Starting phenix.real_space_refine on Mon Mar 18 11:46:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nog_0468/03_2024/6nog_0468.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nog_0468/03_2024/6nog_0468.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nog_0468/03_2024/6nog_0468.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nog_0468/03_2024/6nog_0468.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nog_0468/03_2024/6nog_0468.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nog_0468/03_2024/6nog_0468.pdb" } resolution = 3.9 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5986 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 292 5.49 5 S 27 5.16 5 C 8489 2.51 5 N 2751 2.21 5 O 3370 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E GLU 50": "OE1" <-> "OE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E ASP 123": "OD1" <-> "OD2" Residue "F ASP 24": "OD1" <-> "OD2" Residue "F ASP 85": "OD1" <-> "OD2" Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C ASP 90": "OD1" <-> "OD2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "G GLU 56": "OE1" <-> "OE2" Residue "G ASP 72": "OD1" <-> "OD2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D GLU 93": "OE1" <-> "OE2" Residue "D TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 93": "OE1" <-> "OE2" Residue "L ASP 52": "OD1" <-> "OD2" Residue "K GLU 16": "OE1" <-> "OE2" Residue "K GLU 56": "OE1" <-> "OE2" Residue "K GLU 69": "OE1" <-> "OE2" Residue "K ARG 80": "NH1" <-> "NH2" Residue "K TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 161": "OD1" <-> "OD2" Residue "K GLU 215": "OE1" <-> "OE2" Residue "K PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 229": "NH1" <-> "NH2" Residue "K ARG 231": "NH1" <-> "NH2" Residue "K ARG 265": "NH1" <-> "NH2" Residue "K ARG 282": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14929 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "E" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 800 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 723 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "H" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "L" Number of atoms: 593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 593 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "K" Number of atoms: 2431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2431 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 288} Chain breaks: 3 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Time building chain proxies: 7.29, per 1000 atoms: 0.49 Number of scatterers: 14929 At special positions: 0 Unit cell: (118.104, 138.32, 118.104, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 292 15.00 O 3370 8.00 N 2751 7.00 C 8489 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 6.79 Conformation dependent library (CDL) restraints added in 1.7 seconds 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2116 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 9 sheets defined 63.2% alpha, 5.5% beta 135 base pairs and 245 stacking pairs defined. Time for finding SS restraints: 5.96 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 75 removed outlier: 3.843A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA A 75 " --> pdb=" O VAL A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.700A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.913A pdb=" N ARG A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.925A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 113 removed outlier: 3.604A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 4.103A pdb=" N ILE E 130 " --> pdb=" O LEU E 126 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.768A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.417A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 4.095A pdb=" N ARG B 92 " --> pdb=" O TYR B 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.586A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 50 through 75 Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.820A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY F 94 " --> pdb=" O LEU F 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.527A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 72 removed outlier: 4.137A pdb=" N ASP C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.635A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 removed outlier: 4.026A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.986A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.747A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG G 88 " --> pdb=" O GLN G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.524A pdb=" N ASN G 94 " --> pdb=" O ASP G 90 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU G 96 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 46 removed outlier: 3.783A pdb=" N VAL D 41 " --> pdb=" O TYR D 37 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS D 46 " --> pdb=" O TYR D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 83 removed outlier: 3.653A pdb=" N SER D 60 " --> pdb=" O SER D 56 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU D 80 " --> pdb=" O GLU D 76 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N HIS D 82 " --> pdb=" O SER D 78 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR D 83 " --> pdb=" O ARG D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.504A pdb=" N ARG D 99 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU D 100 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU D 101 