Starting phenix.real_space_refine on Mon Aug 5 06:31:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut8_42533/08_2024/8ut8_42533.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut8_42533/08_2024/8ut8_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut8_42533/08_2024/8ut8_42533.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut8_42533/08_2024/8ut8_42533.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut8_42533/08_2024/8ut8_42533.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut8_42533/08_2024/8ut8_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 Residue "A GLU 21": "OE1" <-> "OE2" Residue "C GLU 21": "OE1" <-> "OE2" Residue "C PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 111": "OE1" <-> "OE2" Residue "D GLU 103": "OE1" <-> "OE2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "E GLU 71": "OE1" <-> "OE2" Residue "E PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 57": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 8.48, per 1000 atoms: 0.67 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 - 3.50 Amino acid : False - 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: 4.39 Conformation dependent library (CDL) restraints added in 1.9 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: 1.80 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: 3.94 Time building geometry restraints manager: 4.83 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: 95.76 - 103.41: 57 103.41 - 111.06: 4653 111.06 - 118.71: 5611 118.71 - 126.36: 7004 126.36 - 134.00: 155 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: 11.010 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: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 37.030 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.180 ------------------------------------------------------------------------------- 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 12909 Z= 0.410 Angle : 1.147 12.120 17480 Z= 0.625 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 1.370 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: 0.2725 time to fit residues: 99.7636 Evaluate side-chains 216 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 1.303 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 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 12909 Z= 0.225 Angle : 0.650 7.554 17480 Z= 0.347 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 *********************** 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 fitting. rotamer outliers: 20 poor density : 225 time to evaluate : 1.393 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: 0.7543 (t0) cc_final: 0.7288 (t0) REVERT: A 201 GLN cc_start: 0.8216 (tp40) cc_final: 0.7993 (mt0) REVERT: B 53 ASN cc_start: 0.7862 (OUTLIER) cc_final: 0.7255 (m-40) REVERT: B 54 ARG cc_start: 0.7902 (ttp80) cc_final: 0.7274 (tmm160) REVERT: B 115 MET cc_start: 0.8464 (tpt) cc_final: 0.7850 (tpt) REVERT: B 120 GLU cc_start: 0.7291 (mm-30) cc_final: 0.7024 (pt0) REVERT: C 155 MET cc_start: 0.6828 (ttm) cc_final: 0.6525 (ttm) REVERT: D 37 ASP cc_start: 0.7220 (t0) cc_final: 0.6995 (t0) REVERT: D 60 ASN cc_start: 0.7975 (t0) cc_final: 0.7583 (t0) REVERT: D 117 LYS cc_start: 0.7994 (ptpp) cc_final: 0.7663 (ptpp) REVERT: E 109 ASP cc_start: 0.7854 (t0) cc_final: 0.7560 (t0) REVERT: F 161 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7313 (ptmt) outliers start: 20 outliers final: 13 residues processed: 232 average time/residue: 0.2672 time to fit residues: 87.2278 Evaluate side-chains 205 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 190 time to evaluate : 1.328 ------------------------------------------------------------------------------- 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 82 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 123 optimal weight: 0.0470 chunk 100 optimal weight: 0.0670 chunk 40 optimal weight: 0.7980 chunk 148 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 chunk 132 optimal weight: 1.9990 chunk 147 optimal weight: 10.0000 chunk 50 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 HIS ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 ASN B 159 HIS B 169 ASN ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 GLN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12909 Z= 0.166 Angle : 0.564 7.433 17480 Z= 0.299 Chirality : 0.041 0.219 1984 Planarity : 0.003 0.047 2315 Dihedral : 4.882 33.922 2117 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.20 % Allowed : 12.70 % Favored : 85.10 % 