Starting phenix.real_space_refine on Sat Oct 11 07:13:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ut8_42533/10_2025/8ut8_42533.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ut8_42533/10_2025/8ut8_42533.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ut8_42533/10_2025/8ut8_42533.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ut8_42533/10_2025/8ut8_42533.map" model { file = "/net/cci-nas-00/data/ceres_data/8ut8_42533/10_2025/8ut8_42533.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ut8_42533/10_2025/8ut8_42533.cif" } resolution = 3.2 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= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 66 5.16 5 C 7833 2.51 5 N 2266 2.21 5 O 2542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12707 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2422 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 13, 'TRANS': 303} Chain: "B" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1359 Classifications: {'peptide': 167} Link IDs: {'TRANS': 166} Chain: "C" Number of atoms: 2414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2414 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 13, 'TRANS': 302} Chain: "D" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1359 Classifications: {'peptide': 167} Link IDs: {'TRANS': 166} Chain: "E" Number of atoms: 2414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2414 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 13, 'TRANS': 302} Chain: "F" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1359 Classifications: {'peptide': 167} Link IDs: {'TRANS': 166} Chain: "G" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 630 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 126} Link IDs: {'TRANS': 125} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 126 Planarities with less than four sites: {'UNK:plan-1': 126} Unresolved non-hydrogen planarities: 126 Chain: "H" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 540 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'TRANS': 107} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 108 Planarities with less than four sites: {'UNK:plan-1': 108} Unresolved non-hydrogen planarities: 108 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.74, per 1000 atoms: 0.29 Number of scatterers: 12707 At special positions: 0 Unit cell: (84.825, 109.475, 144.275, 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 66 16.00 O 2542 8.00 N 2266 7.00 C 7833 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 268 " distance=2.04 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 66 " distance=2.02 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 272 " - pdb=" SG CYS A 296 " distance=2.02 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.02 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 268 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 66 " distance=2.04 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 129 " distance=2.03 Simple disulfide: pdb=" SG CYS C 272 " - pdb=" SG CYS C 296 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS E 42 " - pdb=" SG CYS E 268 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 66 " distance=2.03 Simple disulfide: pdb=" SG CYS E 87 " - pdb=" SG CYS E 129 " distance=2.03 Simple disulfide: pdb=" SG CYS E 272 " - pdb=" SG CYS E 296 " distance=2.04 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " 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 Links applied BETA1-3 " NAG I 1 " - " NAG I 2 " BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG A 401 " - " ASN A 28 " " NAG B 301 " - " ASN B 154 " " NAG C 401 " - " ASN C 12 " " NAG C 402 " - " ASN C 28 " " NAG D 301 " - " ASN D 154 " " NAG E 401 " - " ASN E 28 " " NAG E 402 " - " ASN E 231 " " NAG F 301 " - " ASN F 154 " " NAG I 1 " - " ASN B 82 " " NAG J 1 " - " ASN D 82 " " NAG K 1 " - " ASN F 82 " Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 603.5 milliseconds Enol-peptide restraints added in 1.2 microseconds 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3104 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 36 sheets defined 27.8% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 57 through 62 removed outlier: 3.595A pdb=" N THR A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 70 removed outlier: 5.271A pdb=" N GLN A 68 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU A 70 " --> pdb=" O ASP A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 104 removed outlier: 3.863A pdb=" N GLU A 104 " --> pdb=" O GLN A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'B' and resid 38 through 55 Processing helix chain 'B' and resid 74 through 126 Processing helix chain 'B' and resid 146 through 154 Processing helix chain 'B' and resid 162 through 169 Processing helix chain 'C' and resid 55 through 60 removed outlier: 4.031A pdb=" N ILE C 60 " --> pdb=" O LEU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 70 removed outlier: 3.823A pdb=" N ASP C 67 " --> pdb=" O PRO C 64 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLN C 68 " --> pdb=" O GLN C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 106 removed outlier: 4.246A pdb=" N GLY C 106 " --> pdb=" O LEU C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 186 Processing helix chain 'D' and resid 37 through 56 Processing helix chain 'D' and resid 74 through 127 Processing helix chain 'D' and resid 145 through 154 removed outlier: 3.554A pdb=" N MET D 149 " --> pdb=" O ASP D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 171 removed outlier: 3.698A pdb=" N ALA D 166 " --> pdb=" O TYR D 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 62 Processing helix chain 'E' and resid 63 through 70 removed outlier: 5.404A pdb=" N GLN E 68 " --> pdb=" O GLN E 65 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU E 70 " --> pdb=" O ASP E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 103 Processing helix chain 'E' and resid 178 through 186 Processing helix chain 'F' and resid 37 through 56 Processing helix chain 'F' and resid 74 through 127 Processing helix chain 'F' and resid 128 through 130 No H-bonds