Starting phenix.real_space_refine on Sun Jul 21 00:37:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut8_42533/07_2024/8ut8_42533.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut8_42533/07_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_42533/07_2024/8ut8_42533.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut8_42533/07_2024/8ut8_42533.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut8_42533/07_2024/8ut8_42533.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut8_42533/07_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-5388/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: 7.79, per 1000 atoms: 0.61 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: 4.75 Conformation dependent library (CDL) restraints added in 2.0 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: 1.79 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: 3.53 Time building geometry restraints manager: 5.25 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 2.440 nonbonded pdb=" OE2 GLU E 34 " pdb=" OG1 THR E 36 " model vdw 2.136 2.440 nonbonded pdb=" OE1 GLU E 31 " pdb=" OG SER E 304 " model vdw 2.185 2.440 nonbonded pdb=" OE1 GLU C 139 " pdb=" NH1 ARG C 247 " model vdw 2.200 2.520 ... (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 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: 0.010 Normalize map: mean=0, sd=1: 2.810 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: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 35.690 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.060 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.320 ------------------------------------------------------------------------------- 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 : 1.397 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: 0.2779 time to fit residues: 101.8495 Evaluate side-chains 216 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 1.328 ------------------------------------------------------------------------------- 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: 6.9990 chunk 42 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 148 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 GLN B 95 ASN ** C 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS F 60 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12909 Z= 0.300 Angle : 0.668 8.147 17480 Z= 0.353 Chirality : 0.043 0.222 1984 Planarity : 0.004 0.046 2315 Dihedral : 5.341 40.867 2117 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.04 % Allowed : 11.24 % Favored : 86.73 % 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: 1.30 (0.27), residues: 325 sheet: 0.58 (0.31), residues: 287 loop : -0.82 (0.19), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 171 HIS 0.007 0.002 HIS C 8 PHE 0.031 0.002 PHE E 242 TYR 0.021 0.002 TYR B 119 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 251 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 226 time to evaluate : 1.230 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: 0.7601 (t0) cc_final: 0.7373 (t0) REVERT: B 54 ARG cc_start: 0.7921 (ttp80) cc_final: 0.7339 (tmm160) REVERT: B 115 MET cc_start: 0.8510 (tpt) cc_final: 0.7809 (tpt) REVERT: B 120 GLU cc_start: 0.7258 (mm-30) cc_final: 0.7007 (pt0) REVERT: B 149 MET cc_start: 0.6906 (mmt) cc_final: 0.6551 (mmt) REVERT: C 155 MET cc_start: 0.6850 (ttm) cc_final: 0.6527 (ttm) REVERT: D 60 ASN cc_start: 0.8070 (t0) cc_final: 0.7663 (t0) REVERT: D 117 LYS cc_start: 0.8040 (ptpp) cc_final: 0.7688 (ptpp) REVERT: E 34 GLU cc_start: 0.7289 (tp30) cc_final: 0.7033 (tp30) REVERT: E 68 GLN cc_start: 0.7915 (pm20) cc_final: 0.7680 (pm20) REVERT: F 161 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7345 (ptmt) outliers start: 25 outliers final: 18 residues processed: 236 average time/residue: 0.2733 time to fit residues: 89.8895 Evaluate side-chains 212 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 193 time to evaluate : 1.377 ------------------------------------------------------------------------------- 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 B residue 148 CYS 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 194 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 194 THR 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: 4.9990 chunk 45 optimal weight: 0.7980 chunk 123 optimal weight: 0.0170 chunk 100 optimal weight: 0.0020 chunk 40 