Starting phenix.real_space_refine on Thu Jun 27 11:58:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut8_42533/06_2024/8ut8_42533_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut8_42533/06_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_42533/06_2024/8ut8_42533.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut8_42533/06_2024/8ut8_42533.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut8_42533/06_2024/8ut8_42533_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut8_42533/06_2024/8ut8_42533_updated.pdb" } 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-5370/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: 7.91, per 1000 atoms: 0.62 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: 5.02 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... running ksdssp... Secondary structure from input PDB file: 29 helices and 33 sheets defined 24.5% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.45 Creating SS restraints... Processing helix chain 'A' and resid 57 through 61 Processing helix chain 'A' and resid 64 through 69 removed outlier: 5.271A pdb=" N GLN A 68 " --> pdb=" O GLN A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 103 Processing helix chain 'A' and resid 181 through 184 No H-bonds generated for 'chain 'A' and resid 181 through 184' Processing helix chain 'B' and resid 39 through 56 Processing helix chain 'B' and resid 75 through 125 Processing helix chain 'B' and resid 147 through 153 Processing helix chain 'B' and resid 163 through 168 Processing helix chain 'C' and resid 56 through 59 Processing helix chain 'C' and resid 64 through 69 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 95 through 103 Processing helix chain 'C' and resid 179 through 185 Processing helix chain 'D' and resid 38 through 55 Processing helix chain 'D' and resid 75 through 129 removed outlier: 6.905A pdb=" N GLU D 128 " --> pdb=" O ARG D 124 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASN D 129 " --> pdb=" O GLN D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 153 Processing helix chain 'D' and resid 163 through 170 Processing helix chain 'E' and resid 56 through 61 removed outlier: 4.007A pdb=" N THR E 61 " --> pdb=" O GLY E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 69 removed outlier: 5.404A pdb=" N GLN E 68 " --> pdb=" O GLN E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 104 removed outlier: 3.816A pdb=" N GLU E 104 " --> pdb=" O GLN E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 185 Processing helix chain 'F' and resid 38 through 55 Processing helix chain 'F' and resid 75 through 129 removed outlier: 6.800A pdb=" N GLU F 128 " --> pdb=" O ARG F 124 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ASN F 129 " --> pdb=" O GLN F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 153 Processing helix chain 'F' and resid 163 through 170 Processing helix chain 'G' and resid 62 through 64 No H-bonds generated for 'chain 'G' and resid 62 through 64' Processing helix chain 'G' and resid 88 through 90 No H-bonds generated for 'chain 'G' and resid 88 through 90' Processing helix chain 'G' and resid 109 through 112 Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 81 through 83 No H-bonds generated for 'chain 'H' and resid 81 through 83' Processing sheet with id= A, first strand: chain 'A' and resid 14 through 16 Processing sheet with id= B, first strand: chain 'A' and resid 29 through 31 Processing sheet with id= C, first strand: chain 'A' and resid 40 through 42 removed outlier: 7.238A pdb=" N GLN A 263 " --> pdb=" O ILE A 41 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 48 through 51 removed outlier: 6.857A pdb=" N LEU A 76 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LEU A 51 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE A 78 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N MET A 256 " --> pdb=" O ILE A 77 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N GLU A 79 " --> pdb=" O MET A 256 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE A 258 " --> pdb=" O GLU A 79 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 90 through 92 removed outlier: 6.082A pdb=" N ILE A 221 " --> pdb=" O LYS A 91 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 108 through 112 Processing sheet with id= G, first strand: chain 'A' and resid 140 through 142 Processing sheet with id= H, first strand: chain 'A' and resid 155 through 160 Processing sheet with id= I, first strand: chain 'A' and resid 272 through 274 removed outlier: 3.794A pdb=" N CYS A 272 " --> pdb=" O ILE A 279 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 22 through 26 removed outlier: 4.576A pdb=" N TYR B 22 " --> pdb=" O ASP B 37 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 130 through 132 Processing sheet with id= L, first strand: chain 'C' and resid 14 through 16 Processing sheet with id= M, first strand: chain 'C' and resid 29 through 31 Processing sheet with id= N, first strand: chain 'C' and resid 48 through 50 removed outlier: 7.348A pdb=" N LEU C 76 " --> pdb=" O VAL C 49 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'C' and resid 90 through 92 removed outlier: 5.843A pdb=" N ILE C 221 " --> pdb=" O LYS C 91 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 109 through 112 Processing sheet with id= Q, first strand: chain 'C' and resid 140 through 142 Processing sheet with id= R, first strand: chain 'C' and resid 155 through 159 Processing sheet with id= S, 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= T, first strand: chain 'D' and resid 23 through 27 Processing sheet with id= U, first strand: chain 'D' and resid 130 through 132 Processing sheet with id= V, first strand: chain 'E' and resid 14 through 16 Processing sheet with id= W, first strand: chain 'E' and resid 29 through 31 Processing sheet with id= X, first strand: chain 'E' and resid 48 through 50 removed outlier: 6.642A pdb=" N LEU E 76 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N MET E 256 " --> pdb=" O ILE E 77 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N GLU E 79 " --> pdb=" O MET E 256 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE E 258 " --> pdb=" O GLU E 79 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'E' and resid 108 through 112 Processing sheet with id= Z, first strand: chain 'E' and resid 155 through 160 Processing sheet with id= AA, first strand: chain 'E' and resid 167 through 175 Processing sheet with id= AB, first strand: chain 'F' and resid 23 through 26 Processing sheet with id= AC, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.296A pdb=" N UNK G 122 " --> pdb=" O UNK G 10 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N UNK G 12 " --> pdb=" O UNK G 122 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N UNK G 124 " --> pdb=" O UNK G 12 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N UNK G 38 " --> pdb=" O UNK G 47 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N UNK G 47 " --> pdb=" O UNK G 38 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'G' and resid 18 through 22 Processing sheet with id= AE, first strand: chain 'H' and resid 10 through 13 removed outlier: 5.941A pdb=" N UNK H 105 " --> pdb=" O UNK H 11 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N UNK H 13 " --> pdb=" O UNK H 105 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N UNK H 107 " --> pdb=" O UNK H 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'H' and resid 19 through 24 Processing sheet with id= AG, first strand: chain 'H' and resid 98 through 101 removed outlier: 4.275A pdb=" N UNK H 89 " --> pdb=" O UNK H 101 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N UNK H 38 " --> pdb=" O UNK H 47 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N UNK H 47 " --> pdb=" O UNK H 38 " (cutoff:3.500A) 422 hydrogen bonds defined for protein. 1131 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: 3.34 Time building geometry restraints manager: 5.50 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: 257 2.65 - 3.21: 11445 3.21 - 3.77: 19510 3.77 - 4.34: 26894 4.34 - 4.90: 44508 Nonbonded interactions: 102614 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 102609 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: 0.000 Normalize map: mean=0, sd=1: 3.300 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: 9.920 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 35.940 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.100 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.950 ------------------------------------------------------------------------------- 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= 0.417 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 : 1.354 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: 0.2760 