generated for 'chain 'F' and resid 128 through 130' Processing helix chain 'F' and resid 145 through 154 Processing helix chain 'F' and resid 162 through 171 Processing helix chain 'G' and resid 61 through 65 Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.556A pdb=" N UNK G 91 " --> pdb=" O UNK G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 113 removed outlier: 3.731A pdb=" N UNK G 113 " --> pdb=" O UNK G 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 32 No H-bonds generated for 'chain 'H' and resid 30 through 32' Processing helix chain 'H' and resid 80 through 84 Processing sheet with id=AA1, first strand: chain 'B' and resid 33 through 37 removed outlier: 4.576A pdb=" N TYR B 22 " --> pdb=" O ASP B 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 16 Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AA4, first strand: chain 'A' and resid 33 through 34 Processing sheet with id=AA5, first strand: chain 'A' and resid 40 through 42 removed outlier: 5.448A pdb=" N ILE A 41 " --> pdb=" O ASP A 265 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 48 through 51 removed outlier: 6.646A pdb=" N VAL A 49 " --> pdb=" O ILE A 78 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 90 through 92 removed outlier: 6.900A pdb=" N LYS A 91 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N TRP A 225 " --> pdb=" O LYS A 91 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N VAL A 170 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ARG A 247 " --> pdb=" O VAL A 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 90 through 92 removed outlier: 6.900A pdb=" N LYS A 91 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N TRP A 225 " --> pdb=" O LYS A 91 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N VAL A 170 " --> pdb=" O PRO A 245 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 155 through 160 Processing sheet with id=AB1, first strand: chain 'A' and resid 277 through 279 removed outlier: 3.794A pdb=" N CYS A 272 " --> pdb=" O ILE A 279 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 32 through 36 removed outlier: 3.610A pdb=" N GLY D 23 " --> pdb=" O GLY C 6 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 14 through 16 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 31 Processing sheet with id=AB5, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AB6, first strand: chain 'C' and resid 41 through 42 removed outlier: 5.397A pdb=" N ILE C 41 " --> pdb=" O ASP C 265 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 48 through 50 removed outlier: 6.326A pdb=" N VAL C 49 " --> pdb=" O ILE C 78 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ILE C 77 " --> pdb=" O ILE C 258 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 72 through 73 removed outlier: 6.922A pdb=" N ARG C 247 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N VAL C 170 " --> pdb=" O ARG C 247 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 140 through 142 Processing sheet with id=AC1, first strand: chain 'C' and resid 155 through 159 Processing sheet with id=AC2, first strand: chain 'C' and resid 272 through 274 removed outlier: 3.757A pdb=" N CYS C 272 " --> pdb=" O ILE C 279 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 33 through 36 removed outlier: 3.661A pdb=" N LYS E 2 " --> pdb=" O GLN F 27 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 14 through 16 Processing sheet with id=AC5, first strand: chain 'E' and resid 29 through 31 Processing sheet with id=AC6, first strand: chain 'E' and resid 33 through 34 Processing sheet with id=AC7, first strand: chain 'E' and resid 41 through 42 removed outlier: 5.591A pdb=" N ILE E 41 " --> pdb=" O ASP E 265 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'E' and resid 48 through 50 removed outlier: 5.922A pdb=" N ILE E 77 " --> pdb=" O ILE E 258 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 108 through 112 removed outlier: 7.076A pdb=" N ARG E 247 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N VAL E 170 " --> pdb=" O ARG E 247 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 126 through 130 removed outlier: 4.461A pdb=" N CYS E 129 " --> pdb=" O SER E 135 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AD3, first strand: chain 'E' and resid 155 through 160 Processing sheet with id=AD4, first strand: chain 'E' and resid 277 through 278 removed outlier: 3.562A pdb=" N VAL E 293 " --> pdb=" O TYR E 273 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 9 through 12 removed outlier: 5.008A pdb=" N UNK G 33 " --> pdb=" O UNK G 99 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N UNK G 32 " --> pdb=" O UNK G 52 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N UNK G 52 " --> pdb=" O UNK G 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N UNK G 34 " --> pdb=" O UNK G 50 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N UNK G 50 " --> pdb=" O UNK G 34 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N UNK G 36 " --> pdb=" O UNK G 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 18 through 22 Processing sheet with id=AD7, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AD8, first strand: chain 'H' and resid 10 through 13 removed outlier: 3.589A pdb=" N UNK H 107 " --> pdb=" O UNK H 11 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 54 through 55 removed outlier: 6.462A pdb=" N UNK H 36 " --> pdb=" O UNK H 48 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N UNK H 50 " --> pdb=" O UNK H 34 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N UNK H 34 " --> pdb=" O UNK H 50 " (cutoff:3.500A) 531 hydrogen bonds defined for protein. 