optimal weight: 4.9990 chunk 148 optimal weight: 10.0000 chunk 160 optimal weight: 9.9990 chunk 132 optimal weight: 1.9990 chunk 147 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 overall best weight: 0.7428 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN A 259 GLN B 27 GLN B 159 HIS C 154 GLN ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7508 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12909 Z= 0.180 Angle : 0.566 7.451 17480 Z= 0.299 Chirality : 0.041 0.232 1984 Planarity : 0.003 0.047 2315 Dihedral : 4.873 37.044 2117 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.44 % Allowed : 12.46 % 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: -0.05 (0.20), residues: 1438 helix: 1.56 (0.27), residues: 319 sheet: 0.53 (0.31), residues: 287 loop : -0.90 (0.19), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 171 HIS 0.013 0.001 HIS C 8 PHE 0.015 0.002 PHE E 92 TYR 0.015 0.001 TYR D 157 ARG 0.004 0.000 ARG C 303 *********************** 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 246 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 216 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASN cc_start: 0.7594 (t0) cc_final: 0.7355 (t0) REVERT: B 115 MET cc_start: 0.8403 (tpt) cc_final: 0.7636 (tpt) REVERT: B 120 GLU cc_start: 0.7241 (mm-30) cc_final: 0.7008 (pt0) REVERT: C 155 MET cc_start: 0.6841 (ttm) cc_final: 0.6542 (ttm) REVERT: D 60 ASN cc_start: 0.8092 (t0) cc_final: 0.7497 (t0) REVERT: E 109 ASP cc_start: 0.7871 (t0) cc_final: 0.7660 (t0) REVERT: F 19 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.7101 (p0) REVERT: F 161 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7252 (ptmt) outliers start: 30 outliers final: 17 residues processed: 234 average time/residue: 0.2482 time to fit residues: 82.4663 Evaluate side-chains 210 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 191 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 231 ASN Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 146 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: 7.9990 chunk 76 optimal weight: 5.9990 chunk 16 optimal weight: 0.3980 chunk 70 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 148 optimal weight: 10.0000 chunk 157 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 141 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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** B 27 GLN B 62 GLN B 125 GLN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 GLN D 47 GLN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 12909 Z= 0.344 Angle : 0.656 8.671 17480 Z= 0.341 Chirality : 0.045 0.411 1984 Planarity : 0.004 0.043 2315 Dihedral : 5.487 39.671 2117 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.99 % Allowed : 12.62 % Favored : 83.39 % 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: 1.35 (0.28), residues: 319 sheet: 0.27 (0.33), residues: 257 loop : -1.04 (0.19), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 171 HIS 0.009 0.002 HIS C 8 PHE 0.017 0.002 PHE E 238 TYR 0.020 0.002 TYR D 119 ARG 0.003 0.001 ARG A 121 *********************** 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 250 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 201 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 HIS cc_start: 0.7655 (t70) cc_final: 0.6935 (p-80) REVERT: A 155 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.7288 (mpp) REVERT: A 247 ARG cc_start: 0.7693 (ptp-110) cc_final: 0.7465 (ptm160) REVERT: B 115 MET cc_start: 0.8383 (tpt) cc_final: 0.7571 (tpt) REVERT: B 120 GLU cc_start: 0.7301 (mm-30) cc_final: 0.7045 (pt0) REVERT: C 75 ASP cc_start: 0.5941 (m-30) cc_final: 0.5722 (m-30) REVERT: C 227 MET cc_start: 0.7632 (tpt) cc_final: 0.7364 (tpt) REVERT: D 60 ASN cc_start: 0.8324 (t0) cc_final: 0.7793 (t0) REVERT: E 2 LYS cc_start: 0.7226 (ttpt) cc_final: 0.6995 (tttp) REVERT: E 34 GLU cc_start: 0.7474 (tp30) cc_final: 0.7233 (tp30) REVERT: E 109 ASP cc_start: 0.7829 (t0) cc_final: 0.7602 (t0) REVERT: F 137 CYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7565 (m) REVERT: F 143 LYS cc_start: 0.8168 (tptt) cc_final: 0.7557 (tptm) REVERT: F 161 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7140 (ptmt) outliers start: 49 outliers final: 33 residues processed: 233 average time/residue: 0.2615 time to fit residues: 86.0500 Evaluate side-chains 219 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 