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 122 removed outlier: 4.504A pdb=" N THR D 119 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N CYS D 120 " --> pdb=" O LYS D 116 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TYR D 121 " --> pdb=" O ALA D 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 46 removed outlier: 3.769A pdb=" N VAL H 41 " --> pdb=" O TYR H 37 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS H 46 " --> pdb=" O TYR H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 83 removed outlier: 3.777A pdb=" N LEU H 80 " --> pdb=" O GLU H 76 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA H 81 " --> pdb=" O ALA H 77 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N HIS H 82 " --> pdb=" O SER H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 102 removed outlier: 3.965A pdb=" N THR H 96 " --> pdb=" O ARG H 92 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU H 100 " --> pdb=" O THR H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 122 removed outlier: 3.848A pdb=" N CYS H 120 " --> pdb=" O LYS H 116 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR H 122 " --> pdb=" O VAL H 118 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 35 Processing helix chain 'L' and resid 37 through 39 No H-bonds generated for 'chain 'L' and resid 37 through 39' Processing helix chain 'L' and resid 55 through 60 removed outlier: 3.577A pdb=" N TYR L 59 " --> pdb=" O LEU L 56 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN L 60 " --> pdb=" O SER L 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 33 through 48 Processing helix chain 'K' and resid 48 through 57 Processing helix chain 'K' and resid 67 through 91 Processing helix chain 'K' and resid 103 through 119 Processing helix chain 'K' and resid 140 through 151 removed outlier: 3.518A pdb=" N VAL K 144 " --> pdb=" O SER K 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 167 through 177 Processing helix chain 'K' and resid 188 through 210 Processing helix chain 'K' and resid 225 through 234 removed outlier: 3.511A pdb=" N ARG K 229 " --> pdb=" O SER K 225 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLU K 230 " --> pdb=" O GLU K 226 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG K 231 " --> pdb=" O GLU K 227 " (cutoff:3.500A) Processing helix chain 'K' and resid 246 through 258 Processing helix chain 'K' and resid 286 through 289 Processing helix chain 'K' and resid 319 through 329 removed outlier: 3.544A pdb=" N GLU K 323 " --> pdb=" O ARG K 319 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 96 through 97 removed outlier: 7.099A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.709A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA4, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.510A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'L' and resid 12 through 16 removed outlier: 3.512A pdb=" N LEU L 15 " --> pdb=" O ILE L 3 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE L 45 " --> pdb=" O LYS L 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 6 through 9 removed outlier: 3.522A pdb=" N LEU K 7 " --> pdb=" O TYR K 20 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 26 through 28 Processing sheet with id=AA9, first strand: chain 'K' and resid 216 through 220 removed outlier: 6.225A pdb=" N HIS K 182 " --> pdb=" O THR K 217 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N GLU K 219 " --> pdb=" O HIS K 182 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N GLY K 184 " --> pdb=" O GLU K 219 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N PHE K 159 " --> pdb=" O TYR K 183 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N VAL K 185 " --> pdb=" O PHE K 159 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ASP K 161 " --> pdb=" O VAL K 185 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL K 160 " --> pdb=" O PHE K 239 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE K 238 " --> pdb=" O VAL K 267 " (cutoff:3.500A) 480 hydrogen bonds defined for protein. 1407 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 350 hydrogen bonds 700 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 245 stacking parallelities Total time for adding SS restraints: 5.02 Time building geometry restraints manager: 7.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2744 1.33 - 1.45: 5049 1.45 - 1.57: 7375 1.57 - 1.69: 583 1.69 - 1.82: 47 Bond restraints: 15798 Sorted by residual: bond pdb=" N PRO G 80 " pdb=" CD PRO G 80 " ideal model delta sigma weight residual 1.473 1.422 0.051 1.40e-02 5.10e+03 1.35e+01 bond pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " ideal model delta sigma weight residual 1.422 1.495 -0.073 3.00e-02 1.11e+03 5.90e+00 bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.422 1.494 -0.072 3.00e-02 1.11e+03 5.75e+00 bond pdb=" C HIS H 49 " pdb=" N PRO H 50 " ideal model delta sigma weight residual 1.336 1.308 0.028 1.20e-02 6.94e+03 5.60e+00 bond pdb=" C GLY G 46 " pdb=" N ALA G 47 " ideal model delta sigma weight residual 1.332 1.300 0.032 1.38e-02 5.25e+03 5.22e+00 ... (remaining 15793 not shown) Histogram of bond angle deviations from ideal: 97.72 - 105.32: 1454 105.32 - 112.91: 8725 112.91 - 120.51: 7275 120.51 - 128.11: 4736 128.11 - 135.70: 411 Bond angle restraints: 22601 Sorted by residual: angle pdb=" C ARG F 23 " pdb=" N ASP F 24 " pdb=" CA ASP F 24 " ideal model delta sigma weight residual 122.46 129.87 -7.41 1.41e+00 5.03e-01 2.76e+01 angle pdb=" N GLY G 105 " pdb=" CA GLY G 105 " pdb=" C GLY G 105 " ideal model delta sigma weight residual 113.18 124.85 -11.67 2.37e+00 1.78e-01 2.43e+01 angle pdb=" C ASP G 90 " pdb=" N GLU G 91 " pdb=" CA GLU G 91 " ideal model delta sigma weight residual 120.54 127.15 -6.61 1.35e+00 5.49e-01 2.40e+01 angle pdb=" N GLY C 46 " pdb=" CA GLY C 46 " pdb=" C GLY C 46 " ideal model delta sigma weight residual 114.66 120.63 -5.97 1.24e+00 6.50e-01 2.32e+01 angle pdb=" N ASP F 24 " pdb=" CA ASP F 24 " pdb=" C ASP F 24 " ideal model delta sigma weight residual 111.30 117.58 -6.28 1.36e+00 5.41e-01 2.13e+01 ... (remaining 22596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.82: 7037 31.82 - 63.65: 1668 63.65 - 95.47: 50 95.47 - 127.29: 0 127.29 - 159.12: 3 Dihedral angle restraints: 8758 sinusoidal: 5489 harmonic: 3269 Sorted by residual: dihedral pdb=" CA ARG A 63 " pdb=" C ARG A 63 " pdb=" N LYS A 64 " pdb=" CA LYS A 64 " ideal model delta harmonic sigma weight residual -180.00 -151.77 -28.23 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA ARG E 63 " pdb=" C ARG E 63 " pdb=" N LYS E 64 " pdb=" CA LYS E 64 " ideal model delta harmonic sigma weight residual 180.00 -155.74 -24.26 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual 180.00 -157.19 -22.81 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 8755 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2041 0.071 - 0.142: 445 0.142 - 0.213: 63 0.213 - 0.284: 12 0.284 - 0.355: 8 Chirality restraints: 2569 Sorted by residual: chirality pdb=" CG LEU K 107 " pdb=" CB LEU K 107 " pdb=" CD1 LEU K 107 " pdb=" CD2 LEU K 107 " both_signs ideal model delta sigma weight residual False -2.59 -2.94 0.36 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CB ILE K 151 " pdb=" CA ILE K 151 " pdb=" CG1 ILE K 151 " pdb=" CG2 ILE K 151 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CA LEU K 299 " pdb=" N LEU K 299 " pdb=" C LEU K 299 " pdb=" CB LEU K 299 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.68e+00 ... (remaining 2566 not shown) Planarity restraints: 1855 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU H 102 " -0.048 5.00e-02 4.00e+02 7.15e-02 8.19e+00 pdb=" N PRO H 103 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO H 103 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO H 103 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE K 266 " 0.013 2.00e-02 2.50e+03 2.70e-02 7.31e+00 pdb=" C ILE K 266 " -0.047 2.00e-02 2.50e+03 pdb=" O ILE K 266 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL K 267 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 91 " -0.036 2.00e-02 2.50e+03 1.59e-02 6.96e+00 pdb=" N9 DA I 91 " 0.030 2.00e-02 2.50e+03 pdb=" C8 DA I 91 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DA I 91 " 0.011 2.00e-02 2.50e+03 pdb=" C5 DA I 91 " -0.009 2.00e-02 2.50e+03 pdb=" C6 DA I 91 " -0.005 2.00e-02 2.50e+03 pdb=" N6 DA I 91 " -0.012 2.00e-02 2.50e+03 pdb=" N1 DA I 91 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 91 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DA I 91 " 0.009 2.00e-02 2.50e+03 pdb=" C4 DA I 91 " 0.009 2.00e-02 2.50e+03 ... (remaining 1852 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2724 2.77 - 3.30: 12860 3.30 - 3.84: 28212 3.84 - 4.37: 30410 4.37 - 4.90: 43971 Nonbonded interactions: 118177 Sorted by model distance: nonbonded pdb=" OG1 THR K 154 " pdb=" OD1 ASP K 155 " model vdw 2.239 2.440 nonbonded pdb=" O TYR G 39 " pdb=" OG SER H 78 " model vdw 2.274 2.440 nonbonded pdb=" O ASP K 161 " pdb=" OG SER K 164 " model vdw 2.293 2.440 nonbonded pdb=" O TYR C 39 " pdb=" OG SER D 78 " model vdw 2.302 2.440 nonbonded pdb=" OD1 ASN K 242 " pdb=" OG SER K 268 " model vdw 2.327 2.440 ... (remaining 118172 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' selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 25 through 102) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 14 through 117) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 32 through 124) } 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 group one per residue 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 4.200 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 42.560 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 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:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 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 : 0.009 0.073 15798 Z= 0.556 Angle : 1.118 12.415 22601 Z= 0.660 Chirality : 0.062 0.355 2569 Planarity : 0.008 0.072 1855 Dihedral : 26.638 159.118 6642 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.84 % Allowed : 7.67 % Favored : 91.49 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.63 % 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: -1.83 (0.22), residues: 1098 helix: -1.16 (0.17), residues: 634 sheet: 0.01 (0.56), residues: 79 loop : -1.28 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP K 208 HIS 0.008 0.003 HIS E 113 PHE 0.032 0.004 PHE K 159 TYR 0.030 0.004 TYR K 27 ARG 0.010 0.001 ARG K 203 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 386 time to evaluate : 1.467 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: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8253 (mt) cc_final: 0.7951 (mt) REVERT: A 80 THR cc_start: 0.8160 (t) cc_final: 0.7703 (t) REVERT: A 86 SER cc_start: 0.8987 (m) cc_final: 0.8662 (t) REVERT: A 108 ASN cc_start: 0.8699 (t0) cc_final: 0.8482 (t0) REVERT: E 41 TYR cc_start: 0.8336 (m-80) cc_final: 0.8041 (m-80) REVERT: F 25 ASN cc_start: 0.8048 (m110) cc_final: 0.7809 (m-40) REVERT: F 63 GLU