Starting phenix.real_space_refine on Wed Jul 30 19:11:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ut8_42533/07_2025/8ut8_42533.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ut8_42533/07_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_42533/07_2025/8ut8_42533.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ut8_42533/07_2025/8ut8_42533.map" model { file = "/net/cci-nas-00/data/ceres_data/8ut8_42533/07_2025/8ut8_42533.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ut8_42533/07_2025/8ut8_42533.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 9.18, per 1000 atoms: 0.72 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: 3.05 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.85 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: 4.25 Time building geometry restraints manager: 3.64 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: 6.480 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: 0.700 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 33.260 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.080 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:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.650 ------------------------------------------------------------------------------- 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 : 3.28 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (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 TRP 0.029 0.003 TRP D 21 HIS 0.012 0.003 HIS A 7 PHE 0.040 0.004 PHE E 238 TYR 0.026 0.003 TYR C 200 ARG 0.013 0.001 ARG C 121 Details of bonding type rmsd link_NAG-ASN : bond 0.00207 ( 11) link_NAG-ASN : angle 1.99294 ( 33) link_BETA1-4 : bond 0.00113 ( 2) link_BETA1-4 : angle 2.14162 ( 6) hydrogen bonds : bond 0.15220 ( 521) hydrogen bonds : angle 7.28636 ( 1407) SS BOND : bond 0.00756 ( 15) SS BOND : angle 2.79595 ( 30) link_BETA1-3 : bond 0.00753 ( 1) link_BETA1-3 : angle 7.95630 ( 3) covalent geometry : bond 0.00651 (12909) covalent geometry : angle 1.14744 (17480) *********************** 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 : 1.436 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: 0.7639 (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: 0.2834 time to fit residues: 104.2393 Evaluate side-chains 216 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 83 optimal weight: 0.0870 chunk 66 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 overall best weight: 1.0166 ------------------------------------------------------------------------------- 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** D 106 HIS F 26 HIS F 60 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.173915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.152408 restraints weight = 19273.112| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 2.65 r_work: 0.3806 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.1509 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= 0.157 Angle : 0.665 10.227 17552 Z= 0.350 Chirality : 0.042 0.224 1984 Planarity : 0.004 0.050 2315 Dihedral : 5.279 45.024 2117 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.63 % Allowed : 11.16 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.20), residues: 1438 helix: 1.46 (0.26), residues: 319 sheet: 0.65 (0.30), residues: 287 loop : -0.76 (0.19), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 171 HIS 0.006 0.001 HIS C 8 PHE 0.026 0.002 PHE E 242 TYR 0.017 0.002 TYR D 157 ARG 0.007 0.001 ARG B 127 Details of bonding type rmsd link_NAG-ASN : bond 0.00247 ( 11) link_NAG-ASN : angle 1.94655 ( 33) link_BETA1-4 : bond 0.00243 ( 2) link_BETA1-4 : angle 1.99523 ( 6) hydrogen bonds : bond 0.04905 ( 521) hydrogen bonds : angle 5.79064 ( 1407) SS BOND : bond 0.00403 ( 15) SS BOND : angle 1.69259 ( 30) link_BETA1-3 : bond 0.00321 ( 1) link_BETA1-3 : angle 6.40693 ( 3) covalent geometry : bond 0.00339 (12909) covalent geometry : angle 0.65044 (17480) *********************** 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 245 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 225 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASN cc_start: 0.7367 (t0) cc_final: 0.7134 (t0) REVERT: B 53 ASN cc_start: 0.7915 (OUTLIER) cc_final: 0.7270 (m-40) REVERT: B 54 ARG cc_start: 0.7833 (ttp80) cc_final: 0.7252 (tmm160) REVERT: B 115 MET cc_start: 0.8419 (tpt) cc_final: 0.7781 (tpt) REVERT: D 37 ASP cc_start: 0.7314 (t0) cc_final: 0.7112 (t0) REVERT: D 