183 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER 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 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 12 ASN 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 212 THR Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 137 CYS Chi-restraints excluded: chain F residue 146 ASP 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: 5.9990 chunk 2 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 134 optimal weight: 4.9990 chunk 108 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 chunk 141 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN ** 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: 0.7660 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 12909 Z= 0.331 Angle : 0.637 10.144 17480 Z= 0.331 Chirality : 0.046 0.686 1984 Planarity : 0.004 0.042 2315 Dihedral : 5.244 40.920 2117 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.99 % Allowed : 13.03 % Favored : 82.98 % 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: -0.57 (0.21), residues: 1438 helix: 1.19 (0.28), residues: 320 sheet: -0.16 (0.33), residues: 241 loop : -1.07 (0.19), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 171 HIS 0.008 0.001 HIS C 8 PHE 0.015 0.002 PHE C 69 TYR 0.026 0.002 TYR E 137 ARG 0.006 0.001 ARG C 247 *********************** 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 247 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 198 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 HIS cc_start: 0.7665 (t70) cc_final: 0.7040 (p-80) REVERT: B 120 GLU cc_start: 0.7277 (mm-30) cc_final: 0.7038 (pt0) REVERT: C 227 MET cc_start: 0.7665 (tpt) cc_final: 0.7421 (tpt) REVERT: D 60 ASN cc_start: 0.8430 (t0) cc_final: 0.7909 (t0) REVERT: D 74 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7407 (tp30) REVERT: E 2 LYS cc_start: 0.7337 (ttpt) cc_final: 0.7093 (tttp) REVERT: E 4 CYS cc_start: 0.6467 (m) cc_final: 0.5974 (m) REVERT: E 155 MET cc_start: 0.7801 (mtm) cc_final: 0.7352 (ptp) REVERT: E 164 LYS cc_start: 0.8137 (mmtt) cc_final: 0.7884 (ttmm) REVERT: F 19 ASP cc_start: 0.7800 (OUTLIER) cc_final: 0.7285 (p0) REVERT: F 137 CYS cc_start: 0.7848 (OUTLIER) cc_final: 0.7094 (m) REVERT: F 143 LYS cc_start: 0.8236 (tptt) cc_final: 0.7441 (tptm) REVERT: F 161 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7079 (ptmt) outliers start: 49 outliers final: 33 residues processed: 227 average time/residue: 0.2504 time to fit residues: 80.8625 Evaluate side-chains 214 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 178 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 93 VAL 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 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 86 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 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 260 SER Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 117 LYS Chi-restraints excluded: chain F residue 137 CYS Chi-restraints excluded: chain F residue 146 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: 0.0870 chunk 141 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 157 optimal weight: 10.0000 chunk 130 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 13 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 overall best weight: 1.3562 ------------------------------------------------------------------------------- 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** B 27 GLN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN ** E 286 GLN ** 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: 0.7631 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12909 Z= 0.235 Angle : 0.576 8.292 17480 Z= 0.301 Chirality : 0.043 0.503 1984 Planarity : 0.003 0.042 2315 Dihedral : 5.050 38.948 2117 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.66 % Allowed : 14.82 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.39 (0.28), residues: 319 sheet: -0.35 (0.33), residues: 243 loop : -1.08 (0.19), residues: 876 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 0.013 0.001 PHE D 24 TYR 0.023 0.002 TYR A 159 ARG 0.006 0.000 ARG F 25 *********************** 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 248 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 203 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 HIS cc_start: 0.7668 (t70) cc_final: 0.7039 (p-80) REVERT: B 