cc_start: 0.8364 (tt0) cc_final: 0.8164 (tt0) REVERT: F 88 TYR cc_start: 0.8458 (m-10) cc_final: 0.8190 (m-10) REVERT: C 68 ASN cc_start: 0.8668 (t0) cc_final: 0.8417 (t0) REVERT: G 68 ASN cc_start: 0.8479 (m-40) cc_final: 0.7210 (m-40) REVERT: G 74 LYS cc_start: 0.8702 (mttm) cc_final: 0.8368 (mtmm) REVERT: D 79 ARG cc_start: 0.8552 (ttp-110) cc_final: 0.8153 (mtm-85) REVERT: D 105 GLU cc_start: 0.7944 (tp30) cc_final: 0.7667 (tm-30) REVERT: D 109 HIS cc_start: 0.8099 (m90) cc_final: 0.7611 (m-70) REVERT: D 121 TYR cc_start: 0.8029 (t80) cc_final: 0.7672 (t80) REVERT: H 59 MET cc_start: 0.9006 (tpp) cc_final: 0.8615 (tpp) REVERT: H 85 LYS cc_start: 0.8632 (mtmt) cc_final: 0.8415 (mmtt) REVERT: L 6 LYS cc_start: 0.8458 (tttt) cc_final: 0.7744 (mmtt) REVERT: L 8 LEU cc_start: 0.4657 (mm) cc_final: 0.4074 (tt) REVERT: L 29 LYS cc_start: 0.8544 (mttt) cc_final: 0.8217 (tptp) REVERT: L 39 ASP cc_start: 0.7768 (p0) cc_final: 0.7447 (m-30) REVERT: L 71 LEU cc_start: 0.6967 (mt) cc_final: 0.6582 (mt) REVERT: K 27 TYR cc_start: 0.4974 (m-80) cc_final: 0.3654 (t80) REVERT: K 49 PRO cc_start: 0.6899 (Cg_exo) cc_final: 0.6654 (Cg_endo) outliers start: 8 outliers final: 1 residues processed: 389 average time/residue: 0.3894 time to fit residues: 197.6321 Evaluate side-chains 185 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 184 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 5.9990 chunk 103 optimal weight: 0.4980 chunk 57 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 69 optimal weight: 0.1980 chunk 55 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 79 optimal weight: 8.9990 chunk 123 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN F 25 ASN G 24 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN D 49 HIS D 84 ASN D 95 GLN H 47 GLN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 251 HIS K 252 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 15798 Z= 0.221 Angle : 0.637 7.341 22601 Z= 0.372 Chirality : 0.037 0.178 2569 Planarity : 0.005 0.056 1855 Dihedral : 29.237 159.162 4429 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 4.20 % Allowed : 15.02 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.59 (0.25), residues: 1098 helix: 1.01 (0.20), residues: 648 sheet: 0.69 (0.59), residues: 79 loop : -0.65 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP K 228 HIS 0.009 0.001 HIS K 117 PHE 0.031 0.002 PHE L 4 TYR 0.012 0.002 TYR B 51 ARG 0.007 0.001 ARG F 78 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 203 time to evaluate : 1.182 Fit side-chains revert: symmetry clash REVERT: E 41 TYR cc_start: 0.8528 (m-80) cc_final: 0.8257 (m-80) REVERT: E 60 LEU cc_start: 0.8962 (mt) cc_final: 0.8756 (mt) REVERT: E 90 MET cc_start: 0.8907 (mmp) cc_final: 0.8699 (mmm) REVERT: E 105 GLU cc_start: 0.7942 (tp30) cc_final: 0.7724 (tp30) REVERT: F 25 ASN cc_start: 0.8075 (m-40) cc_final: 0.7612 (m110) REVERT: F 35 ARG cc_start: 0.8961 (ttm-80) cc_final: 0.8734 (ttm-80) REVERT: F 63 GLU cc_start: 0.8313 (tt0) cc_final: 0.8029 (tt0) REVERT: F 82 THR cc_start: 0.8785 (p) cc_final: 0.8579 (m) REVERT: C 61 GLU cc_start: 0.8365 (tt0) cc_final: 0.8118 (tt0) REVERT: G 16 THR cc_start: 0.9418 (OUTLIER) cc_final: 0.8958 (p) REVERT: G 56 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7784 (tm-30) REVERT: G 74 LYS cc_start: 0.8748 (mttm) cc_final: 0.8454 (mtmm) REVERT: D 121 TYR cc_start: 0.8247 (t80) cc_final: 0.7995 (t80) REVERT: H 34 LYS cc_start: 0.8884 (ttmm) cc_final: 0.8521 (mmtm) REVERT: H 85 LYS cc_start: 0.8666 (mtmt) cc_final: 0.8452 (mmtt) REVERT: H 91 SER cc_start: 0.8683 (t) cc_final: 0.8367 (p) REVERT: L 6 LYS cc_start: 0.8460 (tttt) cc_final: 0.7719 (mmtt) REVERT: L 8 LEU cc_start: 0.4781 (mm) cc_final: 0.4372 (tt) REVERT: L 12 THR cc_start: 0.5432 (OUTLIER) cc_final: 0.5062 (t) REVERT: L 39 ASP cc_start: 0.7626 (p0) cc_final: 0.7189 (t0) REVERT: K 31 HIS cc_start: 0.4955 (OUTLIER) cc_final: 0.4367 (m90) REVERT: K 49 PRO cc_start: 0.6852 (Cg_exo) cc_final: 0.6609 (Cg_endo) REVERT: K 252 GLN cc_start: 0.8879 (mt0) cc_final: 0.8662 (mm-40) outliers start: 40 outliers final: 20 residues processed: 229 average time/residue: 0.2679 time to fit residues: 89.0267 Evaluate side-chains 177 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 154 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain K residue 31 HIS Chi-restraints excluded: chain K residue 157 ASP Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 289 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 chunk 133 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 122 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 99 optimal weight: 8.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 85 GLN F 25 ASN C 38 ASN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN D 47 GLN ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 HIS K 113 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 15798 Z= 0.407 Angle : 0.714 7.360 22601 Z= 0.406 Chirality : 0.042 0.169 2569 Planarity : 0.005 0.043 1855 Dihedral : 29.256 154.422 4428 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 5.04 % Allowed : 17.86 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.83 (0.25), residues: 1098 helix: 1.15 (0.20), residues: 660 sheet: 0.70 (0.57), residues: 79 loop : -0.50 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP K 228 HIS 0.010 0.002 HIS C 31 PHE 0.016 0.002 PHE C 25 TYR 0.032 0.002 TYR D 83 ARG 0.006 0.001 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 156 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.9278 (m) cc_final: 0.8947 (t) REVERT: E 105 GLU cc_start: 0.8005 (tp30) cc_final: 0.7703 (tp30) REVERT: B 84 MET cc_start: 0.8367 (tpp) cc_final: 0.8107 (tpp) REVERT: F 25 ASN cc_start: 0.8618 (m110) cc_final: 0.8005 (m110) REVERT: F 63 GLU cc_start: 0.8376 (tt0) cc_final: 0.8126 (tt0) REVERT: C 61 GLU cc_start: 0.8443 (tt0) cc_final: 0.8050 (tt0) REVERT: C 84 GLN cc_start: 0.9079 (OUTLIER) cc_final: 0.8077 (tt0) REVERT: G 56 GLU cc_start: 0.8318 (tm-30) cc_final: 0.8114 (tm-30) REVERT: G 64 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7801 (tm-30) REVERT: G 74 LYS cc_start: 0.8985 (mttm) cc_final: 0.8707 (mtmm) REVERT: G 110 ASN cc_start: 0.8239 (OUTLIER) cc_final: 0.7902 (m110) REVERT: D 35 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8199 (tp30) REVERT: D 76 GLU cc_start: 0.9198 (tp30) cc_final: 0.8742 (tp30) REVERT: H 34 LYS cc_start: 0.8840 (ttmm) cc_final: 0.8512 (mmtm) REVERT: H 35 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.8011 (tm-30) REVERT: H 85 LYS cc_start: 0.8824 (mtmt) cc_final: 0.8485 (mmtt) REVERT: L 6 LYS cc_start: 0.8481 (tttt) cc_final: 0.7626 (mptt) REVERT: L 8 LEU cc_start: 0.4732 (mm) cc_final: 0.4155 (tt) REVERT: L 29 LYS cc_start: 0.8506 (mttt) cc_final: 0.8278 (tptt) REVERT: L 33 LYS cc_start: 0.6453 (OUTLIER) cc_final: 0.6174 (ptmt) REVERT: L 39 ASP cc_start: 0.7676 (p0) cc_final: 0.7179 (t0) REVERT: K 20 TYR cc_start: 0.5760 (m-10) cc_final: 0.4934 (m-80) REVERT: K 27 TYR cc_start: 0.5139 (m-80) cc_final: 0.4718 (m-10) REVERT: K 31 HIS cc_start: 0.4638 (OUTLIER) cc_final: 0.4199 (m90) REVERT: K 252 GLN cc_start: 0.8892 (mt0) cc_final: 0.8675 (mm-40) outliers start: 48 outliers final: 26 residues processed: 187 average time/residue: 0.2499 time to fit residues: 69.6357 Evaluate side-chains 173 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 142 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 85 GLN Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain L residue 33 LYS Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain K residue 31 HIS Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 317 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 83 optimal weight: 7.9990 chunk 124 optimal weight: 8.9990 chunk 131 optimal weight: 6.9990 chunk 117 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 109 optimal weight: 8.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 GLN K 31 HIS K 109 HIS K 113 GLN ** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.4781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 15798 Z= 0.309 Angle : 0.633 8.939 22601 Z= 0.368 Chirality : 0.038 0.163 2569 Planarity : 0.004 0.041 1855 Dihedral : 29.101 154.890 4428 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 5.78 % Allowed : 18.38 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.13 (0.26), residues: 1098 helix: 1.39 (0.20), residues: 661 sheet: 0.72 (0.58), residues: 79 loop : -0.34 (0.35), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP K 228 HIS 0.019 0.002 HIS K 31 PHE 0.012 0.002 PHE K 326 TYR 0.023 0.002 TYR D 83 ARG 0.005 0.001 ARG E 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 155 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.9226 (m) cc_final: 0.8824 (t) REVERT: E 105 GLU cc_start: 0.8013 (tp30) cc_final: 0.7674 (tp30) REVERT: E 120 MET cc_start: 0.8085 (mtp) cc_final: 0.7757 (mtp) REVERT: B 84 MET cc_start: 0.8224 (tpp) cc_final: 0.8015 (tpp) REVERT: F 63 GLU cc_start: 0.8278 (tt0) cc_final: 0.8049 (tt0) REVERT: C 61 GLU cc_start: 0.8488 (tt0) cc_final: 0.8147 (tt0) REVERT: C 84 GLN cc_start: 0.9067 (OUTLIER) cc_final: 0.8131 (tt0) REVERT: G 56 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8073 (tm-30) REVERT: G 64 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7767 (tm-30) REVERT: G 74 LYS cc_start: 0.8974 (mttm) cc_final: 0.8693 (mtmm) REVERT: D 35 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8225 (tp30) REVERT: D 76 GLU cc_start: 0.9222 (tp30) cc_final: 0.8827 (tp30) REVERT: H 59 MET cc_start: 0.9005 (tpp) cc_final: 0.8799 (tpp) REVERT: H 85 LYS cc_start: 0.8831 (mtmt) cc_final: 0.8476 (mmtt) REVERT: H 116 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8589 (ttmm) REVERT: L 6 LYS cc_start: 0.8503 (tttt) cc_final: 0.7632 (mptt) REVERT: L 15 LEU cc_start: 0.6654 (mp) cc_final: 0.5348 (tt) REVERT: L 29 LYS cc_start: 0.8429 (mttt) cc_final: 0.8144 (tmtt) REVERT: L 39 ASP cc_start: 0.7506 (p0) cc_final: 0.7000 (t0) REVERT: L 69 LEU cc_start: 0.5974 (tp) cc_final: 0.5696 (tp) REVERT: K 20 TYR cc_start: 0.6030 (m-10) cc_final: 0.5229 (m-80) REVERT: K 149 ASP cc_start: 0.8033 (m-30) cc_final: 0.7637 (p0) REVERT: K 216 TYR cc_start: 0.4524 (p90) cc_final: 0.4272 (p90) REVERT: K 238 ILE cc_start: 0.9116 (OUTLIER) cc_final: 0.8777 (mp) REVERT: K 252 GLN cc_start: 0.8903 (mt0) cc_final: 0.8665 (mm-40) outliers start: 55 outliers final: 37 residues processed: 193 average time/residue: 0.2335 time to fit residues: 67.9096 Evaluate side-chains 180 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 140 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain K residue 113 GLN Chi-restraints excluded: chain K residue 117 HIS Chi-restraints excluded: chain K residue 151 ILE Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 289 THR Chi-restraints excluded: chain K residue 317 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 chunk 33 optimal weight: 0.0670 chunk 44 optimal weight: 0.7980 overall best weight: 1.