1407 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.06 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4365 1.34 - 1.47: 2932 1.47 - 1.59: 5515 1.59 - 1.71: 1 1.71 - 1.84: 96 Bond restraints: 12909 Sorted by residual: bond pdb=" N ARG E 40 " pdb=" CA ARG E 40 " ideal model delta sigma weight residual 1.454 1.489 -0.034 1.27e-02 6.20e+03 7.35e+00 bond pdb=" CA ARG A 130 " pdb=" CB ARG A 130 " ideal model delta sigma weight residual 1.531 1.617 -0.086 3.28e-02 9.30e+02 6.89e+00 bond pdb=" CB MET A 311 " pdb=" CG MET A 311 " ideal model delta sigma weight residual 1.520 1.452 0.068 3.00e-02 1.11e+03 5.16e+00 bond pdb=" CA UNK H 44 " pdb=" CB UNK H 44 " ideal model delta sigma weight residual 1.530 1.485 0.045 2.00e-02 2.50e+03 4.97e+00 bond pdb=" CA UNK H 65 " pdb=" CB UNK H 65 " ideal model delta sigma weight residual 1.530 1.486 0.044 2.00e-02 2.50e+03 4.90e+00 ... (remaining 12904 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 16553 2.42 - 4.85: 821 4.85 - 7.27: 92 7.27 - 9.70: 11 9.70 - 12.12: 3 Bond angle restraints: 17480 Sorted by residual: angle pdb=" N ASP E 267 " pdb=" CA ASP E 267 " pdb=" C ASP E 267 " ideal model delta sigma weight residual 111.28 117.54 -6.26 1.09e+00 8.42e-01 3.30e+01 angle pdb=" C UNK H 102 " pdb=" N UNK H 103 " pdb=" CA UNK H 103 " ideal model delta sigma weight residual 121.70 111.59 10.11 1.80e+00 3.09e-01 3.15e+01 angle pdb=" N CYS C 87 " pdb=" CA CYS C 87 " pdb=" C CYS C 87 " ideal model delta sigma weight residual 111.02 102.62 8.40 1.52e+00 4.33e-01 3.05e+01 angle pdb=" N GLY B 8 " pdb=" CA GLY B 8 " pdb=" C GLY B 8 " ideal model delta sigma weight residual 112.77 119.15 -6.38 1.28e+00 6.10e-01 2.48e+01 angle pdb=" C UNK H 12 " pdb=" N UNK H 13 " pdb=" CA UNK H 13 " ideal model delta sigma weight residual 121.70 112.75 8.95 1.80e+00 3.09e-01 2.47e+01 ... (remaining 17475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 7331 17.97 - 35.95: 451 35.95 - 53.92: 126 53.92 - 71.90: 35 71.90 - 89.87: 16 Dihedral angle restraints: 7959 sinusoidal: 3137 harmonic: 4822 Sorted by residual: dihedral pdb=" CB CYS C 87 " pdb=" SG CYS C 87 " pdb=" SG CYS C 129 " pdb=" CB CYS C 129 " ideal model delta sinusoidal sigma weight residual 93.00 157.96 -64.96 1 1.00e+01 1.00e-02 5.54e+01 dihedral pdb=" CB CYS D 144 " pdb=" SG CYS D 144 " pdb=" SG CYS D 148 " pdb=" CB CYS D 148 " ideal model delta sinusoidal sigma weight residual -86.00 -149.97 63.97 1 1.00e+01 1.00e-02 5.39e+01 dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 66 " pdb=" CB CYS C 66 " ideal model delta sinusoidal sigma weight residual 93.00 29.45 63.55 1 1.00e+01 1.00e-02 5.32e+01 ... (remaining 7956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1613 0.071 - 0.142: 313 0.142 - 0.213: 48 0.213 - 0.284: 7 0.284 - 0.356: 3 Chirality restraints: 1984 Sorted by residual: chirality pdb=" CA UNK H 103 " pdb=" N UNK H 103 " pdb=" C UNK H 103 " pdb=" CB UNK H 103 " both_signs ideal model delta sigma weight residual False 2.52 2.16 0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" CB THR B 49 " pdb=" CA THR B 49 " pdb=" OG1 THR B 49 " pdb=" CG2 THR B 49 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN B 82 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.38e+00 ... (remaining 1981 not shown) Planarity restraints: 2326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 58 " -0.018 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C GLY A 58 " 0.062 2.00e-02 2.50e+03 pdb=" O GLY A 58 " -0.023 2.00e-02 2.50e+03 pdb=" N THR A 59 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 57 " -0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C LEU A 57 " 0.060 2.00e-02 2.50e+03 pdb=" O LEU A 57 " -0.022 2.00e-02 2.50e+03 pdb=" N GLY A 58 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNK H 38 " 0.015 2.00e-02 2.50e+03 3.10e-02 9.64e+00 pdb=" C UNK H 38 " -0.054 2.00e-02 2.50e+03 pdb=" O UNK H 38 " 0.020 2.00e-02 2.50e+03 pdb=" N UNK H 39 " 0.018 2.00e-02 2.50e+03 ... (remaining 2323 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 244 2.65 - 3.21: 11382 3.21 - 3.77: 19389 3.77 - 4.34: 26735 4.34 - 4.90: 44468 Nonbonded interactions: 102218 Sorted by model distance: nonbonded pdb=" OE1 GLU A 139 " pdb=" CD ARG A 247 " model vdw 2.087 3.440 nonbonded pdb=" OG SER E 198 " pdb=" OD2 ASP E 232 " model vdw 2.124 3.040 nonbonded pdb=" OE2 GLU E 34 " pdb=" OG1 THR E 36 " model vdw 2.136 3.040 nonbonded pdb=" OE1 GLU E 31 " pdb=" OG SER E 304 " model vdw 2.185 3.040 nonbonded pdb=" OE1 GLU C 139 " pdb=" NH1 ARG C 247 " model vdw 2.200 3.120 ... (remaining 102213 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 316 or resid 401 through 402)) selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = (chain 'G' and resid 20 through 127) selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.590 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 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 0.086 12938 Z= 0.304 Angle : 1.159 12.687 17552 Z= 0.628 Chirality : 0.059 0.356 1984 Planarity : 0.006 0.091 2315 Dihedral : 13.814 89.871 4810 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.10 (0.20), residues: 1438 helix: 0.88 (0.25), residues: 316 sheet: 0.65 (0.29), residues: 287 loop : -0.42 (0.19), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 121 TYR 0.026 0.003 TYR C 200 PHE 0.040 0.004 PHE E 238 TRP 0.029 0.003 TRP D 21 HIS 0.012 0.003 HIS A 7 Details of bonding type rmsd covalent geometry : bond 0.00651 (12909) covalent geometry : angle 1.14744 (17480) SS BOND : bond 0.00756 ( 15) SS BOND : angle 2.79595 ( 30) hydrogen bonds : bond 0.15220 ( 521) hydrogen bonds : angle 7.28636 ( 1407) link_BETA1-3 : bond 0.00753 ( 1) link_BETA1-3 : angle 7.95630 ( 3) link_BETA1-4 : bond 0.00113 ( 2) link_BETA1-4 : angle 2.14162 ( 6) link_NAG-ASN : bond 0.00207 ( 11) link_NAG-ASN : angle 1.99294 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 ARG cc_start: 0.7817 (ttp80) cc_final: 0.7365 (tmm160) REVERT: B 115 MET cc_start: 0.8503 (tpt) cc_final: 0.8195 (tpt) REVERT: B 120 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6916 (pt0) REVERT: B 153 ARG cc_start: 0.8114 (mtp85) cc_final: 0.7638 (mtt90) REVERT: C 92 PHE cc_start: 0.6528 (m-80) cc_final: 0.5993 (m-80) REVERT: C 173 ILE cc_start: 0.7497 (mm) cc_final: 0.7275 (mm) REVERT: C 227 MET cc_start: 0.7377 (mmp) cc_final: 0.7116 (tpt) REVERT: D 60 ASN cc_start: 0.7878 (t0) cc_final: 0.7505 (t0) REVERT: D 117 LYS cc_start: 0.8111 (ptpp) cc_final: 0.7147 (ptpp) REVERT: E 222 ASP cc_start: 0.6879 (p0) cc_final: 0.6677 (p0) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.1321 time to fit residues: 48.8457 Evaluate side-chains 