Starting phenix.real_space_refine on Sat Aug 23 16:08:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jqn_36576/08_2025/8jqn_36576.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jqn_36576/08_2025/8jqn_36576.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jqn_36576/08_2025/8jqn_36576.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jqn_36576/08_2025/8jqn_36576.map" model { file = "/net/cci-nas-00/data/ceres_data/8jqn_36576/08_2025/8jqn_36576.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jqn_36576/08_2025/8jqn_36576.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 5334 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 54 5.16 5 C 5610 2.51 5 N 1555 2.21 5 O 1700 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8919 Number of models: 1 Model: "" Number of chains: 6 Chain: "H" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 903 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 774 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 97} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "h" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 887 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "l" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 776 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 97} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "a" Number of atoms: 2794 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 352, 2788 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 332} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 13 Conformer: "B" Number of residues, atoms: 352, 2788 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 332} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 13 bond proxies already assigned to first conformer: 2860 Chain: "A" Number of atoms: 2785 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 354, 2778 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 334} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 64 Planarities with less than four sites: {'GLU:plan': 3, 'TRP:plan': 1, 'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 38 Conformer: "B" Number of residues, atoms: 354, 2778 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 334} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 64 Planarities with less than four sites: {'GLU:plan': 3, 'TRP:plan': 1, 'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 38 bond proxies already assigned to first conformer: 2848 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ASER a 58 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER a 58 " occ=0.50 residue: pdb=" N AVAL A 60 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL A 60 " occ=0.50 Time building chain proxies: 3.08, per 1000 atoms: 0.35 Number of scatterers: 8919 At special positions: 0 Unit cell: (124.95, 79.05, 163.2, 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 54 16.00 O 1700 8.00 N 1555 7.00 C 5610 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 96 " distance=2.04 Simple disulfide: pdb=" SG CYS l 22 " - pdb=" SG CYS l 87 " distance=2.03 Simple disulfide: pdb=" SG CYS a 4 " - pdb=" SG CYS a 15 " distance=2.03 Simple disulfide: pdb=" SG CYS a 55 " - pdb=" SG CYS a 143 " distance=2.03 Simple disulfide: pdb=" SG CYS a 179 " - pdb=" SG CYS a 223 " distance=2.03 Simple disulfide: pdb=" SG CYS a 280 " - pdb=" SG CYS a 329 " distance=2.03 Simple disulfide: pdb=" SG CYS a 291 " - pdb=" SG CYS a 312 " distance=2.03 Simple disulfide: pdb=" SG CYS a 313 " - pdb=" SG CYS a 316 " distance=2.03 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 15 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 143 " distance=2.03 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 223 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 312 " distance=2.04 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 316 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 520.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2102 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 18 sheets defined 16.1% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.736A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.586A 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 'L' and resid 78 through 82 removed outlier: 3.611A pdb=" N ASP L 81 " --> pdb=" O GLN L 78 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU L 82 " --> pdb=" O VAL L 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 82' Processing helix chain 'h' and resid 28 through 32 removed outlier: 3.692A pdb=" N TYR h 32 " --> pdb=" O PHE h 29 " (cutoff:3.500A) Processing helix chain 'h' and resid 62 through 65 Processing helix chain 'h' and resid 87 through 91 Processing helix chain 'h' and resid 101 through 105 removed outlier: 3.779A pdb=" N GLY h 105 " --> pdb=" O GLY h 102 " (cutoff:3.500A) Processing helix chain 'l' and resid 78 through 82 removed outlier: 3.573A pdb=" N ASP l 81 " --> pdb=" O GLN l 78 " (cutoff:3.500A) Processing helix chain 'a' and resid 38 through 52 Processing helix chain 'a' and resid 61 through 82 removed outlier: 5.263A pdb=" N GLY a 73 " --> pdb=" O ARG a 69 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N GLU a 74 " --> pdb=" O SER a 70 " (cutoff:3.500A) Processing helix chain 'a' and resid 144 through 146 No H-bonds generated for 'chain 'a' and resid 144 through 146' Processing helix chain 'a' and resid 157 through 160 removed outlier: 4.478A pdb=" N PHE a 160 " --> pdb=" O ASP a 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 157 through 160' Processing helix chain 'a' and resid 180 through 183 removed outlier: 3.779A pdb=" N VAL a 183 " --> pdb=" O ASP a 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 180 through 183' Processing helix chain 'a' and resid 226 through 230 Processing helix chain 'a' and resid 244 through 248 Processing helix chain 'a' and resid 252 through 256 removed outlier: 3.779A pdb=" N THR a 256 " --> pdb=" O HIS a 253 " (cutoff:3.500A) Processing helix chain 'a' and resid 341 through 345 removed outlier: 3.577A pdb=" N ASN a 344 " --> pdb=" O PRO a 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 52 Processing helix chain 'A' and resid 61 through 82 removed outlier: 5.076A pdb=" N GLY A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N GLU A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 180 through 183 removed outlier: 3.897A pdb=" N VAL A 183 " --> pdb=" O ASP A 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 183' Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 237 through 241 removed outlier: 3.822A pdb=" N LEU A 241 " --> pdb=" O