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 85 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 GLN ** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 234 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.5095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15798 Z= 0.260 Angle : 0.604 7.603 22601 Z= 0.352 Chirality : 0.036 0.153 2569 Planarity : 0.004 0.037 1855 Dihedral : 29.031 153.404 4428 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 5.25 % Allowed : 20.27 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.30 (0.26), residues: 1098 helix: 1.53 (0.20), residues: 660 sheet: 0.68 (0.60), residues: 79 loop : -0.24 (0.35), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP K 228 HIS 0.006 0.001 HIS C 31 PHE 0.011 0.001 PHE K 202 TYR 0.016 0.002 TYR D 83 ARG 0.004 0.000 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 151 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.9132 (m) cc_final: 0.8725 (t) REVERT: E 105 GLU cc_start: 0.8057 (tp30) cc_final: 0.7706 (tp30) REVERT: E 120 MET cc_start: 0.8035 (mtp) cc_final: 0.7682 (mtp) REVERT: E 133 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7706 (mt-10) REVERT: F 63 GLU cc_start: 0.8233 (tt0) cc_final: 0.8009 (tt0) REVERT: C 61 GLU cc_start: 0.8449 (tt0) cc_final: 0.8106 (tt0) REVERT: C 95 LYS cc_start: 0.8679 (mttt) cc_final: 0.8217 (mttm) REVERT: G 64 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7777 (tm-30) REVERT: G 74 LYS cc_start: 0.8984 (mttm) cc_final: 0.8713 (mtmm) REVERT: D 35 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8204 (mm-30) REVERT: D 76 GLU cc_start: 0.9213 (tp30) cc_final: 0.8783 (tp30) REVERT: D 121 TYR cc_start: 0.8707 (t80) cc_final: 0.8464 (t80) REVERT: H 85 LYS cc_start: 0.8904 (mtmt) cc_final: 0.8503 (mmtt) REVERT: H 116 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8569 (ttmm) REVERT: L 6 LYS cc_start: 0.8489 (tttt) cc_final: 0.7638 (mptt) REVERT: L 39 ASP cc_start: 0.7473 (p0) cc_final: 0.6954 (t0) REVERT: K 20 TYR cc_start: 0.6134 (m-10) cc_final: 0.5578 (m-80) REVERT: K 238 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8769 (mp) REVERT: K 243 PHE cc_start: 0.7671 (OUTLIER) cc_final: 0.7396 (m-10) outliers start: 50 outliers final: 33 residues processed: 188 average time/residue: 0.2420 time to fit residues: 68.8518 Evaluate side-chains 168 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 131 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain E residue 85 GLN Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain K residue 55 MET Chi-restraints excluded: chain K residue 151 ILE Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 243 PHE Chi-restraints excluded: chain K residue 289 THR Chi-restraints excluded: chain K residue 317 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 131 optimal weight: 6.9990 chunk 109 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 126 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.5529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 15798 Z= 0.380 Angle : 0.678 9.542 22601 Z= 0.386 Chirality : 0.040 0.166 2569 Planarity : 0.005 0.036 1855 Dihedral : 29.229 151.747 4428 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 6.20 % Allowed : 20.27 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.95 (0.25), residues: 1098 helix: 1.24 (0.20), residues: 666 sheet: 0.71 (0.60), residues: 80 loop : -0.46 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 228 HIS 0.007 0.001 HIS C 31 PHE 0.020 0.002 PHE E 84 TYR 0.030 0.002 TYR D 83 ARG 0.004 0.001 ARG L 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 134 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 SER cc_start: 0.8576 (OUTLIER) cc_final: 0.8079 (t) REVERT: A 87 SER cc_start: 0.9236 (m) cc_final: 0.8893 (t) REVERT: E 105 GLU cc_start: 0.8119 (tp30) cc_final: 0.7779 (tp30) REVERT: E 120 MET cc_start: 0.8154 (mtp) cc_final: 0.7848 (mtp) REVERT: E 133 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7765 (mt-10) REVERT: C 61 GLU cc_start: 0.8469 (tt0) cc_final: 0.8144 (tt0) REVERT: C 84 GLN cc_start: 0.9124 (OUTLIER) cc_final: 0.8176 (tt0) REVERT: G 64 GLU cc_start: 0.8383 (tm-30) cc_final: 0.7859 (tm-30) REVERT: G 74 LYS cc_start: 0.9027 (mttm) cc_final: 0.8720 (mtmm) REVERT: D 35 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8109 (mm-30) REVERT: D 76 GLU cc_start: 0.9238 (tp30) cc_final: 0.8835 (tp30) REVERT: H 59 MET cc_start: 0.9084 (tpp) cc_final: 0.8526 (tpp) REVERT: H 85 LYS cc_start: 0.8848 (mtmt) cc_final: 0.8455 (mmtt) REVERT: H 116 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8606 (ttmm) REVERT: L 6 LYS cc_start: 0.8447 (tttt) cc_final: 0.7666 (mptt) REVERT: L 39 ASP cc_start: 0.7377 (p0) cc_final: 0.6581 (t0) REVERT: K 149 ASP cc_start: 0.8073 (m-30) cc_final: 0.7674 (p0) REVERT: K 181 HIS cc_start: 0.7548 (OUTLIER) cc_final: 0.7212 (t-90) REVERT: K 238 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8852 (mp) REVERT: K 243 PHE cc_start: 0.7676 (OUTLIER) cc_final: 0.7388 (m-10) outliers start: 59 outliers final: 42 residues processed: 184 average time/residue: 0.2402 time to fit residues: 66.2014 Evaluate side-chains 173 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 124 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 85 GLN Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain K residue 55 MET Chi-restraints excluded: chain K residue 117 HIS Chi-restraints excluded: chain K residue 142 ASP Chi-restraints excluded: chain K residue 157 ASP Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 181 HIS Chi-restraints excluded: chain K residue 217 