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: 0.04 (0.20), residues: 1438 helix: 1.57 (0.27), residues: 316 sheet: 0.53 (0.31), residues: 292 loop : -0.78 (0.19), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 171 HIS 0.012 0.001 HIS C 8 PHE 0.015 0.002 PHE E 92 TYR 0.016 0.001 TYR B 119 ARG 0.004 0.000 ARG E 121 *********************** 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 261 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 234 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7657 (tp30) cc_final: 0.7390 (mm-30) REVERT: A 22 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7444 (mpt180) REVERT: A 28 ASN cc_start: 0.7559 (t0) cc_final: 0.7294 (t0) REVERT: A 213 GLN cc_start: 0.7193 (OUTLIER) cc_final: 0.6828 (mm-40) REVERT: A 247 ARG cc_start: 0.7947 (mtt180) cc_final: 0.7721 (mtt180) REVERT: B 120 GLU cc_start: 0.7289 (mm-30) cc_final: 0.7061 (pt0) REVERT: C 34 GLU cc_start: 0.7583 (tp30) cc_final: 0.7113 (tp30) REVERT: C 155 MET cc_start: 0.6814 (ttm) cc_final: 0.6542 (ttm) REVERT: C 295 LYS cc_start: 0.8718 (mttt) cc_final: 0.8457 (mmtp) REVERT: D 60 ASN cc_start: 0.8029 (t0) cc_final: 0.7652 (t0) REVERT: D 117 LYS cc_start: 0.7959 (ptpp) cc_final: 0.7592 (ptpp) REVERT: E 34 GLU cc_start: 0.7498 (tp30) cc_final: 0.7110 (tp30) REVERT: F 19 ASP cc_start: 0.7509 (OUTLIER) cc_final: 0.7088 (p0) REVERT: F 115 MET cc_start: 0.7362 (tpt) cc_final: 0.6571 (tpt) REVERT: F 161 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7230 (ptmt) outliers start: 27 outliers final: 10 residues processed: 248 average time/residue: 0.2609 time to fit residues: 91.0883 Evaluate side-chains 212 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 198 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain 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 126 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain F residue 19 ASP 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 146 optimal weight: 8.9990 chunk 111 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 148 optimal weight: 10.0000 chunk 157 optimal weight: 10.0000 chunk 77 optimal weight: 0.0010 chunk 141 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 overall best weight: 2.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 125 GLN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN D 61 GLN D 125 GLN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 12909 Z= 0.403 Angle : 0.722 9.509 17480 Z= 0.376 Chirality : 0.048 0.568 1984 Planarity : 0.005 0.044 2315 Dihedral : 5.798 41.034 2117 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.09 % Allowed : 13.27 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.46 (0.21), residues: 1438 helix: 1.01 (0.28), residues: 326 sheet: 0.14 (0.32), residues: 274 loop : -1.02 (0.19), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 142 HIS 0.011 0.002 HIS A 7 PHE 0.018 0.003 PHE C 69 TYR 0.024 0.002 TYR D 119 ARG 0.007 0.001 ARG A 131 *********************** 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 255 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 217 time to evaluate : 1.438 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 21 GLU cc_start: 0.7819 (tp30) cc_final: 0.7591 (mm-30) REVERT: A 22 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7349 (mpt180) REVERT: A 28 ASN cc_start: 0.7820 (t0) cc_final: 0.7617 (t0) REVERT: A 139 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7396 (mm-30) REVERT: A 247 ARG cc_start: 0.8255 (mtt180) cc_final: 0.7979 (mtt180) REVERT: B 120 GLU cc_start: 0.7324 (mm-30) cc_final: 0.7064 (pt0) REVERT: B 149 MET cc_start: 0.7004 (mmt) cc_final: 0.6737 (mmt) REVERT: C 25 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.6264 (tm-30) REVERT: C 75 ASP cc_start: 0.6128 (m-30) cc_final: 0.5888 (m-30) REVERT: C 155 MET cc_start: 0.6976 (ttm) cc_final: 0.6554 (ttm) REVERT: C 227 MET cc_start: 0.7601 (tpt) cc_final: 0.7374 (tpt) REVERT: D 47 GLN cc_start: 0.8046 (tt0) cc_final: 0.7743 (tt0) REVERT: D 60 ASN cc_start: 0.8379 (t0) cc_final: 0.7910 (t0) REVERT: D 61 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.7693 (tp40) REVERT: D 167 MET cc_start: 0.5935 (mtt) cc_final: 0.5733 (mtm) REVERT: E 34 GLU cc_start: 0.7684 (tp30) cc_final: 0.7312 (tp30) REVERT: F 143 LYS cc_start: 0.8204 (tptt) cc_final: 0.7411 (tptm) REVERT: F 161 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7140 (ptmt) outliers start: 38 outliers final: 29 residues processed: 237 average time/residue: 0.2641 time to fit residues: 87.5709 Evaluate side-chains 217 