GLU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.615A pdb=" N THR A 256 " --> pdb=" O HIS A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 345 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.512A pdb=" N TYR H 94 " --> pdb=" O THR H 112 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL H 37 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N MET H 34 " --> pdb=" O PHE H 50 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N PHE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.772A pdb=" N ALA L 83 " --> pdb=" O VAL L 105 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N TRP L 34 " --> pdb=" O VAL L 46 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.772A pdb=" N ALA L 83 " --> pdb=" O VAL L 105 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 17 through 23 removed outlier: 3.507A pdb=" N MET L 69 " --> pdb=" O SER L 66 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'h' and resid 3 through 7 Processing sheet with id=AA7, first strand: chain 'h' and resid 11 through 12 removed outlier: 3.607A pdb=" N TYR h 94 " --> pdb=" O THR h 112 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N MET h 34 " --> pdb=" O PHE h 50 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N PHE h 50 " --> pdb=" O MET h 34 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TRP h 36 " --> pdb=" O VAL h 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'l' and resid 9 through 12 removed outlier: 6.652A pdb=" N TRP l 34 " --> pdb=" O VAL l 46 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'l' and resid 9 through 12 Processing sheet with id=AB1, first strand: chain 'l' and resid 18 through 23 removed outlier: 3.515A pdb=" N ALA l 18 " --> pdb=" O ILE l 74 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'a' and resid 2 through 7 removed outlier: 5.130A pdb=" N HIS A 1 " --> pdb=" O GLY A 18 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N HIS a 2 " --> pdb=" O VAL A 6 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'a' and resid 87 through 90 removed outlier: 6.790A pdb=" N THR a 87 " --> pdb=" O PHE a 133 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL a 135 " --> pdb=" O THR a 87 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL a 89 " --> pdb=" O VAL a 135 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N GLY a 56 " --> pdb=" O ALA a 149 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'a' and resid 153 through 155 Processing sheet with id=AB5, first strand: chain 'a' and resid 329 through 331 removed outlier: 4.474A pdb=" N PHE a 277 " --> pdb=" O LYS a 213 " (cutoff:3.500A) removed outlier: 9.127A pdb=" N LYS a 213 " --> pdb=" O PHE a 277 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N LEU a 212 " --> pdb=" O GLU a 205 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N GLU a 205 " --> pdb=" O LEU a 212 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG a 214 " --> pdb=" O GLU a 203 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU A 192 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N GLU A 205 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU A 212 " --> pdb=" O GLU A 205 " (cutoff:3.500A) removed outlier: 9.055A pdb=" N LYS A 213 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N PHE A 277 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'a' and resid 284 through 287 removed outlier: 6.454A pdb=" N LYS a 284 " --> pdb=" O TRP a 311 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N CYS a 313 " --> pdb=" O LYS a 284 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N HIS a 286 " --> pdb=" O CYS a 313 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 32 through 35 removed outlier: 3.515A pdb=" N ASP A 157 " --> pdb=" O TRP A 168 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 87 through 90 removed outlier: 6.325A pdb=" N THR A 87 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL A 135 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL A 89 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N GLY A 56 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 285 through 287 296 hydrogen bonds defined for protein. 729 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.27 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1480 1.31 - 1.44: 2628 1.44 - 1.57: 4972 1.57 - 1.70: 0 1.70 - 1.82: 76 Bond restraints: 9156 Sorted by residual: bond pdb=" CA SER L 89 " pdb=" CB SER L 89 " ideal model delta sigma weight residual 1.534 1.436 0.098 1.34e-02 5.57e+03 5.40e+01 bond pdb=" C VAL a 167 " pdb=" O VAL a 167 " ideal model delta sigma weight residual 1.237 1.184 0.053 1.11e-02 8.12e+03 2.30e+01 bond pdb=" CA SER L 93 " pdb=" CB SER L 93 " ideal model delta sigma weight residual 1.530 1.458 0.072 1.68e-02 3.54e+03 1.84e+01 bond pdb=" N ARG A 336 " pdb=" CA ARG A 336 " ideal model delta sigma weight residual 1.453 1.488 -0.035 8.30e-03 1.45e+04 1.75e+01 bond pdb=" C SER L 89 " pdb=" O SER L 89 " ideal model delta sigma weight residual 1.235 1.193 0.042 1.08e-02 8.57e+03 1.52e+01 ... (remaining 9151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 12120 1.94 - 3.88: 295 3.88 - 5.83: 26 5.83 - 7.77: 7 7.77 - 9.71: 2 Bond angle restraints: 12450 Sorted by residual: angle pdb=" N ASP A 208 " pdb=" CA ASP A 208 " pdb=" C ASP A 208 " ideal model delta sigma weight residual 114.12 104.50 9.62 1.39e+00 5.18e-01 4.79e+01 angle pdb=" C LYS A 206 " pdb=" CA LYS A 206 " pdb=" CB LYS A 206 " ideal model delta sigma weight residual 110.16 100.45 9.71 1.66e+00 3.63e-01 3.42e+01 angle pdb=" C HIS a 158 " pdb=" CA HIS a 158 " pdb=" CB HIS a 158 " ideal model delta sigma weight residual 111.50 117.81 -6.31 1.29e+00 6.01e-01 2.39e+01 angle pdb=" N THR a 165 " pdb=" CA THR a 165 " pdb=" C THR a 165 " ideal model delta sigma weight residual 114.64 108.42 6.22 1.52e+00 4.33e-01 1.67e+01 angle pdb=" N ASN L 95 " pdb=" CA ASN L 95 " pdb=" C ASN L 95 " ideal model delta sigma weight residual 114.31 109.19 5.12 1.29e+00 6.01e-01 1.57e+01 ... (remaining 12445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 5011 17.53 - 35.06: 324 35.06 - 52.59: 59 52.59 - 70.12: 14 70.12 - 87.66: 4 Dihedral angle restraints: 5412 sinusoidal: 2116 harmonic: 3296 Sorted by residual: dihedral pdb=" CB CYS a 291 " pdb=" SG CYS a 291 " pdb=" SG CYS a 312 " pdb=" CB CYS a 312 " ideal model delta sinusoidal sigma weight residual -86.00 -130.96 44.96 1 1.00e+01 1.00e-02 2.81e+01 dihedral pdb=" C HIS a 164 " pdb=" N HIS a 164 " pdb=" CA HIS a 164 " pdb=" CB HIS a 164 " ideal model delta harmonic sigma weight residual -122.60 -111.91 -10.69 0 