120 GLU cc_start: 0.7234 (mm-30) cc_final: 0.6982 (pt0) REVERT: C 227 MET cc_start: 0.7659 (tpt) cc_final: 0.7426 (tpt) REVERT: D 60 ASN cc_start: 0.8413 (t0) cc_final: 0.7925 (t0) REVERT: D 74 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7419 (tp30) REVERT: E 2 LYS cc_start: 0.7285 (ttpt) cc_final: 0.7035 (tttp) REVERT: E 34 GLU cc_start: 0.7457 (tp30) cc_final: 0.7223 (tp30) REVERT: E 164 LYS cc_start: 0.8170 (mmtt) cc_final: 0.7876 (ttmm) REVERT: F 19 ASP cc_start: 0.7775 (OUTLIER) cc_final: 0.7281 (p0) REVERT: F 143 LYS cc_start: 0.8220 (tptt) cc_final: 0.7418 (tptm) REVERT: F 161 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7064 (ptmt) outliers start: 45 outliers final: 34 residues processed: 231 average time/residue: 0.2560 time to fit residues: 84.7165 Evaluate side-chains 219 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 183 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER 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 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 7 HIS Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain D residue 26 HIS Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain D residue 145 ASP 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 E residue 260 SER Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 146 ASP 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: 9.9990 chunk 17 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 chunk 115 optimal weight: 0.0980 chunk 132 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 157 optimal weight: 10.0000 chunk 98 optimal weight: 0.0980 chunk 95 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 239 ASN B 27 GLN B 62 GLN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN E 217 GLN ** E 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7579 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12909 Z= 0.175 Angle : 0.553 7.508 17480 Z= 0.288 Chirality : 0.042 0.489 1984 Planarity : 0.003 0.043 2315 Dihedral : 4.753 34.644 2117 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.69 % Allowed : 16.37 % Favored : 80.94 % 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: -0.48 (0.21), residues: 1438 helix: 1.57 (0.28), residues: 319 sheet: -0.46 (0.32), residues: 271 loop : -1.03 (0.19), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 171 HIS 0.008 0.001 HIS C 8 PHE 0.014 0.001 PHE D 24 TYR 0.024 0.002 TYR A 159 ARG 0.005 0.000 ARG F 25 *********************** 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 fitting. rotamer outliers: 33 poor density : 213 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 HIS cc_start: 0.7655 (t70) cc_final: 0.7044 (p-80) REVERT: C 184 LYS cc_start: 0.6909 (OUTLIER) cc_final: 0.6568 (pttm) REVERT: D 60 ASN cc_start: 0.8410 (t0) cc_final: 0.7968 (t0) REVERT: D 62 GLN cc_start: 0.8372 (mt0) cc_final: 0.8125 (mm-40) REVERT: D 74 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7465 (tp30) REVERT: E 34 GLU cc_start: 0.7460 (tp30) cc_final: 0.7207 (tp30) REVERT: E 164 LYS cc_start: 0.8149 (mmtt) cc_final: 0.7882 (ttmm) REVERT: F 19 ASP cc_start: 0.7730 (OUTLIER) cc_final: 0.7271 (p0) REVERT: F 115 MET cc_start: 0.7243 (tpt) cc_final: 0.6343 (tpt) REVERT: F 143 LYS cc_start: 0.8172 (tptt) cc_final: 0.7361 (tptm) REVERT: F 161 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.7090 (ptmt) outliers start: 33 outliers final: 21 residues processed: 233 average time/residue: 0.2509 time to fit residues: 83.2362 Evaluate side-chains 208 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 184 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 155 MET 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 148 CYS Chi-restraints excluded: chain C residue 7 HIS 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 184 LYS Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 242 PHE Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain F residue 19 ASP 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: 2.9990 chunk 93 optimal weight: 0.7980 chunk 47 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 chunk 142 optimal weight: 20.0000 chunk 150 optimal weight: 10.