60 ASN cc_start: 0.7998 (t0) cc_final: 0.7603 (t0) REVERT: D 117 LYS cc_start: 0.7967 (ptpp) cc_final: 0.7651 (ptpp) REVERT: E 109 ASP cc_start: 0.7866 (t0) cc_final: 0.7599 (t0) REVERT: F 161 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7315 (ptmt) outliers start: 20 outliers final: 13 residues processed: 232 average time/residue: 0.3225 time to fit residues: 105.0785 Evaluate side-chains 204 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 189 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 7 HIS Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 126 THR 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 3 ILE 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 130 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 108 optimal weight: 8.9990 chunk 152 optimal weight: 10.0000 chunk 121 optimal weight: 0.3980 chunk 74 optimal weight: 0.9980 chunk 76 optimal weight: 0.2980 chunk 128 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 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 = 0.4104 r_free = 0.4104 target = 0.171868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.150126 restraints weight = 19448.687| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.64 r_work: 0.3777 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12938 Z= 0.147 Angle : 0.601 9.678 17552 Z= 0.313 Chirality : 0.042 0.218 1984 Planarity : 0.003 0.047 2315 Dihedral : 4.916 34.315 2117 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.85 % Allowed : 12.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.20), residues: 1438 helix: 1.37 (0.27), residues: 320 sheet: 0.55 (0.31), residues: 285 loop : -0.85 (0.19), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 171 HIS 0.013 0.001 HIS C 8 PHE 0.015 0.002 PHE E 92 TYR 0.015 0.002 TYR D 157 ARG 0.005 0.001 ARG B 127 Details of bonding type rmsd link_NAG-ASN : bond 0.00406 ( 11) link_NAG-ASN : angle 1.90395 ( 33) link_BETA1-4 : bond 0.00241 ( 2) link_BETA1-4 : angle 1.94226 ( 6) hydrogen bonds : bond 0.04449 ( 521) hydrogen bonds : angle 5.33728 ( 1407) SS BOND : bond 0.00404 ( 15) SS BOND : angle 1.55458 ( 30) link_BETA1-3 : bond 0.00382 ( 1) link_BETA1-3 : angle 6.07333 ( 3) covalent geometry : bond 0.00319 (12909) covalent geometry : angle 0.58688 (17480) *********************** 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 269 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 234 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7725 (tp30) cc_final: 0.7480 (mm-30) REVERT: A 22 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7600 (mpt180) REVERT: A 28 ASN cc_start: 0.7482 (t0) cc_final: 0.7243 (t0) REVERT: A 213 GLN cc_start: 0.7276 (OUTLIER) cc_final: 0.6848 (mm-40) REVERT: A 247 ARG cc_start: 0.8039 (mtt180) cc_final: 0.7815 (mtt180) REVERT: B 120 GLU cc_start: 0.7584 (pt0) cc_final: 0.6964 (mm-30) REVERT: B 149 MET cc_start: 0.7224 (mmt) cc_final: 0.6855 (mmt) REVERT: C 220 ARG cc_start: 0.5499 (mmt-90) cc_final: 0.4708 (ttm-80) REVERT: C 295 LYS cc_start: 0.8749 (mttt) cc_final: 0.8524 (mmtp) REVERT: D 60 ASN cc_start: 0.8168 (t0) cc_final: 0.7563 (t0) REVERT: D 117 LYS cc_start: 0.7961 (ptpp) cc_final: 0.7592 (ptpp) REVERT: E 34 GLU cc_start: 0.7511 (tp30) cc_final: 0.7147 (tp30) REVERT: F 19 ASP cc_start: 0.7334 (OUTLIER) cc_final: 0.6931 (p0) REVERT: F 161 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7181 (ptmt) outliers start: 35 outliers final: 19 residues processed: 252 average time/residue: 0.2675 time to fit residues: 96.1649 Evaluate side-chains 216 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 193 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 155 MET 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 148 CYS Chi-restraints excluded: chain B residue 159 HIS Chi-restraints excluded: chain C residue 7 HIS Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 275 SER 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 3 ILE Chi-restraints excluded: chain E residue 232 ASP Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 49 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 10 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 145 optimal weight: 9.9990 chunk 140 optimal weight: 8.9990 chunk 119 optimal weight: 0.9990 chunk 49 optimal weight: 0.0060 chunk 45 optimal weight: 0.0980 chunk 96 optimal weight: 6.9990 chunk 154 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- 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** B 