2.50e+00 1.60e-01 1.83e+01 dihedral pdb=" C LYS A 206 " pdb=" N LYS A 206 " pdb=" CA LYS A 206 " pdb=" CB LYS A 206 " ideal model delta harmonic sigma weight residual -122.60 -112.01 -10.59 0 2.50e+00 1.60e-01 1.79e+01 ... (remaining 5409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1055 0.055 - 0.110: 217 0.110 - 0.166: 51 0.166 - 0.221: 6 0.221 - 0.276: 1 Chirality restraints: 1330 Sorted by residual: chirality pdb=" CA HIS a 164 " pdb=" N HIS a 164 " pdb=" C HIS a 164 " pdb=" CB HIS a 164 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA LEU L 96 " pdb=" N LEU L 96 " pdb=" C LEU L 96 " pdb=" CB LEU L 96 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.72e-01 chirality pdb=" CA GLN l 78 " pdb=" N GLN l 78 " pdb=" C GLN l 78 " pdb=" CB GLN l 78 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.45e-01 ... (remaining 1327 not shown) Planarity restraints: 1606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA l 77 " -0.022 2.00e-02 2.50e+03 4.50e-02 2.02e+01 pdb=" C ALA l 77 " 0.078 2.00e-02 2.50e+03 pdb=" O ALA l 77 " -0.030 2.00e-02 2.50e+03 pdb=" N GLN l 78 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE h 100 " 0.016 2.00e-02 2.50e+03 1.49e-02 3.90e+00 pdb=" CG PHE h 100 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE h 100 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE h 100 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE h 100 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE h 100 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE h 100 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR l 33 " -0.014 2.00e-02 2.50e+03 1.33e-02 3.54e+00 pdb=" CG TYR l 33 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR l 33 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR l 33 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR l 33 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR l 33 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR l 33 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR l 33 " -0.000 2.00e-02 2.50e+03 ... (remaining 1603 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1509 2.76 - 3.30: 7748 3.30 - 3.83: 13916 3.83 - 4.37: 17037 4.37 - 4.90: 30629 Nonbonded interactions: 70839 Sorted by model distance: nonbonded pdb=" OG SER A 297 " pdb=" O TYR A 331 " model vdw 2.226 3.040 nonbonded pdb=" OD2 ASP A 197 " pdb=" NZ LYS A 221 " model vdw 2.239 3.120 nonbonded pdb=" OE2 GLU L 82 " pdb=" N VAL L 107 " model vdw 2.241 3.120 nonbonded pdb=" OD2 ASP a 197 " pdb=" NZ LYS a 221 " model vdw 2.273 3.120 nonbonded pdb=" OG SER a 297 " pdb=" O TYR a 331 " model vdw 2.273 3.040 ... (remaining 70834 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 28 or (resid 29 and (name N or name CA or name C \ or name O or name CB )) or resid 30 through 57 or resid 59 or resid 61 through \ 257 or (resid 258 and (name N or name CA or name C or name O or name CB )) or re \ sid 259 through 283 or (resid 284 and (name N or name CA or name C or name O or \ name CB )) or resid 285 through 309 or (resid 310 and (name N or name CA or name \ C or name O or name CB )) or resid 311 through 352)) selection = (chain 'a' and (resid 1 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 25 or (resid 26 through 29 and (nam \ e N or name CA or name C or name O or name CB )) or resid 30 or (resid 31 and (n \ ame N or name CA or name C or name O or name CB )) or resid 32 through 57 or res \ id 59 or resid 61 through 121 or (resid 122 and (name N or name CA or name C or \ name O or name CB )) or resid 123 through 124 or (resid 125 through 127 and (nam \ e N or name CA or name C or name O or name CB )) or resid 128 through 288 or (re \ sid 289 and (name N or name CA or name C or name O or name CB )) or resid 290 th \ rough 314 or (resid 315 and (name N or name CA or name C or name O or name CB )) \ or resid 316 through 325 or (resid 326 and (name N or name CA or name C or name \ O or name CB )) or resid 327 through 352)) } ncs_group { reference = (chain 'H' and (resid 2 through 75 or (resid 76 and (name N or name CA or name C \ or name O or name CB )) or resid 77 through 86 or (resid 87 through 88 and (nam \ e N or name CA or name C or name O or name CB )) or resid 89 through 117)) selection = chain 'h' } ncs_group { reference = (chain 'L' and (resid 4 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 108)) selection = (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 108)) } 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: 8.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.450 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 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 0.098 9172 Z= 0.362 Angle : 0.714 9.712 12482 Z= 0.448 Chirality : 0.049 0.276 1330 Planarity : 0.004 0.045 1606 Dihedral : 12.256 87.655 3262 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.80 % Favored : 94.11 % Rotamer: Outliers : 1.37 % Allowed : 0.84 % Favored : 97.79 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.25), residues: 1143 helix: 2.08 (0.59), residues: 73 sheet: -0.62 (0.28), residues: 369 loop : -0.84 (0.24), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG a 261 TYR 0.031 0.002 TYR l 33 PHE 0.035 0.002 PHE h 100 TRP 0.024 0.001 TRP A 168 HIS 0.009 0.001 HIS a 164 Details of bonding type rmsd covalent geometry : bond 0.00683 ( 9156) covalent geometry : angle 0.71240 (12450) SS BOND : bond 0.00331 ( 16) SS BOND : angle 1.19182 ( 32) hydrogen bonds : bond 0.23039 ( 285) hydrogen bonds : angle 8.41074 ( 729) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 210 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 11 VAL cc_start: 0.8306 (t) cc_final: 0.7992 (p) REVERT: H 43 LYS cc_start: 0.6206 (mppt) cc_final: 0.5854 (mtmt) REVERT: H 57 ASN cc_start: 0.8146 (m-40) cc_final: 0.7876 (m110) REVERT: H 71 SER cc_start: 0.8053 (t) cc_final: 0.7654 (p) REVERT: L 29 LYS cc_start: 0.6847 (mttt) cc_final: 0.6375 (mtmt) REVERT: L 62 SER cc_start: 0.7697 (t) cc_final: 0.7354 (m) REVERT: L 69 MET cc_start: 0.6794 (ttm) cc_final: 0.6536 (ttm) REVERT: L 84 ASP cc_start: 0.7431 (m-30) cc_final: 0.7102 (m-30) REVERT: h 78 THR cc_start: 0.6922 (m) cc_final: 0.6652 (t) REVERT: l 29 LYS cc_start: 0.5390 (mmmt) cc_final: 0.5105 (mttp) REVERT: l 60 ARG cc_start: 0.6761 (ptt180) cc_final: 0.6555 (ptt180) REVERT: l 82 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6286 (tp30) REVERT: a 10 LYS cc_start: 0.6736 (mttt) cc_final: 0.6329 (mttp) REVERT: a 11 LYS cc_start: 0.6850 (mtpt) cc_final: 0.5319 (tppt) REVERT: a 24 ASP cc_start: 0.7349 (p0) cc_final: 0.7061 (p0) REVERT: a 72 GLU cc_start: 0.6003 (tt0) cc_final: 0.5793 (tt0) REVERT: a 142 GLU cc_start: 0.6634 (tt0) cc_final: 0.6332 (mt-10) REVERT: a 156 GLU cc_start: 0.6427 (mt-10) cc_final: 0.6223 (mt-10) REVERT: a 165 THR cc_start: 0.5960 (OUTLIER) cc_final: 0.5461 (m) REVERT: a 166 SER cc_start: 0.7125 (OUTLIER) cc_final: 0.6869 (p) REVERT: a 170 LYS cc_start: 0.7620 (ptmm) cc_final: 0.7049 (ptmm) REVERT: a 189 LYS cc_start: 0.7770 (tptm) cc_final: 0.7014 (tptp) REVERT: a 192 GLU cc_start: 0.7096 (mm-30) cc_final: 0.6832 (mm-30) REVERT: a 261 ARG cc_start: 0.7256 (mmm-85) cc_final: 0.6496 (mtp180) REVERT: a 264 MET cc_start: 0.7917 (mmt) cc_final: 0.7313 (mmt) REVERT: a 271 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7342 (mm-30) REVERT: a 279 GLU cc_start: 0.7139 (mt-10) cc_final: 0.6897 (mt-10) REVERT: a 302 THR cc_start: 0.7665 (m) cc_final: 0.7052 (p) REVERT: A 10 LYS cc_start: 0.7677 (mptt) cc_final: 0.7313 (mmtt) REVERT: A 40 ARG cc_start: 0.6548 (mpp80) cc_final: 0.5863 (mtt90) REVERT: A 52 ASP cc_start: 0.6806 (t70) cc_final: 0.6556 (m-30) REVERT: A 109 ASN cc_start: 0.7143 (m-40) cc_final: 0.6847 (t0) REVERT: A 128 LYS cc_start: 0.6815 (tttp) cc_final: 0.6521 (ttmt) REVERT: A 130 ASN cc_start: 0.6839 (p0) cc_final: 0.6200 (m110) REVERT: A 138 ASP cc_start: 0.6764 (t0) cc_final: 0.6554 (m-30) REVERT: A 178 GLU cc_start: 0.6937 (mt-10) cc_final: 0.6719 (mt-10) REVERT: A 209 THR cc_start: 0.7690 (OUTLIER) cc_final: 0.7464 (m) REVERT: A 274 GLU cc_start: 0.7685 (tt0) cc_final: 0.7387 (tt0) REVERT: A 284 LYS cc_start: 0.7909 (tttp) cc_final: 0.7073 (tptp) outliers start: 12 outliers final: 1 residues processed: 218 average time/residue: 0.5061 time to fit residues: 117.4016 Evaluate side-chains 155 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 150 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 82 GLU Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain a residue 166 SER Chi-restraints excluded: chain A residue 209 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 0.0670 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 74 ASN H 101 ASN L 41 GLN a 2 HIS a 82 ASN a 102 GLN a 131 ASN A 85 GLN A 131 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.140750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.102393 restraints weight = 24767.711| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 3.13 r_work: 0.2876 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9172 Z= 0.119 Angle : 0.585 7.614 12482 Z= 0.317 Chirality : 0.044 0.147 1330 Planarity : 0.004 0.039 1606 Dihedral : 5.144 41.045 1265 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.00 % Allowed : 8.61 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.25), residues: 1143 helix: 1.85 (0.58), residues: 77 sheet: -0.52 (0.27), residues: 380 loop : -0.63 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG a 41 TYR 0.027 0.001 TYR H 103 PHE 0.022 0.002 PHE h 100 TRP 0.015 0.001 TRP A 168 HIS 0.006 0.001 HIS a 2 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 9156) covalent geometry : angle 0.57792 (12450) SS BOND : bond 0.00512 ( 16) SS BOND : angle 1.85408 ( 32) hydrogen bonds : bond 0.04679 ( 285) hydrogen bonds : angle 5.88431 ( 729) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7044 (mppt) cc_final: 0.6776 (mtpt) REVERT: H 57 ASN cc_start: 0.8560 (m-40) cc_final: 0.8350 (m110) REVERT: H 71 SER cc_start: 0.8555 (t) cc_final: 0.8341 (p) REVERT: L 29 LYS cc_start: 0.7996 (mttt) cc_final: 0.7558 (mtpt) REVERT: L 62 SER cc_start: 0.8056 (t) cc_final: 0.7718 (p) REVERT: h 78 THR cc_start: 0.8007 (m) cc_final: 0.7795 (t) REVERT: l 29 LYS cc_start: 0.6754 (mmmt) cc_final: 0.6290 (mttp) REVERT: a 10 LYS cc_start: 0.7717 (mttt) cc_final: 0.7310 (mttp) REVERT: a 40 ARG cc_start: 0.7766 (mtm110) cc_final: 0.7435 (mtm-85) REVERT: a 110 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6540 (pt0) REVERT: a 136 ASP cc_start: 0.8238 (p0) cc_final: 0.7880 (p0) REVERT: a 139 THR cc_start: 0.8628 (p) cc_final: 0.8360 (p) REVERT: a 140 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7919 (mt) REVERT: a 170 LYS cc_start: 0.8534 (ptmm) cc_final: 0.8183 (ptmm) REVERT: a 189 LYS cc_start: 0.8673 (tptm) cc_final: 0.8432 (tptp) REVERT: a 261 ARG cc_start: 0.8415 (mmm-85) cc_final: 0.8053 (mtp180) REVERT: a 264 MET cc_start: 0.9076 (mmt) cc_final: 0.8705 (mmt) REVERT: a 271 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7965 (mm-30) REVERT: A 10 LYS cc_start: 0.8277 (mptt) cc_final: 0.7973 (mmmt) REVERT: A 12 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7006 (mm-30) REVERT: A 40 ARG cc_start: 0.7617 (mpp80) cc_final: 0.7122 (mtt90) REVERT: A 109 ASN cc_start: 0.7482 (m-40) cc_final: 0.7239 (t0) REVERT: A 128 LYS cc_start: 0.7260 (tttp) cc_final: 0.6948 (ttmt) REVERT: A 130 ASN cc_start: 0.7226 (p0) cc_final: 0.6422 (m-40) REVERT: A 284 LYS cc_start: 0.8676 (tttp) cc_final: 0.8261 (tptp) outliers start: 18 outliers final: 10 residues processed: 161 average time/residue: 0.6437 time to fit residues: 109.8432 Evaluate side-chains 142 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 103 THR Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 63 MET Chi-restraints excluded: chain a residue 75 LEU Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 110 GLU Chi-restraints excluded: chain a residue 140 LEU Chi-restraints excluded: chain a residue 162 VAL Chi-restraints excluded: chain a residue 346 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 42 optimal weight: 1.9990 chunk 11 optimal weight: 0.0050 chunk 13 optimal weight: 0.4980 chunk 33 optimal weight: 0.0570 chunk 62 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 101 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 overall best weight: 0.7114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 74 ASN L 41 GLN a 2 HIS ** a 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.140669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.103645 restraints weight = 16012.403| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.44 r_work: 0.2933 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2795 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2795 r_free = 0.2795 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2795 r_free = 0.2795 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2795 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 9172 Z= 0.113 Angle : 0.565 10.520 12482 Z= 0.302 Chirality : 0.044 0.196 1330 Planarity : 0.004 0.034 1606 Dihedral : 4.598 33.038 1259 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.31 % Allowed : 11.34 