time to fit residues: 101.2211 Evaluate side-chains 216 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 1.389 ------------------------------------------------------------------------------- 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: 0.7980 chunk 83 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 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: 1.6786 ------------------------------------------------------------------------------- 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 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1513 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= 0.286 Angle : 0.650 8.015 17480 Z= 0.342 Chirality : 0.043 0.219 1984 Planarity : 0.004 0.047 2315 Dihedral : 5.277 40.798 2117 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.79 % Allowed : 11.64 % Favored : 86.56 % 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: 0.04 (0.20), residues: 1438 helix: 1.45 (0.27), residues: 319 sheet: 0.57 (0.31), residues: 287 loop : -0.76 (0.19), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 171 HIS 0.008 0.002 HIS C 8 PHE 0.033 0.002 PHE E 242 TYR 0.023 0.002 TYR B 119 ARG 0.006 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 248 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 226 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: 0.7596 (t0) cc_final: 0.7374 (t0) REVERT: A 201 GLN cc_start: 0.8305 (tp40) cc_final: 0.8022 (mt0) REVERT: B 54 ARG cc_start: 0.7929 (ttp80) cc_final: 0.7355 (tmm160) REVERT: B 115 MET cc_start: 0.8532 (tpt) cc_final: 0.7934 (tpt) REVERT: B 120 GLU cc_start: 0.7272 (mm-30) cc_final: 0.7014 (pt0) REVERT: B 149 MET cc_start: 0.6830 (mmt) cc_final: 0.6587 (mmt) REVERT: C 155 MET cc_start: 0.6834 (ttm) cc_final: 0.6508 (ttm) REVERT: D 37 ASP cc_start: 0.7399 (t0) cc_final: 0.7195 (t0) REVERT: D 60 ASN cc_start: 0.8077 (t0) cc_final: 0.7684 (t0) REVERT: D 117 LYS cc_start: 0.8039 (ptpp) cc_final: 0.7700 (ptpp) REVERT: E 34 GLU cc_start: 0.7249 (tp30) cc_final: 0.6978 (tp30) REVERT: F 161 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7327 (ptmt) outliers start: 22 outliers final: 18 residues processed: 234 average time/residue: 0.2690 time to fit residues: 88.3072 Evaluate side-chains 219 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 200 time to evaluate : 1.445 ------------------------------------------------------------------------------- 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 184 LYS Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 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: 10.0000 chunk 123 optimal weight: 0.0980 chunk 100 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 148 optimal weight: 9.9990 chunk 160 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 chunk 147 optimal weight: 10.0000 chunk 50 optimal weight: 0.4980 chunk 118 optimal weight: 8.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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** ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 GLN B 27 GLN B 125 GLN B 159 HIS C 154 GLN C 182 GLN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2500 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= 0.360 Angle : 0.672 8.764 17480 Z= 0.349 Chirality : 0.045 0.226 1984 Planarity : 0.004 0.044 2315 Dihedral : 5.318 41.049 2117 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.66 % Allowed : 11.56 % Favored : 84.77 % 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: -0.29 (0.21), residues: 1438 helix: 1.53 (0.28), residues: 309 sheet: 0.31 (0.34), residues: 253 loop : -1.02 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 171 HIS 0.014 0.002 HIS C 8 PHE 0.017 0.002 PHE E 236 TYR 0.022 0.002 TYR D 119 ARG 0.006 0.001 ARG A 35 *********************** 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 260 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 215 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.7427 (mpp) cc_final: 0.7116 (mpp) REVERT: B 120 GLU cc_start: 0.7303 (mm-30) cc_final: 0.7049 (pt0) REVERT: B 149 MET cc_start: 0.6821 (mmt) cc_final: 0.6499 (mmt) REVERT: C 75 ASP cc_start: 0.5895 (m-30) cc_final: 0.5676 (m-30) REVERT: D 60 ASN cc_start: 0.8324 (t0) cc_final: 0.7752 (t0) REVERT: D 75 LYS cc_start: 0.8752 (tppt) cc_final: 0.8486 (tppp) REVERT: D 117 LYS cc_start: 0.8103 (ptpp) cc_final: 0.7621 (ptpp) REVERT: E 2 LYS cc_start: 0.7358 (ttpt) cc_final: 0.7077 (tttp) REVERT: E 109 ASP cc_start: 0.7886 (t0) cc_final: 0.7622 (t0) REVERT: F 19 ASP cc_start: 0.7730 (OUTLIER) cc_final: 0.7173 (p0) REVERT: F 161 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7064 (ptmt) REVERT: F 163 ARG cc_start: 0.7631 (mtp180) cc_final: 0.7182 (mtp180) outliers start: 45 outliers final: 28 residues processed: 243 average time/residue: 0.2570 time to fit residues: 89.6681 Evaluate side-chains 211 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 181 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 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 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 126 THR Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 194 THR 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 110 LEU 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 268 CYS Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 161 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 146 optimal weight: 8.9990 chunk 111 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 148 optimal weight: 10.0000 chunk 157 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 141 optimal weight: 10.0000 chunk 42 optimal weight: 0.6980 overall best weight: 2.2984 ------------------------------------------------------------------------------- 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** ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12909 Z= 0.324 Angle : 0.628 9.491 17480 Z= 0.325 Chirality : 0.045 0.480 1984 Planarity : 0.004 0.043 2315 Dihedral : 5.544 41.154 2117 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.34 % Allowed : 14.41 % Favored : 82.25 % 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: -0.45 (0.21), residues: 1438 helix: 1.61 (0.28), residues: 307 sheet: -0.08 (0.34), residues: 239 loop : -1.10 (0.19), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 171 HIS 0.009 0.002 HIS C 8 PHE 0.016 0.002 PHE C 92 TYR 0.021 0.002 TYR D 119 ARG 0.004 0.000 ARG A 291 *********************** 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: 41 poor density : 209 time to evaluate : 1.487 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 8 HIS cc_start: 0.7766 (t70) cc_final: 0.7172 (p-80) REVERT: A 139 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7501 (mm-30) REVERT: A 155 MET cc_start: 0.7299 (OUTLIER) cc_final: 0.6993 (mpp) REVERT: A 173 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8644 (mm) REVERT: A 213 GLN cc_start: 0.7455 (OUTLIER) cc_final: 0.6404 (mm110) REVERT: B 149 MET cc_start: 0.6864 (mmt) cc_final: 0.6497 (mmt) REVERT: C 227 MET cc_start: 0.7675 (tpt) cc_final: 0.7452 (tpt) REVERT: D 60 ASN cc_start: 0.8398 (t0) cc_final: 0.7871 (t0) REVERT: D 117 LYS cc_start: 0.8116 (ptpp) cc_final: 0.7629 (ptpp) REVERT: E 2 LYS cc_start: 0.7487 (ttpt) cc_final: 0.7170 (tttp) REVERT: E 34 GLU cc_start: 0.7489 (tp30) cc_final: 0.7225 (tp30) REVERT: E 164 LYS cc_start: 0.8164 (mmtt) cc_final: 0.7923 (ttmm) REVERT: F 143 LYS cc_start: 0.8183 (tptt) cc_final: 0.7411 (tptm) REVERT: F 161 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7105 (ptmt) outliers start: 41 outliers final: 29 residues processed: 234 average time/residue: 0.2544 time to fit residues: 85.0468 Evaluate side-chains 222 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 189 time to evaluate : 1.388 ------------------------------------------------------------------------------- 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 173 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain C residue 7 HIS Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 126 THR 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 71 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 110 LEU 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 46 ASP Chi-restraints excluded: chain F residue 49 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 131 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 0.6980 chunk 141 optimal weight: 10.0000 chunk 39 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 27 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12909 Z= 0.267 Angle : 0.597 9.915 17480 Z= 0.306 Chirality : 0.044 0.613 1984 Planarity : 0.003 0.043 2315 Dihedral : 5.151 39.865 2117 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.07 % Allowed : 14.66 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.58 (0.28), residues: 312 sheet: -0.54 (0.32), residues: 269 loop : -1.04 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 171 HIS 0.010 0.001 HIS C 8 PHE 0.017 0.002 PHE E 88 TYR 0.020 0.002 TYR D 119 ARG 0.006 0.000 ARG E 121 *********************** 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 253 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 203 time to evaluate : 1.224 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 8 HIS cc_start: 0.7786 (t70) cc_final: 0.7196 (p-80) REVERT: A 155 MET cc_start: 0.7327 (OUTLIER) cc_final: 0.7014 (mpp) REVERT: A 173 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8640 (mm) REVERT: A 213 GLN cc_start: 0.7436 (OUTLIER) cc_final: 0.6476 (mm110) REVERT: A 221 ILE cc_start: 0.8653 (mt) cc_final: 0.8403 (mt) REVERT: A 256 MET cc_start: 0.8441 (ptm) cc_final: 0.8232 (ptm) REVERT: B 115 MET cc_start: 0.8883 (tpt) cc_final: 0.8601 (tpt) REVERT: B 149 MET cc_start: 0.6815 (mmt) cc_final: 0.6489 (mmt) REVERT: C 227 MET cc_start: 0.7646 (tpt) cc_final: 0.7433 (tpt) REVERT: D 60 ASN cc_start: 0.8435 (t0) cc_final: 0.7925 (t0) REVERT: D 117 LYS cc_start: 0.8094 (ptpp) cc_final: 0.7614 (ptpp) REVERT: E 2 LYS cc_start: 0.7468 (ttpt) cc_final: 0.7130 (tttp) REVERT: E 155 MET cc_start: 0.7821 (mtm) cc_final: 0.7393 (ptp) REVERT: E 164 LYS cc_start: 0.8188 (mmtt) cc_final: 0.7916 (ttmm) REVERT: F 19 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7264 (p0) REVERT: F 143 LYS cc_start: 0.8167 (tptt) cc_final: 0.7393 (tptm) REVERT: F 161 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7053 (ptmt) outliers start: 50 outliers final: 31 residues processed: 236 average time/residue: 0.2455 time to fit residues: 82.9756 Evaluate side-chains 222 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 186 time to evaluate : 1.486 ------------------------------------------------------------------------------- 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 173 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain C residue 7 HIS Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 126 THR 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 67 ASP 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 145 ASP Chi-restraints excluded: chain E residue 194 THR 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 49 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 53 optimal weight: 0.0770 chunk 141 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 157 optimal weight: 9.9990 chunk 130 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12909 Z= 0.317 Angle : 0.620 9.538 17480 Z= 0.318 Chirality : 0.044 0.512 1984 Planarity : 0.004 0.042 2315 Dihedral : 5.250 40.301 2117 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.91 % Allowed : 14.90 % Favored : 81.19 % 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: 1.57 (0.28), residues: 306 sheet: -0.67 (0.33), residues: 243 loop : -1.12 (0.19), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 171 HIS 0.009 0.002 HIS C 8 PHE 0.023 0.002 PHE E 88 TYR 0.026 0.002 TYR D 119 ARG 0.004 0.000 ARG A 247 *********************** 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 244 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 196 time to evaluate : 1.411 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 8 HIS cc_start: 0.7709 (t70) cc_final: 0.7179 (p-80) REVERT: A 155 MET cc_start: 0.7291 (OUTLIER) cc_final: 0.6962 (mpp) REVERT: A 173 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8670 (mm) REVERT: A 213 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.6555 (mm110) REVERT: A 247 ARG cc_start: 0.7966 (mtt180) cc_final: 0.7619 (ptt180) REVERT: B 115 MET cc_start: 0.8901 (tpt) cc_final: 0.8635 (tpt) REVERT: B 149 MET cc_start: 0.6842 (mmt) cc_final: 0.6441 (mmt) REVERT: D 60 ASN cc_start: 0.8466 (t0) cc_final: 0.7997 (t0) REVERT: D 117 LYS cc_start: 0.8125 (ptpp) cc_final: 0.7637 (ptpp) REVERT: E 2 LYS cc_start: 0.7503 (ttpt) cc_final: 0.7178 (tttp) REVERT: E 34 GLU cc_start: 0.7451 (tp30) cc_final: 0.7241 (tp30) REVERT: E 164 LYS cc_start: 0.8213 (mmtt) cc_final: 0.7933 (ttmm) REVERT: F 143 LYS cc_start: 0.8213 (tptt) cc_final: 0.7467 (tptm) REVERT: F 161 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7033 (ptmt) outliers start: 48 outliers final: 38 residues processed: 224 average time/residue: 0.2598 time to fit residues: 82.5483 Evaluate side-chains 228 