159 HIS ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN D 76 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 = 0.4107 r_free = 0.4107 target = 0.172228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.150603 restraints weight = 19333.142| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 2.64 r_work: 0.3777 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12938 Z= 0.129 Angle : 0.604 18.215 17552 Z= 0.305 Chirality : 0.045 0.817 1984 Planarity : 0.003 0.045 2315 Dihedral : 5.088 41.439 2117 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.20 % Allowed : 13.93 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.21), residues: 1438 helix: 1.48 (0.27), residues: 317 sheet: 0.43 (0.31), residues: 287 loop : -0.82 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 171 HIS 0.009 0.001 HIS C 8 PHE 0.014 0.001 PHE E 238 TYR 0.017 0.001 TYR A 274 ARG 0.006 0.000 ARG A 131 Details of bonding type rmsd link_NAG-ASN : bond 0.00724 ( 11) link_NAG-ASN : angle 4.12787 ( 33) link_BETA1-4 : bond 0.00468 ( 2) link_BETA1-4 : angle 1.87495 ( 6) hydrogen bonds : bond 0.04270 ( 521) hydrogen bonds : angle 5.17650 ( 1407) SS BOND : bond 0.00779 ( 15) SS BOND : angle 1.31017 ( 30) link_BETA1-3 : bond 0.00327 ( 1) link_BETA1-3 : angle 5.95191 ( 3) covalent geometry : bond 0.00280 (12909) covalent geometry : angle 0.56932 (17480) *********************** 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 237 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 210 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7791 (tp30) cc_final: 0.7556 (mm-30) REVERT: A 22 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7607 (mpt180) REVERT: A 28 ASN cc_start: 0.7486 (t0) cc_final: 0.7240 (t0) REVERT: A 139 GLU cc_start: 0.7385 (mm-30) cc_final: 0.6970 (mm-30) REVERT: A 213 GLN cc_start: 0.7195 (OUTLIER) cc_final: 0.6334 (mm110) REVERT: B 62 GLN cc_start: 0.8789 (tt0) cc_final: 0.8559 (tt0) REVERT: B 116 ASP cc_start: 0.7739 (m-30) cc_final: 0.7268 (m-30) REVERT: B 120 GLU cc_start: 0.7589 (pt0) cc_final: 0.6919 (mm-30) REVERT: B 149 MET cc_start: 0.7230 (mmt) cc_final: 0.6835 (mmt) REVERT: C 220 ARG cc_start: 0.5476 (mmt-90) cc_final: 0.4609 (ttm170) REVERT: C 295 LYS cc_start: 0.8728 (mttt) cc_final: 0.8378 (mppt) REVERT: D 60 ASN cc_start: 0.8185 (t0) cc_final: 0.7622 (t0) REVERT: D 85 ARG cc_start: 0.8004 (ttm-80) cc_final: 0.7783 (ttp80) REVERT: E 34 GLU cc_start: 0.7527 (tp30) cc_final: 0.7167 (tp30) REVERT: F 137 CYS cc_start: 0.7475 (OUTLIER) cc_final: 0.7189 (m) REVERT: F 161 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7215 (ptmt) outliers start: 27 outliers final: 16 residues processed: 225 average time/residue: 0.2657 time to fit residues: 84.3794 Evaluate side-chains 217 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 197 time to evaluate : 1.293 ------------------------------------------------------------------------------- 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 201 GLN 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 C residue 126 THR Chi-restraints excluded: chain C residue 275 SER 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 3 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 17 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 124 optimal weight: 0.2980 chunk 136 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 HIS A 239 ASN B 27 GLN B 125 GLN C 259 GLN ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4123 r_free = 0.4123 target = 0.173793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.152253 restraints weight = 19371.027| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.68 r_work: 0.3773 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12938 Z= 0.116 Angle : 0.572 14.832 17552 Z= 0.291 Chirality : 0.043 0.601 1984 Planarity : 0.003 0.049 2315 Dihedral : 4.768 32.222 2117 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.69 % Allowed : 13.84 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.21), residues: 1438 helix: 1.58 (0.27), residues: 317 sheet: 0.32 (0.31), residues: 287 loop : -0.77 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 171 HIS 0.009 0.001 HIS C 8 PHE 0.014 0.001 PHE D 24 TYR 0.016 0.001 TYR A 274 ARG 0.008 0.000 ARG E 121 Details of bonding type rmsd link_NAG-ASN : bond 0.00607 ( 11) link_NAG-ASN : angle 3.45836 ( 33) link_BETA1-4 : bond 0.00280 ( 2) link_BETA1-4 : angle 1.84856 ( 6) hydrogen bonds : bond 