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.25), residues: 1143 helix: 1.90 (0.58), residues: 77 sheet: -0.36 (0.27), residues: 386 loop : -0.54 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG a 41 TYR 0.023 0.001 TYR H 103 PHE 0.018 0.002 PHE h 100 TRP 0.017 0.001 TRP a 168 HIS 0.005 0.001 HIS h 35 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9156) covalent geometry : angle 0.55691 (12450) SS BOND : bond 0.00442 ( 16) SS BOND : angle 1.97520 ( 32) hydrogen bonds : bond 0.04058 ( 285) hydrogen bonds : angle 5.47259 ( 729) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7087 (mppt) cc_final: 0.6690 (mtmt) REVERT: H 57 ASN cc_start: 0.8688 (m-40) cc_final: 0.8465 (m110) REVERT: H 71 SER cc_start: 0.8581 (t) cc_final: 0.8375 (p) REVERT: L 23 SER cc_start: 0.8825 (p) cc_final: 0.8328 (t) REVERT: L 29 LYS cc_start: 0.7899 (mttt) cc_final: 0.7451 (mtpt) REVERT: L 62 SER cc_start: 0.8034 (t) cc_final: 0.7657 (p) REVERT: l 29 LYS cc_start: 0.6909 (mmmt) cc_final: 0.6404 (mttp) REVERT: l 84 ASP cc_start: 0.8086 (m-30) cc_final: 0.7814 (m-30) REVERT: a 10 LYS cc_start: 0.7739 (mttt) cc_final: 0.7380 (mtmp) REVERT: a 72 GLU cc_start: 0.7626 (tt0) cc_final: 0.7421 (tt0) REVERT: a 140 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7877 (mt) REVERT: a 170 LYS cc_start: 0.8525 (ptmm) cc_final: 0.8193 (ptpp) REVERT: a 189 LYS cc_start: 0.8734 (tptm) cc_final: 0.8474 (tptp) REVERT: a 261 ARG cc_start: 0.8551 (mmm-85) cc_final: 0.8078 (mtp180) REVERT: a 271 GLU cc_start: 0.8322 (mm-30) cc_final: 0.8112 (mm-30) REVERT: A 10 LYS cc_start: 0.8289 (mptt) cc_final: 0.7938 (mmmt) REVERT: A 12 GLU cc_start: 0.7697 (mt-10) cc_final: 0.6976 (mm-30) REVERT: A 40 ARG cc_start: 0.7663 (mpp80) cc_final: 0.7153 (mtt90) REVERT: A 109 ASN cc_start: 0.7486 (m-40) cc_final: 0.7234 (t0) REVERT: A 128 LYS cc_start: 0.7272 (tttp) cc_final: 0.6951 (ttmt) REVERT: A 130 ASN cc_start: 0.7284 (p0) cc_final: 0.6510 (m110) REVERT: A 284 LYS cc_start: 0.8715 (tttp) cc_final: 0.8283 (tptp) outliers start: 21 outliers final: 11 residues processed: 146 average time/residue: 0.6313 time to fit residues: 97.9889 Evaluate side-chains 131 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain h residue 113 LEU Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 63 MET Chi-restraints excluded: chain a residue 75 LEU Chi-restraints excluded: chain a residue 87 THR Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 140 LEU Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain A residue 129 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 39 optimal weight: 8.9990 chunk 60 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 76 optimal weight: 0.6980 chunk 22 optimal weight: 20.0000 chunk 108 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 41 GLN ** a 82 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 = 0.3601 r_free = 0.3601 target = 0.138995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.102080 restraints weight = 29260.722| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.24 r_work: 0.2827 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 9172 Z= 0.151 Angle : 0.620 11.751 12482 Z= 0.331 Chirality : 0.046 0.217 1330 Planarity : 0.005 0.034 1606 Dihedral : 4.857 37.718 1259 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.73 % Allowed : 11.66 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.25), residues: 1143 helix: 1.64 (0.58), residues: 77 sheet: -0.33 (0.27), residues: 374 loop : -0.58 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG a 41 TYR 0.025 0.002 TYR H 103 PHE 0.025 0.002 PHE h 100 TRP 0.022 0.002 TRP a 168 HIS 0.006 0.001 HIS h 35 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 9156) covalent geometry : angle 0.61071 (12450) SS BOND : bond 0.00538 ( 16) SS BOND : angle 2.19308 ( 32) hydrogen bonds : bond 0.04322 ( 285) hydrogen bonds : angle 5.39875 ( 729) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7123 (mppt) cc_final: 0.6784 (mtpt) REVERT: H 57 ASN cc_start: 0.8633 (m-40) cc_final: 0.8396 (m110) REVERT: H 71 SER cc_start: 0.8540 (t) cc_final: 0.8327 (p) REVERT: L 62 SER cc_start: 0.8046 (t) cc_final: 0.7713 (p) REVERT: l 29 LYS cc_start: 0.6874 (mmmt) cc_final: 0.6486 (mttp) REVERT: a 10 LYS cc_start: 0.7652 (mttt) cc_final: 0.7420 (mtmp) REVERT: a 74 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7989 (mt-10) REVERT: a 170 LYS cc_start: 0.8508 (ptmm) cc_final: 0.8190 (ptmm) REVERT: a 189 LYS cc_start: 0.8723 (tptm) cc_final: 0.8487 (tptp) REVERT: a 261 ARG cc_start: 0.8493 (mmm-85) cc_final: 0.8045 (mtp180) REVERT: A 10 LYS cc_start: 0.8342 (mptt) cc_final: 0.7999 (mmmt) REVERT: A 12 GLU cc_start: 0.7624 (mt-10) cc_final: 0.6947 (mm-30) REVERT: A 40 ARG cc_start: 0.7644 (mpp80) cc_final: 0.7066 (mtt90) REVERT: A 109 ASN cc_start: 0.7464 (m-40) cc_final: 0.7261 (t0) REVERT: A 128 LYS cc_start: 0.7318 (tttp) cc_final: 0.6985 (ttmt) REVERT: A 130 ASN cc_start: 0.7218 (p0) cc_final: 0.6479 (m110) REVERT: A 284 LYS cc_start: 0.8631 (tttp) cc_final: 0.8216 (tptp) outliers start: 25 outliers final: 13 residues processed: 138 average time/residue: 0.5473 time to fit residues: 80.5034 Evaluate side-chains 135 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain h residue 113 LEU Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 103 THR Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 63 MET Chi-restraints excluded: chain a residue 74 GLU Chi-restraints excluded: chain a residue 75 LEU Chi-restraints excluded: chain a residue 87 THR Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain A residue 97 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 39 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 109 optimal weight: 0.5980 chunk 32 optimal weight: 0.2980 chunk 91 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 59 optimal weight: 0.0870 chunk 16 optimal weight: 0.2980 overall best weight: 0.4560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 41 GLN a 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.141598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.103534 restraints weight = 26893.273| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 3.20 r_work: 0.2888 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 9172 Z= 0.095 Angle : 0.533 11.893 12482 Z= 0.285 Chirality : 0.043 0.200 1330 Planarity : 0.004 0.034 1606 Dihedral : 4.462 31.948 1259 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.31 % Allowed : 13.03 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.25), residues: 1143 helix: 1.68 (0.58), residues: 77 sheet: -0.24 (0.27), residues: 374 loop : -0.48 (0.25), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 53 TYR 0.021 0.001 TYR H 103 PHE 0.010 0.001 PHE h 100 TRP 0.017 0.001 TRP a 168 HIS 0.005 0.001 HIS h 35 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 9156) covalent geometry : angle 0.52647 (12450) SS BOND : bond 0.00449 ( 16) SS BOND : angle 1.68048 ( 32) hydrogen bonds : bond 0.03436 ( 285) hydrogen bonds : angle 5.15916 ( 729) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7072 (mppt) cc_final: 0.6700 (mtmt) REVERT: H 57 ASN cc_start: 0.8620 (m-40) cc_final: 0.8385 (m110) REVERT: H 71 SER cc_start: 0.8513 (t) cc_final: 0.8222 (p) REVERT: L 62 SER cc_start: 0.7938 (t) cc_final: 0.7599 (m) REVERT: l 29 LYS cc_start: 0.6811 (mmmt) cc_final: 0.6457 (mttp) REVERT: a 10 LYS cc_start: 0.7584 (mttt) cc_final: 0.7370 (mtmp) REVERT: a 72 GLU cc_start: 0.7457 (tt0) cc_final: 0.7237 (tt0) REVERT: a 110 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6631 (pt0) REVERT: a 170 LYS cc_start: 0.8481 (ptmm) cc_final: 0.8148 (ptpp) REVERT: a 189 LYS cc_start: 0.8610 (tptm) cc_final: 0.8381 (tptp) REVERT: a 261 ARG cc_start: 0.8417 (mmm-85) cc_final: 0.7976 (mtp180) REVERT: A 10 LYS cc_start: 0.8286 (mptt) cc_final: 0.7936 (mtmp) REVERT: A 12 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7077 (mm-30) REVERT: A 40 ARG cc_start: 0.7519 (mpp80) cc_final: 0.6934 (mtt90) REVERT: A 128 LYS cc_start: 0.7286 (tttp) cc_final: 0.6961 (ttmt) REVERT: A 130 ASN cc_start: 0.7241 (p0) cc_final: 0.6469 (m110) REVERT: A 237 GLU cc_start: 0.7146 (pm20) cc_final: 0.6457 (mp0) REVERT: A 284 LYS cc_start: 0.8564 (tttp) cc_final: 0.8160 (tptp) outliers start: 21 outliers final: 11 residues processed: 145 average time/residue: 0.5892 time to fit residues: 90.8042 Evaluate side-chains 134 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain h residue 113 LEU Chi-restraints excluded: chain l residue 103 THR Chi-restraints excluded: chain a residue 51 GLU Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 63 MET Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 110 GLU Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain A residue 97 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 98 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 66 optimal weight: 0.4980 chunk 6 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 76 optimal weight: 0.0870 chunk 105 optimal weight: 6.9990 overall best weight: 2.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.138031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.101107 restraints weight = 30065.503| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.36 r_work: 0.2801 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 9172 Z= 0.222 Angle : 0.683 13.724 12482 Z= 0.364 Chirality : 0.049 0.253 1330 Planarity : 0.005 0.037 1606 Dihedral : 5.090 36.608 1259 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.84 % Allowed : 13.45 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.25), residues: 1143 helix: 1.46 (0.57), residues: 77 sheet: -0.14 (0.27), residues: 372 loop : -0.64 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG a 257 TYR 0.027 0.002 TYR H 103 PHE 0.028 0.003 PHE h 100 TRP 0.024 0.002 TRP a 168 HIS 0.007 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00543 ( 9156) covalent geometry : angle 0.67340 (12450) SS BOND : bond 0.00684 ( 16) SS BOND : angle 2.40737 ( 32) hydrogen bonds : bond 0.04758 ( 285) hydrogen bonds : angle 5.41495 ( 729) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7221 (mppt) cc_final: 0.6857 (mtpt) REVERT: H 57 ASN cc_start: 0.8666 (m-40) cc_final: 0.8432 (m110) REVERT: H 71 SER cc_start: 0.8523 (t) cc_final: 0.8294 (p) REVERT: L 62 SER cc_start: 0.8062 (t) cc_final: 0.7744 (m) REVERT: h 104 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8362 (mt-10) REVERT: l 29 LYS cc_start: 0.6953 (mmmt) cc_final: 0.6605 (mttp) REVERT: l 49 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8017 (mt-10) REVERT: a 10 LYS cc_start: 0.7688 (mttt) cc_final: 0.7299 (mtmp) REVERT: a 74 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8063 (mt-10) REVERT: a 110 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6693 (pt0) REVERT: a 170 LYS cc_start: 0.8559 (ptmm) cc_final: 0.8208 (ptmm) REVERT: a 189 LYS cc_start: 0.8765 (tptm) cc_final: 0.8526 (tptp) REVERT: a 261 ARG cc_start: 0.8550 (mmm-85) cc_final: 0.8103 (mtp180) REVERT: A 10 LYS cc_start: 0.8284 (mptt) cc_final: 0.7896 (mtmp) REVERT: A 12 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7100 (mm-30) REVERT: A 40 ARG cc_start: 0.7650 (mpp80) cc_final: 0.7228 (mtt90) REVERT: A 78 ILE cc_start: 0.7541 (OUTLIER) cc_final: 0.7281 (mp) REVERT: A 128 LYS cc_start: 0.7318 (tttp) cc_final: 0.7072 (tttt) REVERT: A 130 ASN cc_start: 0.7263 (p0) cc_final: 0.6487 (m110) REVERT: A 284 LYS cc_start: 0.8661 (tttp) cc_final: 0.8217 (tptp) outliers start: 26 outliers final: 15 residues processed: 137 average time/residue: 0.5556 time to fit residues: 81.0264 Evaluate side-chains 140 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain h residue 104 GLU Chi-restraints excluded: chain h residue 113 LEU Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 49 GLU Chi-restraints excluded: chain l residue 50 ASP Chi-restraints excluded: chain l residue 103 THR Chi-restraints excluded: chain a residue 51 GLU Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 63 MET Chi-restraints excluded: chain a residue 74 GLU Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 110 GLU Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 110 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 106 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 22 optimal weight: 20.0000 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 74 ASN A 151 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.138415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.101343 restraints weight = 29949.667| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.40 r_work: 0.2795 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 9172 Z= 0.185 Angle : 0.648 12.971 12482 Z= 0.346 Chirality : 0.047 0.232 1330 Planarity : 0.005 0.034 1606 Dihedral : 5.098 36.490 1259 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.73 % Allowed : 13.87 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.25), residues: 1143 helix: 1.44 (0.57), residues: 77 sheet: -0.11 (0.27), residues: 372 loop : -0.67 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG a 257 TYR 0.024 0.002 TYR H 103 PHE 0.023 0.002 PHE h 100 TRP 0.026 0.002 TRP a 168 HIS 0.006 