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 186 time to evaluate : 1.420 ------------------------------------------------------------------------------- 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 158 SER Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain C residue 7 HIS Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 117 TYR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 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 67 ASP 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 E residue 3 ILE Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 194 THR 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 E residue 268 CYS Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 117 LYS 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: 3.9990 chunk 89 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 157 optimal weight: 9.9990 chunk 98 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 97 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 217 GLN B 27 GLN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 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: 0.7621 moved from start: 0.3384 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= 0.179 Angle : 0.541 9.268 17480 Z= 0.278 Chirality : 0.042 0.490 1984 Planarity : 0.003 0.042 2315 Dihedral : 4.843 35.885 2117 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.34 % Allowed : 16.12 % Favored : 80.54 % 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: -0.42 (0.21), residues: 1438 helix: 1.82 (0.28), residues: 306 sheet: -0.54 (0.34), residues: 243 loop : -0.99 (0.19), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 171 HIS 0.011 0.001 HIS C 8 PHE 0.020 0.001 PHE E 88 TYR 0.022 0.002 TYR E 137 ARG 0.003 0.000 ARG D 163 *********************** 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 255 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 214 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 HIS cc_start: 0.7712 (t70) cc_final: 0.7194 (p-80) REVERT: A 53 GLN cc_start: 0.8138 (mm-40) cc_final: 0.7824 (mm-40) REVERT: A 155 MET cc_start: 0.7294 (OUTLIER) cc_final: 0.6994 (mpp) REVERT: A 213 GLN cc_start: 0.7353 (OUTLIER) cc_final: 0.6627 (mm110) REVERT: A 247 ARG cc_start: 0.7792 (mtt180) cc_final: 0.7532 (ptt180) REVERT: B 149 MET cc_start: 0.6807 (mmt) cc_final: 0.6503 (mmt) REVERT: C 15 LYS cc_start: 0.8736 (mttp) cc_final: 0.8521 (mmmm) REVERT: C 295 LYS cc_start: 0.8674 (mptt) cc_final: 0.8433 (mmtp) REVERT: D 60 ASN cc_start: 0.8446 (t0) cc_final: 0.8021 (t0) REVERT: D 117 LYS cc_start: 0.8050 (ptpp) cc_final: 0.7655 (ptmt) REVERT: E 2 LYS cc_start: 0.7330 (ttpt) cc_final: 0.7048 (tttp) REVERT: E 164 LYS cc_start: 0.8201 (mmtt) cc_final: 0.7908 (ttmm) REVERT: E 242 PHE cc_start: 0.4435 (OUTLIER) cc_final: 0.4115 (t80) REVERT: F 19 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7235 (p0) REVERT: F 143 LYS cc_start: 0.8150 (tptt) cc_final: 0.7370 (tptm) REVERT: F 161 LYS cc_start: 0.7769 (OUTLIER) cc_final: 0.7040 (ptmt) outliers start: 41 outliers final: 28 residues processed: 237 average time/residue: 0.2405 time to fit residues: 81.9874 Evaluate side-chains 222 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 189 time to evaluate : 1.256 ------------------------------------------------------------------------------- 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 158 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain 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 86 VAL Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 59 THR 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 145 ASP 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 256 MET Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 117 LYS Chi-restraints excluded: chain F residue 146 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: 8.9990 chunk 93 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 99 optimal weight: 0.5980 chunk 107 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 123 optimal weight: 0.0970 chunk 142 optimal weight: 20.0000 chunk 150 optimal weight: 10.0000 overall best weight: 2.5384 ------------------------------------------------------------------------------- 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: 0.7698 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 12909 Z= 0.351 Angle : 0.645 9.682 17480 Z= 0.329 Chirality : 0.045 0.490 1984 