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 184 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 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 53 ASN Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain C residue 7 HIS Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 199 ASN 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 131 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 134 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 chunk 141 optimal weight: 10.0000 chunk 39 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 26 HIS B 27 GLN C 217 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12909 Z= 0.192 Angle : 0.577 9.455 17480 Z= 0.302 Chirality : 0.043 0.609 1984 Planarity : 0.003 0.045 2315 Dihedral : 5.037 34.869 2117 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.44 % Allowed : 14.82 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.35 (0.21), residues: 1438 helix: 1.28 (0.28), residues: 320 sheet: 0.08 (0.32), residues: 271 loop : -0.96 (0.19), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 171 HIS 0.010 0.001 HIS C 8 PHE 0.014 0.001 PHE E 88 TYR 0.023 0.002 TYR A 200 ARG 0.005 0.000 ARG B 127 *********************** 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 240 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 210 time to evaluate : 2.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7794 (tp30) cc_final: 0.7539 (mm-30) REVERT: A 22 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.6958 (mpp-170) REVERT: A 28 ASN cc_start: 0.7672 (t0) cc_final: 0.7446 (t0) REVERT: A 139 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7571 (mm-30) REVERT: B 115 MET cc_start: 0.8564 (mmm) cc_final: 0.8190 (tpp) REVERT: B 119 TYR cc_start: 0.6742 (t80) cc_final: 0.6503 (t80) REVERT: B 149 MET cc_start: 0.7065 (mmt) cc_final: 0.6833 (mmt) REVERT: C 184 LYS cc_start: 0.6743 (OUTLIER) cc_final: 0.6529 (pttm) REVERT: C 227 MET cc_start: 0.7664 (tpt) cc_final: 0.7402 (tpt) REVERT: C 295 LYS cc_start: 0.8636 (mttt) cc_final: 0.8266 (mppt) REVERT: D 60 ASN cc_start: 0.8170 (t0) cc_final: 0.7676 (t0) REVERT: E 155 MET cc_start: 0.7882 (mtm) cc_final: 0.7342 (ptp) REVERT: E 164 LYS cc_start: 0.8060 (mmtt) cc_final: 0.7831 (ttmm) REVERT: F 143 LYS cc_start: 0.8122 (tptt) cc_final: 0.7316 (tptm) REVERT: F 161 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7133 (ptmt) outliers start: 30 outliers final: 18 residues processed: 221 average time/residue: 0.2960 time to fit residues: 91.2494 Evaluate side-chains 217 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 196 time to evaluate : 1.211 ------------------------------------------------------------------------------- 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 201 GLN Chi-restraints excluded: chain A residue 205 VAL 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 113 MET Chi-restraints excluded: chain C residue 117 TYR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 275 SER 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 188 SER Chi-restraints excluded: chain F residue 46 ASP 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 53 optimal weight: 7.9990 chunk 141 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 157 optimal weight: 10.0000 chunk 130 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 12909 Z= 0.298 Angle : 0.616 9.466 17480 Z= 0.322 Chirality : 0.044 0.537 1984 Planarity : 0.004 0.043 2315 Dihedral : 5.122 35.691 2117 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.01 % Allowed : 14.82 % Favored : 82.17 % 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: -0.52 (0.21), residues: 1438 helix: 1.10 (0.28), residues: 326 sheet: -0.15 (0.32), residues: 271 loop : -1.01 (0.19), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 171 HIS 0.010 0.002 HIS D 26 PHE 0.016 0.002 PHE E 92 TYR 0.023 0.002 TYR A 159 ARG 0.009 0.001 ARG E 121 *********************** 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 235 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 198 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7788 (tp30) cc_final: 0.7576 (mm-30) REVERT: A 22 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.6995 (mpp-170) REVERT: A 28 ASN cc_start: 0.7773 (t0) cc_final: 0.7562 (t0) REVERT: A 139 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7857 (mm-30) REVERT: A 247 ARG cc_start: 0.8113 (mtt180) cc_final: 0.7851 (mtt180) REVERT: B 115 MET cc_start: 0.8677 (mmm) cc_final: 0.8298 (tpp) REVERT: B 149 MET cc_start: 0.7019 (mmt) cc_final: 0.6694 (mmt) REVERT: C 25 