215 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN B 95 ASN ** C 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN C 201 GLN ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 HIS F 60 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.165381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.143608 restraints weight = 19580.845| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 2.64 r_work: 0.3699 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 12938 Z= 0.287 Angle : 0.776 11.161 17552 Z= 0.406 Chirality : 0.046 0.229 1984 Planarity : 0.005 0.051 2315 Dihedral : 5.579 37.872 2117 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.36 % Allowed : 11.16 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.21 (0.20), residues: 1438 helix: 1.04 (0.27), residues: 325 sheet: 0.60 (0.31), residues: 277 loop : -0.89 (0.19), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 247 TYR 0.022 0.003 TYR D 157 PHE 0.030 0.003 PHE E 242 TRP 0.017 0.002 TRP C 171 HIS 0.008 0.002 HIS E 8 Details of bonding type rmsd covalent geometry : bond 0.00645 (12909) covalent geometry : angle 0.75893 (17480) SS BOND : bond 0.00637 ( 15) SS BOND : angle 2.16730 ( 30) hydrogen bonds : bond 0.05121 ( 521) hydrogen bonds : angle 5.97023 ( 1407) link_BETA1-3 : bond 0.00461 ( 1) link_BETA1-3 : angle 7.10687 ( 3) link_BETA1-4 : bond 0.00221 ( 2) link_BETA1-4 : angle 2.50371 ( 6) link_NAG-ASN : bond 0.00394 ( 11) link_NAG-ASN : angle 2.23737 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 217 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASN cc_start: 0.7637 (t0) cc_final: 0.7431 (t0) REVERT: B 54 ARG cc_start: 0.7930 (ttp80) cc_final: 0.7340 (tmm160) REVERT: D 60 ASN cc_start: 0.8204 (t0) cc_final: 0.7798 (t0) REVERT: D 117 LYS cc_start: 0.8078 (ptpp) cc_final: 0.7726 (ptpp) REVERT: E 109 ASP cc_start: 0.7875 (t0) cc_final: 0.7644 (t0) REVERT: E 164 LYS cc_start: 0.8482 (mttt) cc_final: 0.8251 (mmtt) REVERT: F 161 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7381 (ptmt) REVERT: F 162 TYR cc_start: 0.6597 (m-10) cc_final: 0.6385 (m-10) outliers start: 29 outliers final: 21 residues processed: 233 average time/residue: 0.1328 time to fit residues: 43.3115 Evaluate side-chains 204 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 182 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain C residue 7 HIS Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 268 CYS Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 161 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 149 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 146 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 chunk 109 optimal weight: 0.0000 chunk 116 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 HIS A 259 GLN B 159 HIS ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 287 ASN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.170723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.149435 restraints weight = 19586.883| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.65 r_work: 0.3754 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12938 Z= 0.133 Angle : 0.609 9.835 17552 Z= 0.318 Chirality : 0.042 0.238 1984 Planarity : 0.003 0.047 2315 Dihedral : 5.050 34.141 2117 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.28 % Allowed : 12.70 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.24 (0.20), residues: 1438 helix: 1.30 (0.27), residues: 317 sheet: 0.39 (0.31), residues: 283 loop : -0.96 (0.19), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 121 TYR 0.026 0.002 TYR A 200 PHE 0.013 0.002 PHE E 92 TRP 0.016 0.001 TRP C 171 HIS 0.012 0.001 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00285 (12909) covalent geometry : angle 0.59465 (17480) SS BOND : bond 0.00452 ( 15) SS BOND : angle 1.65800 ( 30) hydrogen bonds : bond 0.04560 ( 521) hydrogen bonds : angle 5.49381 ( 1407) link_BETA1-3 : bond 0.00305 ( 1) link_BETA1-3 : angle 6.08204 ( 3) link_BETA1-4 : bond 0.00236 ( 2) link_BETA1-4 : angle 1.82111 ( 6) link_NAG-ASN : bond 0.00243 ( 11) link_NAG-ASN : angle 1.91537 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 221 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7824 (tp30) cc_final: 0.7575 (mm-30) REVERT: A 22 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7707 (mpt180) REVERT: A 28 ASN cc_start: 0.7486 (t0) cc_final: 0.7278 (t0) REVERT: A 213 GLN cc_start: 0.7253 (OUTLIER) cc_final: 0.6858 (mm-40) REVERT: B 53 ASN cc_start: 0.7905 (OUTLIER) cc_final: 0.7230 (m-40) REVERT: B 120 GLU cc_start: 0.7527 (pt0) cc_final: 0.6904 (mm-30) REVERT: C 155 MET cc_start: 0.6778 (ttm) cc_final: 0.6432 (ttm) REVERT: C 220 ARG cc_start: 0.5593 (mmt-90) cc_final: 0.4848 (ttm170) REVERT: C 295 LYS cc_start: 0.8747 (mttt) cc_final: 0.8384 (mppt) REVERT: C 303 ARG cc_start: 0.8439 (mtp-110) cc_final: 0.8045 (ttp80) REVERT: D 60 ASN cc_start: 0.8142 (t0) cc_final: 0.7548 (t0) REVERT: E 34 GLU cc_start: 0.7548 (tp30) cc_final: 0.7177 (tp30) REVERT: F 143 LYS cc_start: 0.8111 (tptt) cc_final: 0.7393 (tptm) REVERT: F 161 LYS cc_start: 0.7759 (OUTLIER) cc_final: 0.7137 (ptmt) outliers start: 28 outliers final: 11 residues processed: 234 average time/residue: 0.1272 time to fit residues: 41.9508 Evaluate side-chains 203 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 188 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain F residue 161 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 36 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 116 optimal weight: 0.7980 chunk 90 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 127 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 56 optimal weight: 8.9990 chunk 92 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 GLN B 95 ASN B 125 GLN B 159 HIS ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN D 125 GLN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.166122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.144184 restraints weight = 19830.410| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.67 r_work: 0.3712 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12938 Z= 0.190 