THR Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 243 PHE Chi-restraints excluded: chain K residue 289 THR Chi-restraints excluded: chain K residue 317 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 131 optimal weight: 6.9990 chunk 82 optimal weight: 0.0570 chunk 79 optimal weight: 0.9980 chunk 60 optimal weight: 0.0670 chunk 81 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 GLN ** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.5634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15798 Z= 0.234 Angle : 0.594 8.269 22601 Z= 0.346 Chirality : 0.036 0.154 2569 Planarity : 0.004 0.038 1855 Dihedral : 29.034 150.383 4428 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.73 % Allowed : 21.64 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.34 (0.26), residues: 1098 helix: 1.56 (0.20), residues: 663 sheet: 0.65 (0.58), residues: 82 loop : -0.23 (0.35), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 43 HIS 0.004 0.001 HIS A 113 PHE 0.010 0.001 PHE K 326 TYR 0.022 0.002 TYR D 83 ARG 0.005 0.000 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 143 time to evaluate : 1.250 Fit side-chains revert: symmetry clash REVERT: A 87 SER cc_start: 0.9085 (m) cc_final: 0.8653 (t) REVERT: E 105 GLU cc_start: 0.8145 (tp30) cc_final: 0.7750 (tp30) REVERT: E 120 MET cc_start: 0.8039 (mtp) cc_final: 0.7701 (mtp) REVERT: B 84 MET cc_start: 0.8182 (tpp) cc_final: 0.7902 (tpp) REVERT: C 84 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.8150 (tt0) REVERT: C 95 LYS cc_start: 0.8708 (mttt) cc_final: 0.8229 (mttm) REVERT: G 64 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8114 (tm-30) REVERT: G 74 LYS cc_start: 0.9016 (mttm) cc_final: 0.8716 (mtmm) REVERT: D 35 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8144 (mm-30) REVERT: D 76 GLU cc_start: 0.9169 (tp30) cc_final: 0.8762 (tp30) REVERT: H 59 MET cc_start: 0.9028 (tpp) cc_final: 0.8621 (tpp) REVERT: H 85 LYS cc_start: 0.8797 (mtmt) cc_final: 0.8398 (mmtt) REVERT: H 116 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8576 (ttmm) REVERT: L 6 LYS cc_start: 0.8466 (tttt) cc_final: 0.7668 (mptt) REVERT: L 39 ASP cc_start: 0.7449 (p0) cc_final: 0.6893 (t0) REVERT: K 181 HIS cc_start: 0.7649 (OUTLIER) cc_final: 0.7400 (t-90) REVERT: K 238 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8815 (mp) REVERT: K 252 GLN cc_start: 0.8996 (mt0) cc_final: 0.8659 (mm-40) outliers start: 45 outliers final: 29 residues processed: 174 average time/residue: 0.2498 time to fit residues: 64.4209 Evaluate side-chains 173 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 140 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain K residue 117 HIS Chi-restraints excluded: chain K residue 181 HIS Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 317 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 50.0000 chunk 39 optimal weight: 0.8980 chunk 25 optimal weight: 0.0170 chunk 83 optimal weight: 0.5980 chunk 89 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 12 optimal weight: 0.4980 chunk 103 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 125 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 85 GLN E 108 ASN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 109 HIS ** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 234 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.5793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15798 Z= 0.173 Angle : 0.574 13.971 22601 Z= 0.331 Chirality : 0.034 0.181 2569 Planarity : 0.004 0.040 1855 Dihedral : 28.812 149.007 4428 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.52 % Allowed : 23.95 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.64 (0.26), residues: 1098 helix: 1.83 (0.20), residues: 657 sheet: 0.84 (0.58), residues: 82 loop : -0.17 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 43 HIS 0.006 0.001 HIS A 113 PHE 0.008 0.001 PHE A 84 TYR 0.013 0.001 TYR D 121 ARG 0.008 0.000 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 159 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.9250 (t0) cc_final: 0.8973 (t0) REVERT: E 105 GLU cc_start: 0.8163 (tp30) cc_final: 0.7755 (tp30) REVERT: E 120 MET cc_start: 0.8009 (mtp) cc_final: 0.7635 (mtp) REVERT: C 84 GLN cc_start: 0.9086 (OUTLIER) cc_final: 0.8149 (tt0) REVERT: G 74 LYS cc_start: 0.8980 (mttm) cc_final: 0.8721 (mtmm) REVERT: D 35 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8219 (mm-30) REVERT: H 59 MET cc_start: 0.8964 (tpp) cc_final: 0.8594 (tpp) REVERT: H 85 LYS cc_start: 0.8763 (mtmt) cc_final: 0.8382 (mmtt) REVERT: L 6 LYS cc_start: 0.8453 (tttt) cc_final: 0.7747 (mmtm) REVERT: L 39 ASP cc_start: 0.7347 (p0) cc_final: 0.6914 (t0) REVERT: K 202 PHE cc_start: 0.7503 (t80) cc_final: 0.7230 (t80) REVERT: K 252 GLN cc_start: 0.8956 (mt0) cc_final: 0.8632 (mm-40) outliers start: 24 outliers final: 11 residues processed: 171 average time/residue: 0.3022 time to fit residues: 77.9447 Evaluate side-chains 161 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 149 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain E residue 85 GLN Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain K residue 317 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 10.0000 chunk 125 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 115 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 chunk 80 optimal weight: 40.0000 chunk 129 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 85 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 GLN ** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 