Planarity : 0.004 0.043 2315 Dihedral : 5.230 38.342 2117 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.42 % Allowed : 17.18 % Favored : 79.40 % 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: 1.68 (0.29), residues: 306 sheet: -0.71 (0.33), residues: 243 loop : -1.12 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 171 HIS 0.009 0.002 HIS C 8 PHE 0.025 0.002 PHE E 88 TYR 0.022 0.002 TYR E 137 ARG 0.004 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 232 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 190 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 HIS cc_start: 0.7767 (t70) cc_final: 0.7251 (p-80) REVERT: A 139 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7623 (mm-30) REVERT: A 155 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.6922 (mpp) REVERT: A 213 GLN cc_start: 0.7451 (OUTLIER) cc_final: 0.6639 (mm110) REVERT: A 247 ARG cc_start: 0.7845 (mtt180) cc_final: 0.7590 (ptt180) REVERT: B 149 MET cc_start: 0.6831 (mmt) cc_final: 0.6478 (mmt) REVERT: D 60 ASN cc_start: 0.8488 (t0) cc_final: 0.8075 (t0) REVERT: D 62 GLN cc_start: 0.8435 (mt0) cc_final: 0.7991 (mm-40) REVERT: D 117 LYS cc_start: 0.8140 (ptpp) cc_final: 0.7682 (ptpp) REVERT: E 2 LYS cc_start: 0.7490 (ttpt) cc_final: 0.7187 (tttp) REVERT: E 34 GLU cc_start: 0.7544 (tp30) cc_final: 0.7253 (tp30) REVERT: E 164 LYS cc_start: 0.8274 (mmtt) cc_final: 0.8032 (ttmm) REVERT: F 19 ASP cc_start: 0.7827 (OUTLIER) cc_final: 0.7046 (p0) REVERT: F 137 CYS cc_start: 0.8321 (m) cc_final: 0.8008 (m) REVERT: F 143 LYS cc_start: 0.8218 (tptt) cc_final: 0.7477 (tptm) REVERT: F 161 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7056 (ptmt) outliers start: 42 outliers final: 30 residues processed: 219 average time/residue: 0.2479 time to fit residues: 77.5845 Evaluate side-chains 219 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 185 time to evaluate : 1.284 ------------------------------------------------------------------------------- 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 158 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain C residue 7 HIS Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 110 LEU 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 256 MET Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain E residue 268 CYS Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 52 LEU 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: 1.9990 chunk 146 optimal weight: 8.9990 chunk 150 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 132 optimal weight: 0.6980 chunk 138 optimal weight: 4.9990 chunk 145 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 12909 Z= 0.311 Angle : 0.622 9.901 17480 Z= 0.319 Chirality : 0.045 0.481 1984 Planarity : 0.003 0.042 2315 Dihedral : 5.257 38.402 2117 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.75 % Allowed : 17.35 % Favored : 78.91 % 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: 1.67 (0.28), residues: 306 sheet: -0.75 (0.33), residues: 243 loop : -1.14 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 171 HIS 0.010 0.002 HIS C 8 PHE 0.022 0.002 PHE E 88 TYR 0.027 0.002 TYR E 137 ARG 0.003 0.000 ARG B 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: 46 poor density : 194 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: A 139 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7563 (mm-30) REVERT: A 155 MET cc_start: 0.7278 (OUTLIER) cc_final: 0.6941 (mpp) REVERT: A 173 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8597 (mm) REVERT: A 247 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7552 (ptt180) REVERT: B 149 MET cc_start: 0.6882 (mmt) cc_final: 0.6520 (mmt) REVERT: C 313 ASN cc_start: 0.7657 (t0) cc_final: 0.7081 (t0) REVERT: D 60 ASN cc_start: 0.8484 (t0) cc_final: 0.8082 (t0) REVERT: D 62 GLN cc_start: 0.8413 (mt0) cc_final: 0.7980 (mm-40) REVERT: D 117 LYS cc_start: 0.8126 (ptpp) cc_final: 0.7746 (ptmt) REVERT: E 2 LYS cc_start: 0.7445 (ttpt) cc_final: 0.7207 (tttp) REVERT: E 34 GLU cc_start: 0.7554 (tp30) cc_final: 0.7304 (tp30) REVERT: E 164 LYS cc_start: 0.8314 (mmtt) cc_final: 0.8064 (ttmm) REVERT: F 19 ASP cc_start: 0.7795 (OUTLIER) cc_final: 0.6986 (p0) REVERT: F 143 LYS cc_start: 0.8216 (tptt) cc_final: 0.7431 (tptm) REVERT: F 161 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7049 (ptmt) outliers start: 46 outliers final: 37 residues processed: 222 average