Angle : 0.655 18.122 17552 Z= 0.332 Chirality : 0.045 0.665 1984 Planarity : 0.004 0.044 2315 Dihedral : 5.351 38.833 2117 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.42 % Allowed : 12.21 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.39 (0.20), residues: 1438 helix: 1.25 (0.27), residues: 320 sheet: 0.07 (0.31), residues: 290 loop : -1.01 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 131 TYR 0.028 0.002 TYR A 200 PHE 0.017 0.002 PHE E 238 TRP 0.011 0.001 TRP C 171 HIS 0.009 0.002 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00420 (12909) covalent geometry : angle 0.62131 (17480) SS BOND : bond 0.00481 ( 15) SS BOND : angle 1.66551 ( 30) hydrogen bonds : bond 0.04488 ( 521) hydrogen bonds : angle 5.42993 ( 1407) link_BETA1-3 : bond 0.00135 ( 1) link_BETA1-3 : angle 6.23288 ( 3) link_BETA1-4 : bond 0.00172 ( 2) link_BETA1-4 : angle 2.14031 ( 6) link_NAG-ASN : bond 0.01161 ( 11) link_NAG-ASN : angle 4.08462 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 206 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7885 (tp30) cc_final: 0.7655 (mm-30) REVERT: A 22 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7623 (mpt180) REVERT: A 213 GLN cc_start: 0.7191 (OUTLIER) cc_final: 0.6886 (mm-40) REVERT: B 26 HIS cc_start: 0.5792 (m90) cc_final: 0.5531 (m90) REVERT: B 120 GLU cc_start: 0.7645 (pt0) cc_final: 0.6939 (mm-30) REVERT: B 149 MET cc_start: 0.7162 (mmt) cc_final: 0.6839 (mmt) REVERT: C 295 LYS cc_start: 0.8784 (mttt) cc_final: 0.8416 (mppt) REVERT: C 303 ARG cc_start: 0.8503 (mtp-110) cc_final: 0.8102 (ttp80) REVERT: D 60 ASN cc_start: 0.8270 (t0) cc_final: 0.7717 (t0) REVERT: D 61 GLN cc_start: 0.8389 (tp40) cc_final: 0.8081 (tp40) REVERT: D 117 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7912 (ttpt) REVERT: E 34 GLU cc_start: 0.7626 (tp30) cc_final: 0.7272 (tp30) REVERT: F 19 ASP cc_start: 0.7532 (OUTLIER) cc_final: 0.7108 (p0) REVERT: F 137 CYS cc_start: 0.7642 (OUTLIER) cc_final: 0.7177 (m) REVERT: F 143 LYS cc_start: 0.8159 (tptt) cc_final: 0.7452 (tptm) REVERT: F 161 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7142 (ptmt) outliers start: 42 outliers final: 28 residues processed: 227 average time/residue: 0.1159 time to fit residues: 37.8987 Evaluate side-chains 220 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 186 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain C residue 7 HIS Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 268 CYS Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 137 CYS Chi-restraints excluded: chain F residue 161 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 72 optimal weight: 9.9990 chunk 36 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 150 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 123 optimal weight: 0.6980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 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 = 0.4027 r_free = 0.4027 target = 0.164631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.143181 restraints weight = 19703.617| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.63 r_work: 0.3690 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12938 Z= 0.197 Angle : 0.649 14.821 17552 Z= 0.329 Chirality : 0.045 0.607 1984 Planarity : 0.003 0.042 2315 Dihedral : 5.233 35.895 2117 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.26 % Allowed : 13.11 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.57 (0.20), residues: 1438 helix: 1.04 (0.27), residues: 326 sheet: -0.13 (0.32), residues: 269 loop : -1.05 (0.19), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 121 TYR 0.029 0.002 TYR A 200 PHE 0.015 0.002 PHE E 238 TRP 0.011 0.001 TRP C 171 HIS 0.011 0.002 HIS B 159 Details of bonding type rmsd covalent geometry : bond 0.00441 (12909) covalent geometry : angle 0.61898 (17480) SS BOND : bond 0.00643 ( 15) SS BOND : angle 1.58953 ( 30) hydrogen bonds : bond 0.04461 ( 521) hydrogen bonds : angle 5.43773 ( 1407) link_BETA1-3 : bond 0.00034 ( 1) link_BETA1-3 : angle 6.22390 ( 3) link_BETA1-4 : bond 0.00196 ( 2) link_BETA1-4 : angle 2.10890 ( 6) link_NAG-ASN : bond 0.00628 ( 11) link_NAG-ASN : angle 3.77036 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 211 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7885 (tp30) cc_final: 0.7681 (mm-30) REVERT: A 22 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7560 (mpt180) REVERT: A 213 GLN cc_start: 0.7161 (OUTLIER) cc_final: 0.6294 (mm110) REVERT: B 120 GLU cc_start: 0.7618 (pt0) cc_final: 0.6991 (mm-30) REVERT: B 149 MET cc_start: 0.7300 (mmt) cc_final: 0.6950 (mmt) REVERT: C 227 MET cc_start: 0.7527 (tpt) cc_final: 0.7277 (tpt) REVERT: C 295 LYS cc_start: 0.8795 (mttt) cc_final: 0.8417 (mppt) REVERT: D 60 ASN cc_start: 0.8335 (t0) cc_final: 0.7810 (t0) REVERT: D 61 GLN cc_start: 0.8375 (tp40) cc_final: 0.8114 (tp40) REVERT: E 34 GLU cc_start: 0.7716 (tp30) cc_final: 0.7362 (tp30) REVERT: F 19 ASP cc_start: 0.7588 (OUTLIER) cc_final: 0.7163 (p0) REVERT: F 137 CYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7187 (m) REVERT: F 143 LYS cc_start: 0.8211 (tptt) cc_final: 0.7483 (tptm) REVERT: F 161 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7125 (ptmt) outliers start: 40 outliers final: 31 residues processed: 230 average time/residue: 0.1225 time to fit residues: 39.8440 Evaluate side-chains 226 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 190 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain C residue 7 HIS Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 137 CYS Chi-restraints excluded: chain F residue 161 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 116 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 128 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 153 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN B 159 HIS ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.166713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.145411 restraints weight = 19468.992| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.63 r_work: 0.3703 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12938 Z= 0.146 Angle : 0.605 14.474 17552 