0.04134 ( 521) hydrogen bonds : angle 5.02276 ( 1407) SS BOND : bond 0.00364 ( 15) SS BOND : angle 1.32008 ( 30) link_BETA1-3 : bond 0.00385 ( 1) link_BETA1-3 : angle 5.74540 ( 3) covalent geometry : bond 0.00249 (12909) covalent geometry : angle 0.54408 (17480) *********************** 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 262 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 229 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7758 (tp30) cc_final: 0.7534 (mm-30) REVERT: A 22 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7545 (mpt180) REVERT: A 28 ASN cc_start: 0.7490 (t0) cc_final: 0.7248 (t0) REVERT: A 139 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7313 (mm-30) REVERT: B 116 ASP cc_start: 0.7803 (m-30) cc_final: 0.7296 (m-30) REVERT: B 120 GLU cc_start: 0.7537 (pt0) cc_final: 0.6920 (mm-30) REVERT: B 149 MET cc_start: 0.7280 (mmt) cc_final: 0.6776 (mmt) REVERT: C 25 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7691 (tm-30) REVERT: C 220 ARG cc_start: 0.5469 (mmt-90) cc_final: 0.4607 (ttm170) REVERT: C 295 LYS cc_start: 0.8721 (mttt) cc_final: 0.8391 (mppt) REVERT: D 60 ASN cc_start: 0.8247 (t0) cc_final: 0.7786 (t0) REVERT: D 117 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7654 (ptpp) REVERT: E 34 GLU cc_start: 0.7565 (tp30) cc_final: 0.7213 (tp30) REVERT: F 19 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.7055 (p0) REVERT: F 115 MET cc_start: 0.7201 (tpt) cc_final: 0.6400 (tpt) REVERT: F 137 CYS cc_start: 0.7516 (OUTLIER) cc_final: 0.7219 (m) REVERT: F 161 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7237 (ptmt) outliers start: 33 outliers final: 24 residues processed: 246 average time/residue: 0.2830 time to fit residues: 97.2555 Evaluate side-chains 228 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 1.508 ------------------------------------------------------------------------------- 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 155 MET Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 201 GLN 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 37 ASP 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 C residue 7 HIS Chi-restraints excluded: chain C residue 25 GLU 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 275 SER 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 3 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 115 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 157 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 119 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 142 optimal weight: 20.0000 chunk 83 optimal weight: 0.7980 chunk 135 optimal weight: 4.9990 chunk 125 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** B 27 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.173104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.151820 restraints weight = 19446.795| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 2.66 r_work: 0.3778 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12938 Z= 0.121 Angle : 0.559 14.257 17552 Z= 0.286 Chirality : 0.042 0.534 1984 Planarity : 0.003 0.045 2315 Dihedral : 4.587 31.542 2117 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.34 % Allowed : 14.58 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.21), residues: 1438 helix: 1.53 (0.27), residues: 320 sheet: 0.23 (0.31), residues: 287 loop : -0.77 (0.19), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 171 HIS 0.010 0.001 HIS D 26 PHE 0.015 0.001 PHE C 69 TYR 0.014 0.001 TYR A 274 ARG 0.007 0.001 ARG A 35 Details of bonding type rmsd link_NAG-ASN : bond 0.00632 ( 11) link_NAG-ASN : angle 3.29330 ( 33) link_BETA1-4 : bond 0.00306 ( 2) link_BETA1-4 : angle 1.83225 ( 6) hydrogen bonds : bond 0.04051 ( 521) hydrogen bonds : angle 4.94889 ( 1407) SS BOND : bond 0.00344 ( 15) SS BOND : angle 1.31484 ( 30) link_BETA1-3 : bond 0.00367 ( 1) link_BETA1-3 : angle 5.61277 ( 3) covalent geometry : bond 0.00263 (12909) covalent geometry : angle 0.53305 (17480) *********************** 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 254 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 213 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7494 (mpt180) REVERT: A 28 ASN cc_start: 0.7442 (t0) cc_final: 0.7228 (t0) REVERT: A 247 ARG cc_start: 0.7915 (mtt180) cc_final: 0.7535 (ptt180) REVERT: B 149 MET cc_start: 0.7050 (mmt) cc_final: 0.6807 (mmt) REVERT: C 25 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7676 (tm-30) REVERT: C 220 ARG cc_start: 0.5495 (mmt-90) cc_final: 0.4696 (ttm170) REVERT: C 227 MET cc_start: 0.7492 (tpt) cc_final: 0.7215 (tpt) REVERT: C 295 LYS cc_start: 0.8727 (mttt) cc_final: 0.8394 (mppt) REVERT: D 60 ASN cc_start: 0.8321 (t0) cc_final: 0.7872 (t0) REVERT: D 117 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7700 (ptpp) REVERT: E 34 GLU cc_start: 0.7669 (tp30) cc_final: 0.7328 (tp30) REVERT: E 164 LYS cc_start: 0.8284 (mmtt) cc_final: 0.7921 (ttmm) REVERT: F 19 ASP cc_start: 0.7366 (OUTLIER) cc_final: 0.7023 (p0) REVERT: F 115 MET cc_start: 0.7256 (tpt) cc_final: 0.6359 (tpt) REVERT: F 137 CYS cc_start: 0.7675 (OUTLIER) cc_final: 0.7322 (m) REVERT: F 161 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7215 (ptmt) outliers start: 41 outliers final: 30 residues processed: 234 average time/residue: 0.2602 time to fit residues: 87.3433 Evaluate side-chains 231 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 195 time to evaluate : 1.484 ------------------------------------------------------------------------------- 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 93 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 201 GLN 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 37 ASP 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 25 GLU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 117 TYR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 275 SER 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 129 ASN Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain E residue 3 ILE 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 49 THR 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 27 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 148 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 120 optimal weight: 0.0370 chunk 126 optimal weight: 6.9990 overall best weight: 0.9462 ------------------------------------------------------------------------------- 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 224 HIS B 27 GLN C 259 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.171655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.149936 restraints weight = 19555.462| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.67 r_work: 0.3770 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.3046 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= 0.131 Angle : 0.558 14.073 17552 Z= 0.288 Chirality : 0.042 0.499 1984 Planarity : 0.003 0.044 2315 Dihedral : 4.545 31.524 2117 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.34 % Allowed : 14.66 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.21), residues: 1438 helix: 1.60 (0.27), residues: 320 sheet: 0.27 (0.32), residues: 271 loop : -0.77 (0.19), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 171 HIS 0.008 0.001 HIS C 8 PHE 0.016 0.001 PHE C 69 TYR 0.016 0.001 TYR E 159 ARG 0.005 0.000 ARG A 35 Details of bonding type rmsd link_NAG-ASN : bond 0.00623 ( 11) link_NAG-ASN : angle 3.23363 ( 33) link_BETA1-4 : bond 0.00229 ( 2) link_BETA1-4 : angle 1.87683 ( 6) hydrogen bonds : bond 0.04035 ( 521) hydrogen bonds : angle 4.88517 ( 1407) SS BOND : bond 0.00374 ( 15) SS BOND : angle 1.41823 ( 30) link_BETA1-3 : bond 0.00292 ( 1) link_BETA1-3 : angle 5.59181 ( 3) covalent geometry : bond 0.00292 (12909) covalent geometry : angle 0.53216 (17480) *********************** 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 246 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 205 time to evaluate : 1.288 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: 0.8050 (tpp-160) cc_final: 0.7494 (mpt180) REVERT: A 28 ASN cc_start: 0.7466 (t0) cc_final: 0.7237 (t0) REVERT: A 139 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7546 (mm-30) REVERT: B 116 ASP cc_start: 0.7775 (m-30) cc_final: 0.7545 (m-30) REVERT: B 149 MET cc_start: 0.7039 (mmt) cc_final: 0.6750 (mmt) REVERT: C 25 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7704 (tm-30) REVERT: C 227 MET cc_start: 0.7489 (tpt) cc_final: 0.7253 (tpt) REVERT: C 295 LYS cc_start: 0.8750 (mttt) cc_final: 0.8420 (mppt) REVERT: D 60 ASN cc_start: 0.8319 (t0) cc_final: 0.7876 (t0) REVERT: D 117 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7712 (ptpp) REVERT: E 155 MET cc_start: 0.7863 (mtm) cc_final: 0.7581 (ptp) REVERT: E 164 LYS cc_start: 0.8255 (mmtt) cc_final: 0.7909 (ttmm) REVERT: F 19 ASP cc_start: 0.7367 (OUTLIER) cc_final: 0.7019 (p0) REVERT: F 115 MET cc_start: 0.7239 (tpt) cc_final: 0.6418 (tpt) REVERT: F 161 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7209 (ptmt) outliers start: 41 outliers final: 32 residues processed: 226 average time/residue: 0.2792 time to fit residues: 91.7215 Evaluate side-chains 223 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 187 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 37 ASP 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 25 GLU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 117 TYR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 275 SER 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 129 ASN Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain E residue 3 ILE 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 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 84 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 GLN ** 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 = 0.4075 r_free = 0.4075 target = 0.168193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.146619 restraints weight = 19580.449| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 2.64 r_work: 0.3732 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12938 Z= 0.180 Angle : 0.611 14.092 17552 Z= 0.314 Chirality : 0.044 0.490 1984 Planarity : 0.003 0.045 2315 Dihedral : 4.764 33.884 2117 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.01 % Allowed : 15.96 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.21), residues: 1438 helix: 1.44 (0.28), residues: 320 sheet: 0.17 (0.32), residues: 265 loop : -0.86 (0.19), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 171 HIS 0.006 0.001 HIS C 8 PHE 0.017 0.002 PHE E 238 TYR 0.018 0.002 TYR D 22 ARG 0.006 0.001 ARG A 35 Details of bonding type rmsd link_NAG-ASN : bond 0.00631 ( 11) link_NAG-ASN : angle 3.27182 ( 33) link_BETA1-4 : bond 0.00168 ( 2) link_BETA1-4 : angle 2.00932 ( 6) hydrogen bonds : bond 0.04187 ( 521) hydrogen bonds : angle 5.11090 ( 1407) SS BOND : bond 0.00560 ( 15) SS BOND : angle 1.66998 ( 30) link_BETA1-3 : bond 0.00104 ( 1) link_BETA1-3 : angle 5.80605 ( 3) covalent geometry : bond 0.00408 (12909) covalent geometry : angle 0.58562 (17480) *********************** 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 233 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 196 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7215 (mpp-170) REVERT: A 28 ASN cc_start: 0.7575 (t0) cc_final: 0.7365 (t0) REVERT: A 139 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7855 (mm-30) REVERT: A 247 ARG cc_start: 0.7884 (ptt180) cc_final: 0.7567 (ptt180) REVERT: B 116 ASP cc_start: 0.7839 (m-30) cc_final: 0.7246 (m-30) REVERT: B 120 GLU cc_start: 0.7449 (pt0) cc_final: 0.7000 (mm-30) REVERT: B 149 MET cc_start: 0.7091 (mmt) cc_final: 0.6772 (mmt) REVERT: C 25 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7715 (tm-30) REVERT: C 140 MET cc_start: 0.7179 (OUTLIER) cc_final: 0.5984 (mpp) REVERT: C 295 LYS cc_start: 0.8747 (mttt) cc_final: 0.8522 (mmtp) REVERT: D 60 ASN cc_start: 0.8364 (t0) cc_final: 0.7960 (t0) REVERT: D 61 GLN cc_start: 0.7815 (tp-100) cc_final: 0.6899 (tp40) REVERT: D 97 GLU cc_start: 0.8019 (tt0) cc_final: 0.7726 (mt-10) REVERT: E 155 MET cc_start: 0.7855 (mtm) cc_final: 0.7609 (ptp) REVERT: E 164 LYS cc_start: 0.8311 (mmtt) cc_final: 0.7952 (ttmm) REVERT: F 19 ASP cc_start: 0.7462 (OUTLIER) cc_final: 0.7085 (p0) REVERT: F 143 LYS cc_start: 0.8118 (tptt) cc_final: 0.7473 (tptm) REVERT: F 161 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7198 (ptmt) outliers start: 37 outliers final: 29 residues processed: 211 average time/residue: 0.2561 time to fit residues: 76.8162 Evaluate side-chains 225 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 191 time to evaluate : 1.280 ------------------------------------------------------------------------------- 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 155 MET Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 37 ASP 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 25 GLU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 117 TYR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 303 ARG 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 129 ASN 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 49 THR 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 78 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 159 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 