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 224 HIS A 239 ASN C 94 ASN D 47 GLN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN E 217 GLN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 12909 Z= 0.347 Angle : 0.659 8.895 17480 Z= 0.341 Chirality : 0.046 0.486 1984 Planarity : 0.004 0.046 2315 Dihedral : 5.195 38.109 2117 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.42 % Allowed : 17.02 % Favored : 79.56 % 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: -0.67 (0.21), residues: 1438 helix: 1.45 (0.28), residues: 317 sheet: -0.55 (0.33), residues: 243 loop : -1.17 (0.19), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 171 HIS 0.007 0.002 HIS B 142 PHE 0.016 0.002 PHE E 92 TYR 0.030 0.002 TYR A 159 ARG 0.008 0.001 ARG D 54 *********************** 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 239 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 197 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 HIS cc_start: 0.7651 (t70) cc_final: 0.7042 (p-80) REVERT: C 200 TYR cc_start: 0.8462 (t80) cc_final: 0.8133 (t80) REVERT: D 60 ASN cc_start: 0.8474 (t0) cc_final: 0.8044 (t0) REVERT: D 62 GLN cc_start: 0.8430 (mt0) cc_final: 0.8122 (mm-40) REVERT: D 74 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7453 (tp30) REVERT: E 34 GLU cc_start: 0.7496 (tp30) cc_final: 0.7256 (tp30) REVERT: E 164 LYS cc_start: 0.8231 (mmtt) cc_final: 0.7922 (ttmm) REVERT: F 19 ASP cc_start: 0.7775 (OUTLIER) cc_final: 0.7300 (p0) REVERT: F 115 MET cc_start: 0.7461 (tpt) cc_final: 0.6790 (tpt) REVERT: F 143 LYS cc_start: 0.8275 (tptt) cc_final: 0.7468 (tptm) REVERT: F 161 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7092 (ptmt) outliers start: 42 outliers final: 33 residues processed: 220 average time/residue: 0.2634 time to fit residues: 82.9922 Evaluate side-chains 219 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 184 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 43 SER 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 205 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 26 HIS 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 7 HIS Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 117 TYR Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain D residue 26 HIS Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 242 PHE Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 146 ASP 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: 5.9990 chunk 146 optimal weight: 8.9990 chunk 150 optimal weight: 10.0000 chunk 88 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 chunk 145 optimal weight: 10.0000 chunk 96 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 239 ASN B 62 GLN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN E 217 GLN ** E 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12909 Z= 0.217 Angle : 0.585 8.114 17480 Z= 0.304 Chirality : 0.043 0.470 1984 Planarity : 0.003 0.045 2315 Dihedral : 4.948 35.816 2117 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.77 % Allowed : 17.92 % Favored : 79.32 % 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: 1.65 (0.28), residues: 316 sheet: -0.51 (0.33), residues: 243 loop : -1.14 (0.19), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 171 HIS 0.008 0.001 HIS B 142 PHE 0.017 0.002 PHE A 88 TYR 0.028 0.002 TYR A 159 ARG 0.008 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 224 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 190 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 HIS cc_start: 0.7677 (t70) cc_final: 0.7022 (p-80) REVERT: A 256 MET cc_start: 0.8422 (ptm) cc_final: 0.8167 (ptm) REVERT: C 155 MET cc_start: 0.6462 (ttm) cc_final: 0.6174 (ptp) REVERT: C 184 LYS cc_start: 0.6847 (OUTLIER) cc_final: 0.6532 (pttm) REVERT: C 247 ARG cc_start: 0.6551 (mtt90) cc_final: 0.6275 (mtm-85) REVERT: D 60 ASN cc_start: 0.8435 (t0) cc_final: 0.8003 (t0) REVERT: D 62 GLN cc_start: 0.8401 (mt0) cc_final: 0.8142 (mm-40) REVERT: D 74 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7460 (tp30) REVERT: E 34 GLU cc_start: 0.7485 (tp30) cc_final: 0.7231 (tp30) REVERT: E 164 LYS cc_start: 0.8209 (mmtt) cc_final: 0.7925 (ttmm) REVERT: F 19 ASP cc_start: 0.7747 (OUTLIER) cc_final: 0.7280 (p0) REVERT: F 41 THR cc_start: 0.8663 (m) cc_final: 0.8412 (m) REVERT: F 143 LYS cc_start: 0.8198 (tptt) cc_final: 0.7391 (tptm) REVERT: F 161 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7036 (ptmt) outliers start: 34 outliers final: 27 residues processed: 211 average time/residue: 0.2569 time to fit residues: 78.3428 Evaluate side-chains 214 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 184 