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7653 (tm-30) REVERT: C 184 LYS cc_start: 0.6745 (OUTLIER) cc_final: 0.6540 (pttm) REVERT: C 227 MET cc_start: 0.7635 (tpt) cc_final: 0.7422 (tpt) REVERT: C 295 LYS cc_start: 0.8680 (mttt) cc_final: 0.8295 (mppt) REVERT: D 47 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7629 (tt0) REVERT: D 60 ASN cc_start: 0.8312 (t0) cc_final: 0.7781 (t0) REVERT: E 164 LYS cc_start: 0.8118 (mmtt) cc_final: 0.7865 (ttmm) REVERT: F 19 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7282 (p0) REVERT: F 143 LYS cc_start: 0.8175 (tptt) cc_final: 0.7348 (tptm) REVERT: F 161 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7120 (ptmt) outliers start: 37 outliers final: 28 residues processed: 215 average time/residue: 0.2761 time to fit residues: 82.5014 Evaluate side-chains 221 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 187 time to evaluate : 1.425 ------------------------------------------------------------------------------- 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 288 ILE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 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 61 THR Chi-restraints excluded: chain E residue 242 PHE Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 117 LYS 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 152 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 115 optimal weight: 8.9990 chunk 132 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 157 optimal weight: 10.0000 chunk 98 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 97 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 239 ASN B 27 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12909 Z= 0.179 Angle : 0.558 9.646 17480 Z= 0.293 Chirality : 0.042 0.500 1984 Planarity : 0.003 0.043 2315 Dihedral : 4.833 33.128 2117 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.01 % Allowed : 15.15 % Favored : 81.84 % 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: -0.41 (0.21), residues: 1438 helix: 1.40 (0.27), residues: 320 sheet: -0.19 (0.32), residues: 273 loop : -0.98 (0.19), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 171 HIS 0.008 0.001 HIS C 8 PHE 0.018 0.001 PHE C 69 TYR 0.025 0.002 TYR A 159 ARG 0.007 0.000 ARG E 121 *********************** 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 261 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 224 time to evaluate : 1.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7215 (mpt180) REVERT: A 28 ASN cc_start: 0.7683 (t0) cc_final: 0.7463 (t0) REVERT: A 186 TYR cc_start: 0.6663 (OUTLIER) cc_final: 0.5851 (m-10) REVERT: C 173 ILE cc_start: 0.7581 (mm) cc_final: 0.6977 (tp) REVERT: C 184 LYS cc_start: 0.6620 (OUTLIER) cc_final: 0.6373 (pttm) REVERT: C 227 MET cc_start: 0.7641 (tpt) cc_final: 0.7409 (tpt) REVERT: C 295 LYS cc_start: 0.8627 (mttt) cc_final: 0.8251 (mppt) REVERT: D 60 ASN cc_start: 0.8321 (t0) cc_final: 0.7803 (t0) REVERT: D 117 LYS cc_start: 0.8201 (ptpt) cc_final: 0.7838 (ptpp) REVERT: E 164 LYS cc_start: 0.8076 (mmtt) cc_final: 0.7827 (ttmm) REVERT: F 19 ASP cc_start: 0.7724 (OUTLIER) cc_final: 0.7258 (p0) REVERT: F 143 LYS cc_start: 0.8144 (tptt) cc_final: 0.7488 (tptm) REVERT: F 161 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7120 (ptmt) outliers start: 37 outliers final: 21 residues processed: 241 average time/residue: 0.2680 time to fit residues: 91.0047 Evaluate side-chains 221 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 195 time to evaluate : 1.395 ------------------------------------------------------------------------------- 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 186 TYR 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 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 14 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain E residue 188 SER 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 52 LEU Chi-restraints excluded: chain F residue 152 ILE 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 62 optimal weight: 8.9990 chunk 93 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 142 optimal weight: 20.0000 chunk 150 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 239 ASN B 27 GLN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 17 ASN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 12909 Z= 0.412 Angle : 0.690 10.130 17480 Z= 0.359 Chirality : 0.047 0.504 1984 Planarity : 0.004 0.045 2315 Dihedral : 5.355 36.352 2117 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.34 % Allowed : 15.64 % 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: -0.70 (0.21), residues: 1438 helix: 1.04 (0.28), residues: 323 sheet: -0.36 (0.33), residues: 243 loop : -1.11 (0.19), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 171 HIS 0.007 0.002 HIS A 7 PHE 0.020 0.002 PHE C 69 TYR 0.031 0.002 TYR A 159 ARG 0.006 0.001 ARG B 153 *********************** 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 227 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 186 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7088 (mpp-170) REVERT: A 139 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8231 (mm-30) REVERT: A 186 TYR cc_start: 0.6768 (OUTLIER) cc_final: 0.5934 (m-10) REVERT: C 25 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7615 (tm-30) REVERT: D 47 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7757 (tt0) REVERT: D 60 ASN cc_start: 0.8433 (t0) cc_final: 0.7922 (t0) REVERT: D 61 GLN cc_start: 0.8448 (tp-100) cc_final: 0.8102 (tp40) REVERT: E 34 GLU cc_start: 0.7662 (tp30) cc_final: 0.7261 (tp30) REVERT: E 164 LYS cc_start: 0.8177 (mmtt) cc_final: 0.7917 (ttmm) REVERT: F 143 LYS cc_start: 0.8321 (tptt) cc_final: 0.7704 (tptm) REVERT: F 161 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7051 (ptmt) outliers start: 41 outliers final: 33 residues processed: 206 average time/residue: 0.2624 time to fit residues: 76.5016 Evaluate side-chains 219 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 181 time to evaluate : 1.289 ------------------------------------------------------------------------------- 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 186 TYR 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 52 LEU Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 47 GLN 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 61 THR Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 242 PHE Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain E residue 281 SER Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 152 ILE 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 137 optimal weight: 1.9990 chunk 146 optimal weight: 7.9990 chunk 150 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 132 optimal weight: 0.8980 chunk 138 optimal weight: 0.6980 chunk 145 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 C 259 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12909 Z= 0.200 Angle : 0.589 9.806 17480 Z= 0.308 Chirality : 0.043 0.479 1984 Planarity : 0.003 0.042 2315 Dihedral : 5.012 32.974 2117 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.93 % Allowed : 16.21 % Favored : 80.86 % 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: -0.56 (0.21), residues: 1438 helix: 1.22 (0.28), residues: 323 sheet: -0.45 (0.32), residues: 273 loop : -0.99 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 171 HIS 0.008 0.001 HIS C 8 PHE 0.016 0.001 PHE C 69 TYR 0.033 0.002 TYR C 186 ARG 0.004 0.000 ARG D 54 *********************** 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 240 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 204 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.6973 (mpp-170) REVERT: A 111 GLU cc_start: 0.7230 (tt0) cc_final: 0.6914 (mt-10) REVERT: A 186 TYR cc_start: 0.6628 (OUTLIER) cc_final: 0.5894 (m-10) REVERT: B 26 HIS cc_start: 0.5835 (m-70) cc_final: 0.5535 (m-70) REVERT: C 25 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7649 (tm-30) REVERT: C 160 LYS cc_start: 0.7178 (tptt) cc_final: 0.6959 (tptp) REVERT: C 295 LYS cc_start: 0.8640 (mttt) cc_final: 0.8384 (mmtp) REVERT: D 47 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7647 (tt0) REVERT: D 60 ASN cc_start: 0.8391 (t0) cc_final: 0.7880 (t0) REVERT: E 34 GLU cc_start: 0.7685 (tp30) cc_final: 0.7296 (tp30) REVERT: E 121 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.7402 (mtm-85) REVERT: E 155 MET cc_start: 0.7746 (mtm) cc_final: 0.7521 (ptp) REVERT: E 164 LYS cc_start: 0.8142 (mmtt) cc_final: 0.7881 (ttmm) REVERT: F 19 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7255 (p0) REVERT: F 41 THR cc_start: 0.8404 (m) cc_final: 0.8063 (m) REVERT: F 115 MET cc_start: 0.7354 (tpt) cc_final: 0.6838 (tpt) REVERT: F 143 LYS cc_start: 0.8247 (tptt) cc_final: 0.7412 (tptm) REVERT: F 161 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7055 (ptmt) outliers start: 36 outliers final: 25 residues processed: 222 average time/residue: 0.2544 time to fit residues: 80.0715 Evaluate side-chains 221 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 189 time to evaluate : 1.265 ------------------------------------------------------------------------------- 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 186 TYR 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 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 7 HIS Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 117 TYR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 47 GLN 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 61 THR Chi-restraints excluded: chain E residue 121 ARG Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 242 PHE Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 152 ILE 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 154 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 162 optimal weight: 8.9990 chunk 149 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 102 optimal weight: 0.4980 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 12909 Z= 0.383 Angle : 0.694 11.895 17480 Z= 0.357 Chirality : 0.048 0.491 1984 Planarity : 0.004 0.042 2315 Dihedral : 5.382 35.266 2117 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.69 % Allowed : 17.02 % Favored : 80.29 % 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: -0.73 (0.21), residues: 1438 helix: 1.04 (0.28), residues: 323 sheet: -0.34 (0.34), residues: 233 loop : -1.15 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 171 HIS 0.007 0.002 HIS A 7 PHE 0.020 0.002 PHE C 69 TYR 0.032 0.002 TYR A 159 ARG 0.005 0.001 ARG E 121 ********************** 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 215 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 182 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 HIS cc_start: 0.7757 (t70) cc_final: 0.7126 (p-80) REVERT: A 22 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7131 (mpp-170) REVERT: A 111 GLU cc_start: 0.7239 (tt0) cc_final: 0.6914 (mt-10) REVERT: A 186 TYR cc_start: 0.6740 (OUTLIER) cc_final: 0.6031 (m-10) REVERT: C 25 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7588 (tm-30) REVERT: C 141 LYS cc_start: 0.7264 (OUTLIER) cc_final: 0.6988 (ttmm) REVERT: C 295 LYS cc_start: 0.8695 (mttt) cc_final: 0.8388 (mmtp) REVERT: D 47 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7755 (tt0) REVERT: D 60 ASN cc_start: 0.8440 (t0) cc_final: 0.7904 (t0) REVERT: D 61 GLN cc_start: 0.8452 (tp-100) cc_final: 0.8057 (tp40) REVERT: D 117 LYS cc_start: 0.8306 (ptpt) cc_final: 0.7933 (ptpp) REVERT: E 34 GLU cc_start: 0.7683 (tp30) cc_final: 0.7286 (tp30) REVERT: E 164 LYS cc_start: 0.8212 (mmtt) cc_final: 0.7929 (ttmm) REVERT: F 143 LYS cc_start: 0.8320 (tptt) cc_final: 0.7499 (tptm) REVERT: F 161 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7068 (ptmt) outliers start: 33 outliers final: 25 residues processed: 200 average time/residue: 0.2627 time to fit residues: 74.4126 Evaluate side-chains 207 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 176 time to evaluate : 1.378 ------------------------------------------------------------------------------- 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 186 TYR 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 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 7 HIS Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 242 PHE Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 152 ILE 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 137 optimal weight: 5.9990 chunk 39 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 129 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS C 182 GLN C 259 GLN ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4057 r_free = 0.4057 target = 0.166618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.145052 restraints weight = 19545.893| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.67 r_work: 0.3705 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12909 Z= 0.225 Angle : 0.632 12.812 17480 Z= 0.326 Chirality : 0.045 0.472 1984 Planarity : 0.003 0.042 2315 Dihedral : 5.279 33.390 2117 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.59 % Favored : 95.34 % Rotamer: Outliers : 2.52 % Allowed : 17.18 % Favored : 80.29 % 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: -0.62 (0.21), residues: 1438 helix: 1.18 (0.28), residues: 323 sheet: -0.48 (0.32), residues: 261 loop : -1.03 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 171 HIS 0.008 0.001 HIS C 8 PHE 0.021 0.002 PHE C 69 TYR 0.026 0.002 TYR A 159 ARG 0.008 0.000 ARG D 127 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2952.55 seconds wall clock time: 53 minutes 44.03 seconds (3224.03 seconds total)