0.2980 chunk 104 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.167109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.145524 restraints weight = 19536.792| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.65 r_work: 0.3708 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12938 Z= 0.187 Angle : 0.634 13.965 17552 Z= 0.324 Chirality : 0.044 0.479 1984 Planarity : 0.004 0.044 2315 Dihedral : 4.942 34.752 2117 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.18 % Allowed : 15.72 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.21), residues: 1438 helix: 1.36 (0.28), residues: 320 sheet: -0.14 (0.32), residues: 269 loop : -0.92 (0.20), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 171 HIS 0.007 0.001 HIS C 8 PHE 0.023 0.002 PHE C 69 TYR 0.019 0.002 TYR D 22 ARG 0.005 0.001 ARG A 303 Details of bonding type rmsd link_NAG-ASN : bond 0.00639 ( 11) link_NAG-ASN : angle 3.29647 ( 33) link_BETA1-4 : bond 0.00117 ( 2) link_BETA1-4 : angle 1.99667 ( 6) hydrogen bonds : bond 0.04227 ( 521) hydrogen bonds : angle 5.26702 ( 1407) SS BOND : bond 0.00574 ( 15) SS BOND : angle 1.71352 ( 30) link_BETA1-3 : bond 0.00223 ( 1) link_BETA1-3 : angle 5.76352 ( 3) covalent geometry : bond 0.00425 (12909) covalent geometry : angle 0.60869 (17480) *********************** 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: 39 poor density : 197 time to evaluate : 1.316 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: 0.8140 (OUTLIER) cc_final: 0.7223 (mpp-170) REVERT: A 111 GLU cc_start: 0.7428 (mt-10) cc_final: 0.7221 (mt-10) REVERT: B 26 HIS cc_start: 0.6066 (m-70) cc_final: 0.5682 (m-70) REVERT: B 116 ASP cc_start: 0.7889 (m-30) cc_final: 0.7260 (m-30) REVERT: B 120 GLU cc_start: 0.7436 (pt0) cc_final: 0.6940 (mm-30) REVERT: B 149 MET cc_start: 0.7088 (mmt) cc_final: 0.6796 (mmt) REVERT: C 25 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7687 (tm-30) REVERT: C 140 MET cc_start: 0.7205 (OUTLIER) cc_final: 0.6059 (mpp) REVERT: C 160 LYS cc_start: 0.7307 (tptt) cc_final: 0.7074 (tptp) REVERT: C 295 LYS cc_start: 0.8761 (mttt) cc_final: 0.8532 (mmtp) REVERT: D 60 ASN cc_start: 0.8430 (t0) cc_final: 0.8016 (t0) REVERT: D 61 GLN cc_start: 0.7788 (tp-100) cc_final: 0.6953 (tp40) REVERT: D 97 GLU cc_start: 0.8066 (tt0) cc_final: 0.7776 (mt-10) REVERT: D 149 MET cc_start: 0.5877 (mmt) cc_final: 0.5219 (mmm) REVERT: E 155 MET cc_start: 0.7872 (mtm) cc_final: 0.7619 (ptp) REVERT: E 164 LYS cc_start: 0.8334 (mmtt) cc_final: 0.7969 (ttmm) REVERT: E 295 LYS cc_start: 0.8612 (mtmm) cc_final: 0.8377 (mttp) REVERT: F 19 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.7139 (p0) REVERT: F 143 LYS cc_start: 0.8173 (tptt) cc_final: 0.7487 (tptm) REVERT: F 161 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7168 (ptmt) outliers start: 39 outliers final: 32 residues processed: 214 average time/residue: 0.2600 time to fit residues: 78.8909 Evaluate side-chains 225 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 188 time to evaluate : 1.383 ------------------------------------------------------------------------------- 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 155 MET Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 37 ASP 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 86 ASP Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 117 TYR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 275 SER 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 129 ASN Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 49 THR 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 133 optimal weight: 0.0970 chunk 49 optimal weight: 0.9980 chunk 37 optimal weight: 0.0000 chunk 130 optimal weight: 0.0570 chunk 79 optimal weight: 0.0170 chunk 41 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 159 optimal weight: 10.0000 overall best weight: 0.2138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN B 27 GLN B 62 GLN ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 287 ASN ** F 28 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 = 0.4110 r_free = 0.4110 target = 0.171984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.150797 restraints weight = 19411.835| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 2.65 r_work: 0.3784 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12938 Z= 0.108 Angle : 0.575 14.608 17552 Z= 0.293 Chirality : 0.043 0.577 1984 Planarity : 0.003 0.044 2315 