: 200 average time/residue: 1.2150 time to fit residues: 258.8666 Evaluate side-chains 206 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 0.892 ------------------------------------------------------------------------------- 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 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 61 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 171 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 70 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 53 optimal weight: 0.0030 chunk 28 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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 = 0.3741 r_free = 0.3741 target = 0.122119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.104021 restraints weight = 56441.218| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 4.88 r_work: 0.3250 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- 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 = 0.05 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 9149 Z= 0.173 Angle : 0.653 13.511 12471 Z= 0.338 Chirality : 0.046 0.246 1338 Planarity : 0.005 0.043 1599 Dihedral : 5.530 47.161 1265 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.04 % Allowed : 23.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.25), residues: 1153 helix: 1.23 (0.57), residues: 80 sheet: -0.14 (0.29), residues: 379 loop : -0.72 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP a 122 HIS 0.004 0.001 HIS A 2 PHE 0.009 0.001 PHE A 137 TYR 0.016 0.001 TYR L 48 ARG 0.004 0.000 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.03654 ( 268) hydrogen bonds : angle 5.04844 ( 674) SS BOND : bond 0.00863 ( 16) SS BOND : angle 3.21210 ( 32) covalent geometry : bond 0.00431 ( 9133) covalent geometry : angle 0.63343 (12439) *********************** 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 211 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 184 time to evaluate : 0.997 Fit side-chains REVERT: a 265 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.8215 (mtt-85) REVERT: L 68 THR cc_start: 0.8839 (p) cc_final: 0.8567 (m) REVERT: A 82 ILE cc_start: 0.8454 (mm) cc_final: 0.8215 (tt) REVERT: A 83 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7625 (mt) REVERT: A 143 THR cc_start: 0.8345 (p) cc_final: 0.8048 (p) REVERT: A 150 LYS cc_start: 0.8714 (ptpt) cc_final: 0.8459 (ptmm) REVERT: A 228 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7291 (mt-10) REVERT: A 242 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7542 (mm-30) REVERT: A 249 LYS cc_start: 0.8350 (tttp) cc_final: 0.7961 (tttp) outliers start: 27 outliers final: 19 residues processed: 197 average time/residue: 1.2475 time to fit residues: 261.4763 Evaluate side-chains 201 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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 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 10 VAL Chi-restraints excluded: chain H residue 11 VAL 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 61 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 357 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.1980 chunk 80 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 71 optimal weight: 0.3980 chunk 81 optimal weight: 0.9990 chunk 6 optimal weight: 0.4980 chunk 85 optimal weight: 0.4980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.3749 r_free = 0.3749 target = 0.122748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.103708 restraints weight = 67974.047| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 4.71 r_work: 0.3262 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3254 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3254 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2974 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= 0.145 Angle : 0.640 13.116 12471 Z= 0.330 Chirality : 0.045 0.239 1338 Planarity : 0.005 0.042 1599 Dihedral : 5.389 44.950 1265 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.41 % Allowed : 24.42 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.25), residues: 1153 helix: 1.34 (0.58), residues: 80 sheet: -0.11 (0.29), residues: 383 loop : -0.61 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 122 HIS 0.004 0.001 HIS a 2 PHE 0.007 0.001 PHE a 327 TYR 0.016 0.001 TYR L 48 ARG 0.004 0.000 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.03370 ( 268) hydrogen bonds : angle 4.97036 ( 674) SS BOND : bond 0.00889 ( 16) SS BOND : angle 3.38371 ( 32) covalent geometry : bond 0.00362 ( 9133) covalent geometry : angle 0.61780 (12439) *********************** 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 203 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 182 time to evaluate : 1.397 Fit side-chains REVERT: a 265 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.8155 (mtt-85) REVERT: L 68 THR cc_start: 0.8839 (p) cc_final: 0.8566 (m) REVERT: A 82 ILE cc_start: 0.8403 (mm) cc_final: 0.8182 (tt) REVERT: A 83 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7575 (mt) REVERT: A 150 LYS cc_start: 0.8699 (ptpt) cc_final: 0.8487 (ptmm) REVERT: A 228 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7272 (mt-10) REVERT: A 242 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7534 (mm-30) REVERT: A 249 LYS cc_start: 0.8333 (tttp) cc_final: 0.7964 (tttp) REVERT: A 280 ARG cc_start: 0.8030 (mmm-85) cc_final: 0.7531 (mtt90) outliers start: 21 outliers final: 16 residues processed: 192 average time/residue: 1.6205 time to fit residues: 331.2943 Evaluate side-chains 198 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 0.816 ------------------------------------------------------------------------------- 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 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 l residue 25 ASP Chi-restraints excluded: chain H residue 11 VAL 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 357 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 14 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 67 optimal weight: 0.3980 chunk 0 optimal weight: 0.0970 chunk 95 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN ** 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 = 0.3744 r_free = 0.3744 target = 0.122217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.103967 restraints weight = 57876.390| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 4.96 