Z= 0.308 Chirality : 0.043 0.542 1984 Planarity : 0.003 0.042 2315 Dihedral : 4.979 34.572 2117 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.52 % Allowed : 14.74 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.44 (0.21), residues: 1438 helix: 1.20 (0.28), residues: 323 sheet: 0.04 (0.34), residues: 241 loop : -0.99 (0.19), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 131 TYR 0.030 0.002 TYR A 200 PHE 0.016 0.002 PHE C 69 TRP 0.017 0.001 TRP C 171 HIS 0.010 0.001 HIS B 159 Details of bonding type rmsd covalent geometry : bond 0.00323 (12909) covalent geometry : angle 0.57700 (17480) SS BOND : bond 0.00451 ( 15) SS BOND : angle 1.60450 ( 30) hydrogen bonds : bond 0.04313 ( 521) hydrogen bonds : angle 5.31955 ( 1407) link_BETA1-3 : bond 0.00218 ( 1) link_BETA1-3 : angle 5.86514 ( 3) link_BETA1-4 : bond 0.00191 ( 2) link_BETA1-4 : angle 1.96006 ( 6) link_NAG-ASN : bond 0.00606 ( 11) link_NAG-ASN : angle 3.52445 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 211 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7563 (mpt180) REVERT: A 139 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7146 (mm-30) REVERT: B 116 ASP cc_start: 0.7743 (m-30) cc_final: 0.7260 (m-30) REVERT: B 120 GLU cc_start: 0.7579 (pt0) cc_final: 0.6983 (mm-30) REVERT: C 110 LYS cc_start: 0.8048 (mtpp) cc_final: 0.7596 (mtpp) REVERT: C 155 MET cc_start: 0.6152 (ttm) cc_final: 0.5896 (ttm) REVERT: C 227 MET cc_start: 0.7550 (tpt) cc_final: 0.7311 (tpt) REVERT: C 295 LYS cc_start: 0.8739 (mttt) cc_final: 0.8370 (mppt) REVERT: D 60 ASN cc_start: 0.8334 (t0) cc_final: 0.7810 (t0) REVERT: D 61 GLN cc_start: 0.8357 (tp40) cc_final: 0.8086 (tp40) REVERT: E 34 GLU cc_start: 0.7662 (tp30) cc_final: 0.7319 (tp30) REVERT: E 155 MET cc_start: 0.8024 (mtm) cc_final: 0.7567 (ptp) REVERT: E 164 LYS cc_start: 0.8326 (mmtt) cc_final: 0.7949 (ttmm) REVERT: F 19 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7121 (p0) REVERT: F 137 CYS cc_start: 0.7610 (OUTLIER) cc_final: 0.7193 (m) REVERT: F 143 LYS cc_start: 0.8176 (tptt) cc_final: 0.7446 (tptm) REVERT: F 161 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7143 (ptmt) outliers start: 31 outliers final: 25 residues processed: 227 average time/residue: 0.1220 time to fit residues: 39.4738 Evaluate side-chains 219 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 190 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain C residue 7 HIS Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 242 PHE Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 117 LYS Chi-restraints excluded: chain F residue 137 CYS Chi-restraints excluded: chain F residue 161 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 30 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 154 optimal weight: 10.9990 chunk 160 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 110 optimal weight: 0.0270 chunk 9 optimal weight: 5.9990 chunk 120 optimal weight: 0.4980 overall best weight: 1.9044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 HIS B 159 HIS ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 217 GLN ** F 28 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 = 0.4034 r_free = 0.4034 target = 0.164824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.143563 restraints weight = 19625.707| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.62 r_work: 0.3680 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12938 Z= 0.197 Angle : 0.642 14.504 17552 Z= 0.327 Chirality : 0.044 0.515 1984 Planarity : 0.004 0.060 2315 Dihedral : 5.079 35.215 2117 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.34 % Allowed : 15.15 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.58 (0.21), residues: 1438 helix: 1.13 (0.28), residues: 323 sheet: -0.21 (0.33), residues: 243 loop : -1.05 (0.19), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 121 TYR 0.030 0.002 TYR A 200 PHE 0.016 0.002 PHE E 92 TRP 0.013 0.001 TRP C 171 HIS 0.008 0.001 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00445 (12909) covalent geometry : angle 0.61459 (17480) SS BOND : bond 0.00540 ( 15) SS BOND : angle 1.71542 ( 30) hydrogen bonds : bond 0.04379 ( 521) hydrogen bonds : angle 5.40375 ( 1407) link_BETA1-3 : bond 0.00104 ( 1) link_BETA1-3 : angle 5.94081 ( 3) link_BETA1-4 : bond 0.00119 ( 2) link_BETA1-4 : angle 2.14216 ( 6) link_NAG-ASN : bond 0.00628 ( 11) link_NAG-ASN : angle 3.52499 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 200 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7243 (mpp-170) REVERT: A 256 MET cc_start: 0.8114 (ptm) cc_final: 0.7900 (ptm) REVERT: B 116 ASP cc_start: 0.7709 (m-30) cc_final: 0.7236 (m-30) REVERT: B 120 GLU cc_start: 0.7561 (pt0) cc_final: 0.7004 (mm-30) REVERT: C 227 MET cc_start: 0.7529 (tpt) cc_final: 0.7296 (tpt) REVERT: D 47 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7583 (tt0) REVERT: D 60 ASN cc_start: 0.8409 (t0) cc_final: 0.7955 (t0) REVERT: D 61 GLN cc_start: 0.8392 (tp40) cc_final: 0.8155 (tp40) REVERT: E 34 GLU cc_start: 0.7699 (tp30) cc_final: 0.7471 (tp30) REVERT: E 155 MET cc_start: 0.7999 (mtm) cc_final: 0.7559 (ptp) REVERT: E 164 LYS cc_start: 0.8345 (mmtt) cc_final: 0.7968 (ttmm) REVERT: F 19 ASP cc_start: 0.7557 (OUTLIER) cc_final: 0.7112 (p0) REVERT: F 137 CYS cc_start: 0.7630 (OUTLIER) cc_final: 0.6575 (m) REVERT: F 143 LYS cc_start: 0.8212 (tptt) cc_final: 0.7469 (tptm) REVERT: F 161 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7116 (ptmt) outliers start: 41 outliers final: 30 residues processed: 224 average time/residue: 0.1161 time to fit residues: 37.1974 Evaluate side-chains 218 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 183 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain C residue 7 HIS Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 242 PHE Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 137 CYS Chi-restraints excluded: chain F residue 161 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 47 optimal weight: 10.0000 chunk 157 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 142 optimal weight: 20.0000 chunk 87 optimal weight: 2.9990 chunk 144 