0.001 HIS h 35 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 9156) covalent geometry : angle 0.63792 (12450) SS BOND : bond 0.00631 ( 16) SS BOND : angle 2.30080 ( 32) hydrogen bonds : bond 0.04458 ( 285) hydrogen bonds : angle 5.39431 ( 729) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7327 (mppt) cc_final: 0.6937 (mtpt) REVERT: H 57 ASN cc_start: 0.8630 (m-40) cc_final: 0.8408 (m110) REVERT: H 71 SER cc_start: 0.8529 (t) cc_final: 0.8303 (p) REVERT: L 49 GLU cc_start: 0.8952 (mt-10) cc_final: 0.8696 (mt-10) REVERT: L 62 SER cc_start: 0.8079 (t) cc_final: 0.7750 (m) REVERT: h 104 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8339 (mt-10) REVERT: l 29 LYS cc_start: 0.7103 (mmmt) cc_final: 0.6589 (mttp) REVERT: a 10 LYS cc_start: 0.7713 (mttt) cc_final: 0.7420 (mtmp) REVERT: a 74 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8023 (mt-10) REVERT: a 110 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6684 (pt0) REVERT: a 170 LYS cc_start: 0.8576 (ptmm) cc_final: 0.8192 (ptmm) REVERT: a 189 LYS cc_start: 0.8747 (tptm) cc_final: 0.8514 (tptp) REVERT: a 261 ARG cc_start: 0.8563 (mmm-85) cc_final: 0.8110 (mtp180) REVERT: A 10 LYS cc_start: 0.8283 (mptt) cc_final: 0.7899 (mtmp) REVERT: A 12 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7078 (mm-30) REVERT: A 40 ARG cc_start: 0.7592 (mpp80) cc_final: 0.7147 (mtt90) REVERT: A 128 LYS cc_start: 0.7307 (tttp) cc_final: 0.7044 (tttt) REVERT: A 130 ASN cc_start: 0.7226 (p0) cc_final: 0.6439 (m110) REVERT: A 237 GLU cc_start: 0.7258 (pm20) cc_final: 0.6644 (mp0) REVERT: A 284 LYS cc_start: 0.8658 (tttp) cc_final: 0.8210 (tptp) REVERT: A 309 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7895 (pm20) outliers start: 25 outliers final: 16 residues processed: 142 average time/residue: 0.5230 time to fit residues: 78.8277 Evaluate side-chains 144 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain h residue 104 GLU Chi-restraints excluded: chain h residue 113 LEU Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 103 THR Chi-restraints excluded: chain a residue 51 GLU Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 63 MET Chi-restraints excluded: chain a residue 74 GLU Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 110 GLU Chi-restraints excluded: chain a residue 238 GLU Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 309 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 46 optimal weight: 0.9990 chunk 27 optimal weight: 0.0070 chunk 74 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 39 optimal weight: 0.0670 chunk 6 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.141274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.102901 restraints weight = 21525.989| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.89 r_work: 0.2929 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2921 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2921 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 9172 Z= 0.098 Angle : 0.544 13.045 12482 Z= 0.290 Chirality : 0.043 0.202 1330 Planarity : 0.004 0.034 1606 Dihedral : 4.541 31.049 1259 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.10 % Allowed : 14.71 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.25), residues: 1143 helix: 1.41 (0.58), residues: 77 sheet: -0.04 (0.27), residues: 382 loop : -0.52 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 53 TYR 0.023 0.001 TYR H 103 PHE 0.010 0.001 PHE a 277 TRP 0.021 0.001 TRP a 168 HIS 0.005 0.001 HIS h 35 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 9156) covalent geometry : angle 0.53766 (12450) SS BOND : bond 0.00497 ( 16) SS BOND : angle 1.69064 ( 32) hydrogen bonds : bond 0.03376 ( 285) hydrogen bonds : angle 5.14484 ( 729) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7274 (mppt) cc_final: 0.6885 (mtmt) REVERT: H 57 ASN cc_start: 0.8596 (m-40) cc_final: 0.8354 (m110) REVERT: H 71 SER cc_start: 0.8474 (t) cc_final: 0.8189 (p) REVERT: L 49 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8392 (mt-10) REVERT: L 62 SER cc_start: 0.7980 (t) cc_final: 0.7681 (m) REVERT: l 29 LYS cc_start: 0.6974 (mmmt) cc_final: 0.6560 (mttp) REVERT: a 10 LYS cc_start: 0.7718 (mttt) cc_final: 0.7376 (mtmp) REVERT: a 51 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.6042 (mp0) REVERT: a 110 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6642 (pt0) REVERT: a 170 LYS cc_start: 0.8507 (ptmm) cc_final: 0.8130 (ptmm) REVERT: a 189 LYS cc_start: 0.8601 (tptm) cc_final: 0.8388 (tptp) REVERT: a 261 ARG cc_start: 0.8405 (mmm-85) cc_final: 0.7981 (mtp180) REVERT: A 10 LYS cc_start: 0.8219 (mptt) cc_final: 0.7875 (mtmp) REVERT: A 12 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7118 (mm-30) REVERT: A 40 ARG cc_start: 0.7384 (mpp80) cc_final: 0.6921 (mtt90) REVERT: A 128 LYS cc_start: 0.7266 (tttp) cc_final: 0.7038 (tttt) REVERT: A 130 ASN cc_start: 0.7255 (p0) cc_final: 0.6433 (m110) REVERT: A 237 GLU cc_start: 0.7030 (pm20) cc_final: 0.6660 (mp0) REVERT: A 284 LYS cc_start: 0.8500 (tttp) cc_final: 0.8107 (tptp) REVERT: A 309 GLU cc_start: 0.7933 (pm20) cc_final: 0.7722 (pm20) outliers start: 19 outliers final: 11 residues processed: 143 average time/residue: 0.6053 time to fit residues: 92.0370 Evaluate side-chains 138 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain h residue 113 LEU Chi-restraints excluded: chain l residue 103 THR Chi-restraints excluded: chain a residue 51 GLU Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 63 MET Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 110 GLU Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain A residue 97 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 20 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.138966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.101612 restraints weight = 23255.570| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 3.09 r_work: 0.2864 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 9172 Z= 0.167 Angle : 0.630 13.198 12482 Z= 0.335 Chirality : 0.046 0.224 1330 Planarity : 0.004 0.033 1606 Dihedral : 4.935 37.643 1259 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.10 % Allowed : 14.60 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.25), residues: 1143 helix: 1.44 (0.58), residues: 77 sheet: -0.06 (0.27), residues: 372 loop : -0.56 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 53 TYR 0.026 0.002 TYR H 103 PHE 0.018 0.002 PHE h 100 TRP 0.028 0.002 TRP a 168 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 9156) covalent geometry : angle 0.62089 (12450) SS BOND : bond 