r_work: 0.3252 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3244 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3244 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 9149 Z= 0.162 Angle : 0.658 12.290 12471 Z= 0.339 Chirality : 0.046 0.242 1338 Planarity : 0.005 0.042 1599 Dihedral : 5.375 44.624 1263 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.25), residues: 1153 helix: 1.27 (0.57), residues: 80 sheet: -0.10 (0.29), residues: 384 loop : -0.57 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 122 HIS 0.004 0.001 HIS A 257 PHE 0.008 0.001 PHE A 137 TYR 0.016 0.001 TYR L 48 ARG 0.003 0.000 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.03527 ( 268) hydrogen bonds : angle 4.97769 ( 674) SS BOND : bond 0.00937 ( 16) SS BOND : angle 3.38868 ( 32) covalent geometry : bond 0.00405 ( 9133) covalent geometry : angle 0.63653 (12439) *********************** 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 204 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 182 time to evaluate : 0.945 Fit side-chains REVERT: a 265 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8180 (mtt-85) REVERT: L 68 THR cc_start: 0.8831 (p) cc_final: 0.8557 (m) REVERT: A 82 ILE cc_start: 0.8451 (mm) cc_final: 0.8231 (tt) REVERT: A 83 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7607 (mt) REVERT: A 150 LYS cc_start: 0.8712 (ptpt) cc_final: 0.8452 (ptmm) REVERT: A 228 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7268 (mt-10) REVERT: A 242 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7534 (mm-30) REVERT: A 249 LYS cc_start: 0.8349 (tttp) cc_final: 0.7978 (tttp) outliers start: 22 outliers final: 16 residues processed: 192 average time/residue: 1.3859 time to fit residues: 282.2245 Evaluate side-chains 198 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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 265 ARG Chi-restraints excluded: chain a residue 355 MET 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 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 171 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 48 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 24 optimal weight: 0.1980 chunk 11 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3743 r_free = 0.3743 target = 0.122109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.102935 restraints weight = 68603.811| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 4.78 r_work: 0.3251 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3245 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 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 = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3245 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3023 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= 0.174 Angle : 0.663 12.421 12471 Z= 0.341 Chirality : 0.046 0.248 1338 Planarity : 0.005 0.043 1599 Dihedral : 5.425 44.818 1263 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.20 % Allowed : 24.84 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.25), residues: 1153 helix: 1.21 (0.57), residues: 80 sheet: -0.12 (0.29), residues: 384 loop : -0.57 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP h 33 HIS 0.004 0.001 HIS A 257 PHE 0.009 0.001 PHE A 137 TYR 0.015 0.001 TYR L 48 ARG 0.004 0.000 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.03605 ( 268) hydrogen bonds : angle 4.99334 ( 674) SS BOND : bond 0.00963 ( 16) SS BOND : angle 3.39502 ( 32) covalent geometry : bond 0.00435 ( 9133) covalent geometry : angle 0.64099 (12439) ********************** 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 201 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 182 time to evaluate : 0.986 Fit side-chains REVERT: a 265 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8185 (mtt-85) REVERT: L 68 THR cc_start: 0.8832 (p) cc_final: 0.8562 (m) REVERT: A 82 ILE cc_start: 0.8442 (mm) cc_final: 0.8210 (tt) REVERT: A 83 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7605 (mt) REVERT: A 150 LYS cc_start: 0.8707 (ptpt) cc_final: 0.8455 (ptmm) REVERT: A 228 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7289 (mt-10) REVERT: A 242 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7538 (mm-30) REVERT: A 249 LYS cc_start: 0.8352 (tttp) cc_final: 0.7958 (tttp) outliers start: 19 outliers final: 15 residues processed: 193 average time/residue: 1.3487 time to fit residues: 275.7587 Evaluate side-chains 198 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 181 time to evaluate : 1.138 ------------------------------------------------------------------------------- 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 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 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 171 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 86 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 70 optimal weight: 0.3980 chunk 103 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 0 optimal weight: 0.0870 chunk 78 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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 = 0.3750 r_free = 0.3750 target = 0.122653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.103690 restraints weight = 64542.732| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 4.65 r_work: 0.3267 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3259 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3080 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= 0.154 Angle : 0.652 12.675 12471 Z= 0.335 Chirality : 0.045 0.248 1338 Planarity : 0.005 0.042 1599 Dihedral : 5.330 43.735 1263 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.31 % Allowed : 24.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.25), residues: 1153 helix: 1.28 (0.57), residues: 80 sheet: -0.05 (0.29), residues: 381 loop : -0.52 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP a 122 HIS 0.004 0.001 HIS A 257 PHE 0.008 0.001 PHE a 327 TYR 0.015 0.001 TYR L 48 ARG 0.003 0.000 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.03431 ( 268) hydrogen bonds : angle 4.95132 ( 674) SS BOND : bond 0.00921 ( 16) SS BOND : angle 3.38516 ( 32) covalent geometry : bond 0.00383 ( 9133) covalent geometry : angle 0.62947 (12439) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11419.11 seconds wall clock time: 202 minutes 18.01 seconds (12138.01 seconds total)