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS C 182 GLN E 17 ASN ** F 28 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 = 0.3992 r_free = 0.3992 target = 0.161145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.139668 restraints weight = 19616.163| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.60 r_work: 0.3651 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 12938 Z= 0.244 Angle : 0.692 15.371 17552 Z= 0.352 Chirality : 0.047 0.655 1984 Planarity : 0.004 0.042 2315 Dihedral : 5.328 36.251 2117 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.42 % Allowed : 15.15 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.75 (0.21), residues: 1438 helix: 1.02 (0.28), residues: 323 sheet: -0.46 (0.33), residues: 243 loop : -1.12 (0.19), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 25 TYR 0.025 0.002 TYR D 119 PHE 0.017 0.002 PHE E 238 TRP 0.017 0.002 TRP C 171 HIS 0.012 0.002 HIS B 159 Details of bonding type rmsd covalent geometry : bond 0.00552 (12909) covalent geometry : angle 0.66239 (17480) SS BOND : bond 0.00645 ( 15) SS BOND : angle 1.90780 ( 30) hydrogen bonds : bond 0.04513 ( 521) hydrogen bonds : angle 5.57629 ( 1407) link_BETA1-3 : bond 0.00177 ( 1) link_BETA1-3 : angle 6.15861 ( 3) link_BETA1-4 : bond 0.00177 ( 2) link_BETA1-4 : angle 2.25575 ( 6) link_NAG-ASN : bond 0.00804 ( 11) link_NAG-ASN : angle 3.77535 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 196 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7326 (mpp-170) REVERT: B 116 ASP cc_start: 0.7696 (m-30) cc_final: 0.7167 (m-30) REVERT: B 120 GLU cc_start: 0.7630 (pt0) cc_final: 0.7048 (mm-30) REVERT: B 149 MET cc_start: 0.7388 (mmt) cc_final: 0.6961 (tpt) REVERT: C 25 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7558 (tm-30) REVERT: C 200 TYR cc_start: 0.8268 (t80) cc_final: 0.7970 (t80) REVERT: D 47 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7691 (tt0) REVERT: D 60 ASN cc_start: 0.8431 (t0) cc_final: 0.7982 (t0) REVERT: D 61 GLN cc_start: 0.8429 (tp40) cc_final: 0.8204 (tp40) REVERT: D 117 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7963 (ttpt) REVERT: E 164 LYS cc_start: 0.8415 (mmtt) cc_final: 0.8005 (ttmm) REVERT: F 137 CYS cc_start: 0.7713 (OUTLIER) cc_final: 0.7299 (m) REVERT: F 143 LYS cc_start: 0.8259 (tptt) cc_final: 0.7525 (tptm) REVERT: F 161 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7115 (ptmt) outliers start: 42 outliers final: 31 residues processed: 222 average time/residue: 0.1202 time to fit residues: 38.2875 Evaluate side-chains 222 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 185 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain C residue 7 HIS Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 242 PHE Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 137 CYS Chi-restraints excluded: chain F residue 161 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 92 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 123 optimal weight: 0.0980 chunk 122 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 64 optimal weight: 7.9990 chunk 114 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 162 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 HIS ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS D 168 GLN ** F 28 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 = 0.4043 r_free = 0.4043 target = 0.165893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.144841 restraints weight = 19509.816| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.61 r_work: 0.3702 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12938 Z= 0.136 Angle : 0.625 14.811 17552 Z= 0.318 Chirality : 0.044 0.533 1984 Planarity : 0.003 0.042 2315 Dihedral : 5.041 33.589 2117 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.77 % Allowed : 15.96 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.63 (0.21), residues: 1438 helix: 1.21 (0.28), residues: 323 sheet: -0.55 (0.31), residues: 271 loop : -1.03 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 25 TYR 0.033 0.002 TYR C 186 PHE 0.014 0.001 PHE D 24 TRP 0.017 0.001 TRP C 171 HIS 0.009 0.001 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00295 (12909) covalent geometry : angle 0.59742 (17480) SS BOND : bond 0.00380 ( 15) SS BOND : angle 1.69902 ( 30) hydrogen bonds : bond 0.04305 ( 521) hydrogen bonds : angle 5.30771 ( 1407) link_BETA1-3 : bond 0.00378 ( 1) link_BETA1-3 : angle 5.49186 ( 3) link_BETA1-4 : bond 0.00150 ( 2) link_BETA1-4 : angle 1.85435 ( 6) link_NAG-ASN : bond 0.00706 ( 11) link_NAG-ASN : angle 3.54178 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 202 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7263 (mpp-170) REVERT: A 186 TYR cc_start: 0.6766 (OUTLIER) cc_final: 0.6128 (m-10) REVERT: A 213 GLN cc_start: 0.7087 (OUTLIER) cc_final: 0.6831 (mm110) REVERT: A 272 CYS cc_start: 0.7661 (OUTLIER) cc_final: 0.7156 (p) REVERT: A 296 CYS cc_start: 0.6411 (OUTLIER) cc_final: 0.6180 (p) REVERT: B 26 HIS cc_start: 0.5980 (m-70) cc_final: 0.5762 (m-70) REVERT: B 116 ASP cc_start: 0.7542 (m-30) cc_final: 0.7089 (m-30) REVERT: B 120 GLU cc_start: 0.7453 (pt0) cc_final: 0.6974 (mm-30) REVERT: B 149 MET cc_start: 0.7030 (mmt) cc_final: 0.6776 (tpt) REVERT: C 25 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7557 (tm-30) REVERT: C 173 ILE cc_start: 0.7746 (mm) cc_final: 0.7194 (tp) REVERT: C 295 LYS cc_start: 0.8756 (mttt) cc_final: 0.8549 (mmtp) REVERT: D 47 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7580 (tt0) REVERT: D 60 ASN cc_start: 0.8437 (t0) cc_final: 0.7902 (t0) REVERT: D 61 GLN cc_start: 0.8315 (tp40) cc_final: 0.8084 (tp40) REVERT: D 117 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7901 (ttpt) REVERT: E 34 GLU cc_start: 0.7614 (tp30) cc_final: 0.7305 (tp30) REVERT: E 155 MET cc_start: 0.7993 (mtm) cc_final: 0.7780 (ptp) REVERT: E 164 LYS cc_start: 0.8390 (mmtt) cc_final: 0.7978 (ttmm) REVERT: F 19 ASP cc_start: 0.7535 (OUTLIER) cc_final: 0.7086 (p0) REVERT: F 41 THR cc_start: 0.8463 (m) cc_final: 0.8168 (m) REVERT: F 115 MET cc_start: 0.7308 (tpt) cc_final: 0.6805 (tpt) REVERT: F 137 CYS cc_start: 0.7587 (OUTLIER) cc_final: 0.7252 (m) REVERT: F 143 LYS cc_start: 0.8242 (tptt) cc_final: 0.7520 (tptm) REVERT: F 161 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7107 (ptmt) outliers start: 34 outliers final: 18 residues processed: 221 average time/residue: 0.1153 time to fit residues: 37.0806 Evaluate side-chains 215 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 186 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 186 TYR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain D residue 168 GLN Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 242 PHE Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 137 CYS Chi-restraints excluded: chain F residue 161 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 49 optimal weight: 0.8980 chunk 100 optimal weight: 0.4980 chunk 31 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 148 optimal weight: 10.0000 chunk 58 optimal weight: 0.5980 chunk 135 optimal weight: 4.9990 chunk 157 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN ** F 28 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 = 0.4031 r_free = 0.4031 target = 0.165199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.143700 restraints weight = 19622.736| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.62 r_work: 0.3694 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 12938 Z= 0.153 Angle : 0.652 14.730 17552 Z= 0.331 Chirality : 0.045 0.524 1984 Planarity : 0.004 0.041 2315 Dihedral : 5.062 32.867 2117 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.52 % Allowed : 16.78 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.63 (0.21), residues: 1438 helix: 1.26 (0.28), residues: 323 sheet: -0.57 (0.31), residues: 271 loop : -1.05 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 25 TYR 0.042 0.002 TYR C 186 PHE 0.032 0.002 PHE A 88 TRP 0.020 0.001 TRP C 171 HIS 0.013 0.001 HIS B 159 Details of bonding type rmsd covalent geometry : bond 0.00346 (12909) covalent geometry : angle 0.62615 (17480) SS BOND : bond 0.00487 ( 15) SS BOND : angle 1.80805 ( 30) hydrogen bonds : bond 0.04355 ( 521) hydrogen bonds : angle 5.27882 ( 1407) link_BETA1-3 : bond 0.00077 ( 1) link_BETA1-3 : angle 5.53574 ( 3) link_BETA1-4 : bond 0.00284 ( 2) link_BETA1-4 : angle 1.92371 ( 6) link_NAG-ASN : bond 0.00696 ( 11) link_NAG-ASN : angle 3.51335 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7258 (mpp-170) REVERT: A 186 TYR cc_start: 0.6773 (OUTLIER) cc_final: 0.6102 (m-10) REVERT: A 213 GLN cc_start: 0.7062 (OUTLIER) cc_final: 0.6333 (mm110) REVERT: B 26 HIS cc_start: 0.6077 (m-70) cc_final: 0.5793 (m-70) REVERT: B 116 ASP cc_start: 0.7566 (m-30) cc_final: 0.7092 (m-30) REVERT: B 120 GLU cc_start: 0.7477 (pt0) cc_final: 0.7002 (mm-30) REVERT: B 159 HIS cc_start: 0.6548 (OUTLIER) cc_final: 0.5908 (m90) REVERT: C 25 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7535 (tm-30) REVERT: C 145 SER cc_start: 0.6068 (p) cc_final: 0.5825 (p) REVERT: C 173 ILE cc_start: 0.7761 (mm) cc_final: 0.7190 (tp) REVERT: C 295 LYS cc_start: 0.8744 (mttt) cc_final: 0.8544 (mmtp) REVERT: D 47 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7568 (tt0) REVERT: D 60 ASN cc_start: 0.8429 (t0) cc_final: 0.7990 (t0) REVERT: D 61 GLN cc_start: 0.8300 (tp40) cc_final: 0.8080 (tp40) REVERT: D 117 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7905 (ttpt) REVERT: E 34 GLU cc_start: 0.7616 (tp30) cc_final: 0.7326 (tp30) REVERT: E 155 MET cc_start: 0.8012 (mtm) cc_final: 0.7799 (ptp) REVERT: E 164 LYS cc_start: 0.8374 (mmtt) cc_final: 0.7959 (ttmm) REVERT: E 256 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7857 (tmm) REVERT: F 41 THR cc_start: 0.8462 (m) cc_final: 0.8174 (m) REVERT: F 115 MET cc_start: 0.7343 (tpt) cc_final: 0.6821 (tpt) REVERT: F 137 CYS cc_start: 0.7611 (OUTLIER) cc_final: 0.7267 (m) REVERT: F 143 LYS cc_start: 0.8262 (tptt) cc_final: 0.7510 (tptm) REVERT: F 161 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7143 (ptmt) outliers start: 31 outliers final: 17 residues processed: 213 average time/residue: 0.1205 time to fit residues: 36.9486 Evaluate side-chains 216 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 189 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 186 TYR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain E residue 242 PHE Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 137 CYS Chi-restraints excluded: chain F residue 161 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 106 optimal weight: 0.0570 chunk 83 optimal weight: 4.9990 chunk 141 optimal weight: 10.0000 chunk 138 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 160 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 HIS A 239 ASN B 142 HIS B 159 HIS ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN E 37 ASN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.160509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.138809 restraints weight = 19751.195| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.63 r_work: 0.3633 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 12938 Z= 0.266 Angle : 0.752 14.799 17552 Z= 0.380 Chirality : 0.048 0.520 1984 Planarity : 0.004 0.041 2315 Dihedral : 5.527 36.342 2117 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.69 % Allowed : 16.94 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.93 (0.21), residues: 1438 helix: 0.97 (0.28), residues: 323 sheet: -0.69 (0.33), residues: 243 loop : -1.24 (0.19), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 25 TYR 0.034 0.003 TYR A 159 PHE 0.023 0.002 PHE A 88 TRP 0.019 0.002 TRP C 171 HIS 0.007 0.002 HIS B 159 Details of bonding type rmsd covalent geometry : bond 0.00608 (12909) covalent geometry : angle 0.72446 (17480) SS BOND : bond 0.00973 ( 15) SS BOND : angle 2.30644 ( 30) hydrogen bonds : bond 0.04669 ( 521) hydrogen bonds : angle 5.68485 ( 1407) link_BETA1-3 : bond 0.00326 ( 1) link_BETA1-3 : angle 6.00323 ( 3) link_BETA1-4 : bond 0.00131 ( 2) link_BETA1-4 : angle 2.43300 ( 6) link_NAG-ASN : bond 0.00697 ( 11) link_NAG-ASN : angle 3.66680 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2946.65 seconds wall clock time: 51 minutes 25.63 seconds (3085.63 seconds total)