time/residue: 0.2557 time to fit residues: 80.5719 Evaluate side-chains 222 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 180 time to evaluate : 1.365 ------------------------------------------------------------------------------- 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 158 SER Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 247 ARG 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 14 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain D residue 59 THR 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 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 256 MET Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain E residue 268 CYS 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 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: 0.0670 chunk 107 optimal weight: 6.9990 chunk 162 optimal weight: 8.9990 chunk 149 optimal weight: 10.0000 chunk 129 optimal weight: 0.7980 chunk 13 optimal weight: 0.3980 chunk 99 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 102 optimal weight: 0.6980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN E 213 GLN F 28 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12909 Z= 0.166 Angle : 0.554 9.306 17480 Z= 0.286 Chirality : 0.042 0.461 1984 Planarity : 0.003 0.042 2315 Dihedral : 4.814 32.043 2117 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.28 % Allowed : 18.81 % Favored : 78.91 % 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: 1.80 (0.28), residues: 310 sheet: -0.70 (0.32), residues: 271 loop : -1.06 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 171 HIS 0.011 0.001 HIS C 8 PHE 0.026 0.002 PHE E 88 TYR 0.025 0.002 TYR F 119 ARG 0.004 0.000 ARG B 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 238 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 210 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7598 (mm-30) REVERT: A 155 MET cc_start: 0.7290 (OUTLIER) cc_final: 0.6992 (mpp) REVERT: B 149 MET cc_start: 0.6779 (mmt) cc_final: 0.6518 (mmt) REVERT: C 131 ARG cc_start: 0.4463 (ptp-170) cc_final: 0.3534 (ptp-170) REVERT: C 155 MET cc_start: 0.5848 (tpp) cc_final: 0.5560 (tpt) REVERT: D 60 ASN cc_start: 0.8439 (t0) cc_final: 0.8021 (t0) REVERT: D 62 GLN cc_start: 0.8415 (mt0) cc_final: 0.7961 (mm-40) REVERT: D 117 LYS cc_start: 0.8027 (ptpp) cc_final: 0.7629 (ptmt) REVERT: E 2 LYS cc_start: 0.7352 (ttpt) cc_final: 0.7068 (tttt) REVERT: E 164 LYS cc_start: 0.8325 (mmtt) cc_final: 0.7998 (ttmm) REVERT: F 19 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7005 (p0) REVERT: F 149 MET cc_start: 0.6498 (mmt) cc_final: 0.6270 (mmp) REVERT: F 161 LYS cc_start: 0.7781 (ptmm) cc_final: 0.7066 (ptmt) outliers start: 28 outliers final: 19 residues processed: 227 average time/residue: 0.2587 time to fit residues: 83.7179 Evaluate side-chains 212 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 191 time to evaluate : 1.329 ------------------------------------------------------------------------------- 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 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 14 THR Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 242 PHE Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain E residue 268 CYS Chi-restraints excluded: chain F residue 19 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 113 optimal weight: 8.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 217 GLN E 213 GLN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.164649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.143130 restraints weight = 19608.427| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.63 r_work: 0.3687 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3828 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= 0.215 Angle : 0.576 8.846 17480 Z= 0.295 Chirality : 0.043 0.466 1984 Planarity : 0.003 0.041 2315 Dihedral : 4.787 31.325 2117 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.20 % Allowed : 19.63 % Favored : 78.18 % 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: 1.97 (0.28), residues: 304 sheet: -0.54 (0.34), residues: 243 loop : -1.10 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 171 HIS 0.010 0.002 HIS C 8 PHE 0.015 0.002 PHE C 69 TYR 0.021 0.002 TYR E 137 ARG 0.004 0.000 ARG B 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2913.26 seconds wall clock time: 52 minutes 42.22 seconds (3162.22 seconds total)