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER 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 221 ILE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 26 HIS 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 86 VAL Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain D residue 26 HIS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 242 PHE Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 146 ASP 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: 0.3980 chunk 107 optimal weight: 1.9990 chunk 162 optimal weight: 8.9990 chunk 149 optimal weight: 10.0000 chunk 129 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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** B 27 GLN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN E 217 GLN F 26 HIS ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12909 Z= 0.287 Angle : 0.618 8.482 17480 Z= 0.319 Chirality : 0.044 0.472 1984 Planarity : 0.003 0.043 2315 Dihedral : 5.020 36.123 2117 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.85 % Allowed : 17.83 % Favored : 79.32 % 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: -0.65 (0.21), residues: 1438 helix: 1.60 (0.28), residues: 316 sheet: -0.57 (0.33), residues: 243 loop : -1.19 (0.19), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 171 HIS 0.007 0.001 HIS C 8 PHE 0.015 0.002 PHE A 88 TYR 0.031 0.002 TYR A 159 ARG 0.007 0.001 ARG D 54 ********************** 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 219 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 184 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 HIS cc_start: 0.7680 (t70) cc_final: 0.7038 (p-80) REVERT: C 155 MET cc_start: 0.6564 (ttm) cc_final: 0.6086 (ptp) REVERT: C 184 LYS cc_start: 0.6876 (OUTLIER) cc_final: 0.6563 (pttm) REVERT: C 200 TYR cc_start: 0.8426 (t80) cc_final: 0.8015 (t80) REVERT: D 60 ASN cc_start: 0.8458 (t0) cc_final: 0.8034 (t0) REVERT: D 62 GLN cc_start: 0.8413 (mt0) cc_final: 0.8086 (mm-40) REVERT: D 74 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7462 (tp30) REVERT: E 164 LYS cc_start: 0.8253 (mmtt) cc_final: 0.8025 (ttmm) REVERT: F 19 ASP cc_start: 0.7779 (OUTLIER) cc_final: 0.7294 (p0) REVERT: F 41 THR cc_start: 0.8638 (m) cc_final: 0.8389 (m) REVERT: F 143 LYS cc_start: 0.8262 (tptt) cc_final: 0.7434 (tptm) REVERT: F 161 LYS cc_start: 0.7773 (OUTLIER) cc_final: 0.7077 (ptmt) outliers start: 35 outliers final: 29 residues processed: 207 average time/residue: 0.2713 time to fit residues: 80.6180 Evaluate side-chains 214 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 182 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 43 SER 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 221 ILE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 26 HIS 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 14 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain D residue 26 HIS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 242 PHE Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 146 ASP 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: 2.9990 chunk 39 optimal weight: 0.9990 chunk 119 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 113 optimal weight: 7.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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** B 27 GLN B 62 GLN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN E 217 GLN ** E 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4045 r_free = 0.4045 target = 0.165846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.144608 restraints weight = 19569.128| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.62 r_work: 0.3703 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12909 Z= 0.197 Angle : 0.568 7.717 17480 Z= 0.296 Chirality : 0.043 0.458 1984 Planarity : 0.003 0.042 2315 Dihedral : 4.803 32.947 2117 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.44 % Allowed : 18.57 % Favored : 78.99 % 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: -0.49 (0.21), residues: 1438 helix: 1.74 (0.28), residues: 316 sheet: -0.34 (0.35), residues: 219 loop : -1.13 (0.19), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 171 HIS 0.007 0.001 HIS D 26 PHE 0.014 0.001 PHE D 24 TYR 0.028 0.002 TYR A 159 ARG 0.008 0.000 ARG D 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2989.04 seconds wall clock time: 54 minutes 2.12 seconds (3242.12 seconds total)