0.00611 ( 16) SS BOND : angle 2.14834 ( 32) hydrogen bonds : bond 0.04245 ( 285) hydrogen bonds : angle 5.29440 ( 729) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7393 (mppt) cc_final: 0.6999 (mtmt) REVERT: H 57 ASN cc_start: 0.8595 (m-40) cc_final: 0.8369 (m110) REVERT: H 71 SER cc_start: 0.8481 (t) cc_final: 0.8259 (p) REVERT: L 49 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8653 (mt-10) REVERT: L 62 SER cc_start: 0.8033 (t) cc_final: 0.7729 (m) REVERT: l 29 LYS cc_start: 0.7055 (mmmt) cc_final: 0.6613 (mttm) REVERT: a 10 LYS cc_start: 0.7733 (mttt) cc_final: 0.7499 (mtmp) REVERT: a 51 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.6096 (mp0) REVERT: a 110 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6628 (pt0) REVERT: a 170 LYS cc_start: 0.8583 (ptmm) cc_final: 0.8229 (ptpp) REVERT: a 189 LYS cc_start: 0.8679 (tptm) cc_final: 0.8458 (tptp) REVERT: a 261 ARG cc_start: 0.8478 (mmm-85) cc_final: 0.8058 (mtp180) REVERT: A 10 LYS cc_start: 0.8249 (mptt) cc_final: 0.7902 (mtmp) REVERT: A 12 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7095 (mm-30) REVERT: A 40 ARG cc_start: 0.7558 (mpp80) cc_final: 0.7112 (mtt90) REVERT: A 128 LYS cc_start: 0.7313 (tttp) cc_final: 0.7072 (tttt) REVERT: A 130 ASN cc_start: 0.7224 (p0) cc_final: 0.6465 (m110) REVERT: A 237 GLU cc_start: 0.7074 (pm20) cc_final: 0.6780 (mp0) REVERT: A 284 LYS cc_start: 0.8568 (tttp) cc_final: 0.8149 (tptp) outliers start: 19 outliers final: 14 residues processed: 136 average time/residue: 0.5436 time to fit residues: 78.6263 Evaluate side-chains 138 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain h residue 113 LEU Chi-restraints excluded: chain l residue 103 THR Chi-restraints excluded: chain a residue 51 GLU Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 63 MET Chi-restraints excluded: chain a residue 87 THR Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 110 GLU Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 97 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 96 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 79 optimal weight: 0.0370 chunk 6 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 41 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 overall best weight: 0.7658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.140667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.102740 restraints weight = 23293.867| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 3.19 r_work: 0.2875 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9172 Z= 0.114 Angle : 0.572 12.840 12482 Z= 0.304 Chirality : 0.044 0.205 1330 Planarity : 0.004 0.033 1606 Dihedral : 4.696 33.986 1259 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.68 % Allowed : 15.23 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.25), residues: 1143 helix: 1.42 (0.58), residues: 77 sheet: -0.04 (0.28), residues: 372 loop : -0.49 (0.25), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 53 TYR 0.024 0.001 TYR H 103 PHE 0.011 0.001 PHE a 277 TRP 0.025 0.001 TRP a 168 HIS 0.005 0.001 HIS h 35 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 9156) covalent geometry : angle 0.56453 (12450) SS BOND : bond 0.00524 ( 16) SS BOND : angle 1.84802 ( 32) hydrogen bonds : bond 0.03653 ( 285) hydrogen bonds : angle 5.17220 ( 729) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7391 (mppt) cc_final: 0.7001 (mtmt) REVERT: H 57 ASN cc_start: 0.8602 (m-40) cc_final: 0.8377 (m110) REVERT: H 71 SER cc_start: 0.8498 (t) cc_final: 0.8204 (p) REVERT: L 49 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8521 (mt-10) REVERT: L 62 SER cc_start: 0.8024 (t) cc_final: 0.7728 (m) REVERT: l 69 MET cc_start: 0.8285 (tpp) cc_final: 0.7985 (mmm) REVERT: a 10 LYS cc_start: 0.7726 (mttt) cc_final: 0.7423 (mtmp) REVERT: a 110 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6605 (pt0) REVERT: a 170 LYS cc_start: 0.8504 (ptmm) cc_final: 0.8141 (ptpp) REVERT: a 189 LYS cc_start: 0.8640 (tptm) cc_final: 0.8422 (tptp) REVERT: a 261 ARG cc_start: 0.8447 (mmm-85) cc_final: 0.8008 (mtp180) REVERT: A 10 LYS cc_start: 0.8225 (mptt) cc_final: 0.7856 (mtmp) REVERT: A 12 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7088 (mm-30) REVERT: A 40 ARG cc_start: 0.7453 (mpp80) cc_final: 0.6973 (mtt90) REVERT: A 128 LYS cc_start: 0.7267 (tttp) cc_final: 0.7030 (tttt) REVERT: A 130 ASN cc_start: 0.7239 (p0) cc_final: 0.6409 (m110) REVERT: A 284 LYS cc_start: 0.8570 (tttp) cc_final: 0.8163 (tptp) outliers start: 15 outliers final: 10 residues processed: 133 average time/residue: 0.5760 time to fit residues: 81.4483 Evaluate side-chains 132 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain h residue 113 LEU Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 63 MET Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 110 GLU Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain A residue 97 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 75 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 85 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 73 optimal weight: 0.0270 chunk 36 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 101 optimal weight: 0.4980 chunk 49 optimal weight: 4.9990 chunk 58 optimal weight: 0.0770 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 35 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.142483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.104902 restraints weight = 23784.314| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.10 r_work: 0.2912 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2923 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2923 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 9172 Z= 0.092 Angle : 0.529 12.636 12482 Z= 0.280 Chirality : 0.043 0.194 1330 Planarity : 0.004 0.034 1606 Dihedral : 4.381 29.897 1259 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.47 % Allowed : 15.86 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.26), residues: 1143 helix: 1.53 (0.59), residues: 77 sheet: 0.01 (0.27), residues: 382 loop : -0.39 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 53 TYR 0.023 0.001 TYR H 103 PHE 0.009 0.001 PHE a 277 TRP 0.021 0.001 TRP a 168 HIS 0.005 0.001 HIS h 35 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 9156) covalent geometry : angle 0.52292 (12450) SS BOND : bond 0.00478 ( 16) SS BOND : angle 1.64187 ( 32) hydrogen bonds : bond 0.03209 ( 285) hydrogen bonds : angle 5.01584 ( 729) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3617.14 seconds wall clock time: 62 minutes 4.40 seconds (3724.40 seconds total)