Dihedral : 4.622 29.523 2117 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.12 % Allowed : 17.26 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.21), residues: 1438 helix: 1.59 (0.28), residues: 320 sheet: -0.04 (0.32), residues: 275 loop : -0.81 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 171 HIS 0.008 0.001 HIS C 8 PHE 0.016 0.001 PHE C 69 TYR 0.015 0.001 TYR A 274 ARG 0.007 0.001 ARG C 247 Details of bonding type rmsd link_NAG-ASN : bond 0.00880 ( 11) link_NAG-ASN : angle 3.49474 ( 33) link_BETA1-4 : bond 0.00389 ( 2) link_BETA1-4 : angle 1.64873 ( 6) hydrogen bonds : bond 0.04038 ( 521) hydrogen bonds : angle 4.96532 ( 1407) SS BOND : bond 0.00296 ( 15) SS BOND : angle 1.20750 ( 30) link_BETA1-3 : bond 0.00476 ( 1) link_BETA1-3 : angle 5.20771 ( 3) covalent geometry : bond 0.00229 (12909) covalent geometry : angle 0.54873 (17480) ********************** 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 222 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 196 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7522 (mpt180) REVERT: B 26 HIS cc_start: 0.6060 (m-70) cc_final: 0.5730 (m-70) REVERT: B 116 ASP cc_start: 0.7799 (m-30) cc_final: 0.7534 (m-30) REVERT: C 53 GLN cc_start: 0.7917 (mp10) cc_final: 0.7689 (mm-40) REVERT: C 140 MET cc_start: 0.7201 (OUTLIER) cc_final: 0.6108 (mpp) REVERT: C 295 LYS cc_start: 0.8670 (mttt) cc_final: 0.8340 (mppt) REVERT: C 303 ARG cc_start: 0.8410 (mtp-110) cc_final: 0.7834 (ttp-110) REVERT: D 60 ASN cc_start: 0.8396 (t0) cc_final: 0.8025 (t0) REVERT: D 72 GLU cc_start: 0.5919 (pm20) cc_final: 0.5336 (pm20) REVERT: D 117 LYS cc_start: 0.8036 (ptpt) cc_final: 0.7724 (ptpp) REVERT: D 149 MET cc_start: 0.6053 (mmt) cc_final: 0.5546 (mmm) REVERT: E 155 MET cc_start: 0.7859 (mtm) cc_final: 0.7582 (ptp) REVERT: E 164 LYS cc_start: 0.8288 (mmtt) cc_final: 0.7928 (ttmm) REVERT: F 19 ASP cc_start: 0.7410 (OUTLIER) cc_final: 0.7057 (p0) REVERT: F 143 LYS cc_start: 0.8085 (tptt) cc_final: 0.7419 (tptm) REVERT: F 161 LYS cc_start: 0.7847 (ptmm) cc_final: 0.7181 (ptmt) outliers start: 26 outliers final: 20 residues processed: 206 average time/residue: 0.3611 time to fit residues: 109.9585 Evaluate side-chains 204 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 181 time to evaluate : 1.590 ------------------------------------------------------------------------------- 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 155 MET Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 37 ASP 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 148 CYS Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 117 TYR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain F residue 19 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 143 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 159 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 151 optimal weight: 8.9990 chunk 84 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN B 27 GLN ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** 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 = 0.4096 r_free = 0.4096 target = 0.170074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.148672 restraints weight = 19510.582| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.64 r_work: 0.3753 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12938 Z= 0.141 Angle : 0.592 14.209 17552 Z= 0.301 Chirality : 0.044 0.516 1984 Planarity : 0.003 0.044 2315 Dihedral : 4.625 29.338 2117 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.04 % Allowed : 17.18 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.21), residues: 1438 helix: 1.59 (0.28), residues: 320 sheet: -0.01 (0.32), residues: 259 loop : -0.84 (0.20), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 171 HIS 0.008 0.001 HIS A 7 PHE 0.018 0.002 PHE C 69 TYR 0.014 0.002 TYR D 22 ARG 0.007 0.001 ARG F 25 Details of bonding type rmsd link_NAG-ASN : bond 0.00697 ( 11) link_NAG-ASN : angle 3.54822 ( 33) link_BETA1-4 : bond 0.00176 ( 2) link_BETA1-4 : angle 1.87937 ( 6) hydrogen bonds : bond 0.04056 ( 521) hydrogen bonds : angle 4.96285 ( 1407) SS BOND : bond 0.00439 ( 15) SS BOND : angle 1.44965 ( 30) link_BETA1-3 : bond 0.00177 ( 1) link_BETA1-3 : angle 5.26523 ( 3) covalent geometry : bond 0.00317 (12909) covalent geometry : angle 0.56429 (17480) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6353.21 seconds wall clock time: 112 minutes 55.59 seconds (6775.59 seconds total)