234 ASN K 315 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.5917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 15798 Z= 0.351 Angle : 0.659 10.998 22601 Z= 0.372 Chirality : 0.039 0.157 2569 Planarity : 0.004 0.036 1855 Dihedral : 29.109 149.166 4428 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.94 % Allowed : 23.32 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.31 (0.25), residues: 1098 helix: 1.55 (0.20), residues: 666 sheet: 0.84 (0.57), residues: 82 loop : -0.37 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP K 228 HIS 0.006 0.001 HIS C 31 PHE 0.013 0.002 PHE K 159 TYR 0.026 0.002 TYR D 40 ARG 0.007 0.001 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 142 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 SER cc_start: 0.8533 (OUTLIER) cc_final: 0.8311 (p) REVERT: E 105 GLU cc_start: 0.8129 (tp30) cc_final: 0.7763 (tp30) REVERT: E 120 MET cc_start: 0.8063 (mtp) cc_final: 0.7729 (mtp) REVERT: F 23 ARG cc_start: 0.7408 (ptm-80) cc_final: 0.6876 (ttm-80) REVERT: C 84 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.8170 (tt0) REVERT: G 74 LYS cc_start: 0.9019 (mttm) cc_final: 0.8733 (mtmm) REVERT: D 35 GLU cc_start: 0.8507 (mm-30) cc_final: 0.7997 (mm-30) REVERT: H 59 MET cc_start: 0.9109 (tpp) cc_final: 0.8769 (tpp) REVERT: H 85 LYS cc_start: 0.8853 (mtmt) cc_final: 0.8406 (mmtt) REVERT: L 6 LYS cc_start: 0.8459 (tttt) cc_final: 0.7615 (mptt) REVERT: L 39 ASP cc_start: 0.7307 (p0) cc_final: 0.6865 (t0) REVERT: K 243 PHE cc_start: 0.7512 (OUTLIER) cc_final: 0.7292 (m-10) REVERT: K 252 GLN cc_start: 0.9015 (mt0) cc_final: 0.8628 (mm-40) outliers start: 28 outliers final: 23 residues processed: 163 average time/residue: 0.2484 time to fit residues: 60.6130 Evaluate side-chains 159 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 133 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain K residue 117 HIS Chi-restraints excluded: chain K residue 243 PHE Chi-restraints excluded: chain K residue 317 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 50.0000 chunk 61 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 135 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 83 optimal weight: 0.2980 chunk 66 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 85 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 109 HIS ** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 234 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.5997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15798 Z= 0.205 Angle : 0.588 11.362 22601 Z= 0.337 Chirality : 0.035 0.152 2569 Planarity : 0.004 0.039 1855 Dihedral : 28.908 148.803 4428 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.00 % Allowed : 24.89 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.59 (0.26), residues: 1098 helix: 1.79 (0.20), residues: 658 sheet: 1.00 (0.57), residues: 82 loop : -0.25 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 43 HIS 0.005 0.001 HIS K 213 PHE 0.009 0.001 PHE K 326 TYR 0.019 0.002 TYR B 88 ARG 0.007 0.000 ARG L 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 147 time to evaluate : 1.228 Fit side-chains REVERT: A 108 ASN cc_start: 0.9255 (t0) cc_final: 0.8975 (t0) REVERT: E 105 GLU cc_start: 0.8121 (tp30) cc_final: 0.7742 (tp30) REVERT: E 120 MET cc_start: 0.8016 (mtp) cc_final: 0.7678 (mtp) REVERT: F 23 ARG cc_start: 0.7387 (ptm-80) cc_final: 0.6769 (ttm-80) REVERT: F 24 ASP cc_start: 0.6574 (t0) cc_final: 0.5231 (t0) REVERT: F 25 ASN cc_start: 0.8779 (m110) cc_final: 0.8093 (m110) REVERT: F 84 MET cc_start: 0.7900 (tpp) cc_final: 0.7640 (tpp) REVERT: C 84 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.8166 (tt0) REVERT: G 64 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7956 (tm-30) REVERT: G 74 LYS cc_start: 0.9007 (mttm) cc_final: 0.8722 (mtmm) REVERT: D 35 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8164 (mm-30) REVERT: H 59 MET cc_start: 0.9018 (tpp) cc_final: 0.8726 (tpp) REVERT: H 85 LYS cc_start: 0.8812 (mtmt) cc_final: 0.8364 (mmtt) REVERT: L 6 LYS cc_start: 0.8435 (tttt) cc_final: 0.7607 (mptt) REVERT: L 39 ASP cc_start: 0.7370 (p0) cc_final: 0.6934 (t0) REVERT: K 252 GLN cc_start: 0.9033 (mt0) cc_final: 0.8640 (mm-40) REVERT: K 291 MET cc_start: 0.6776 (tpp) cc_final: 0.6531 (tpp) outliers start: 19 outliers final: 14 residues processed: 157 average time/residue: 0.2671 time to fit residues: 61.0178 Evaluate side-chains 159 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 144 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain K residue 317 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 chunk 45 optimal weight: 0.4980 chunk 110 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 85 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 109 HIS ** K 213 HIS ** 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 = 0.3681 r_free = 0.3681 target = 0.099462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.067033 restraints weight = 43583.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.067690 restraints weight = 34154.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.067697 restraints weight = 25586.882| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.6094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 15798 Z= 0.195 Angle : 0.589 12.540 22601 Z= 0.336 Chirality : 0.035 0.154 2569 Planarity : 0.004 0.036 1855 Dihedral : 28.815 148.260 4428 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.10 % Allowed : 25.00 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.71 (0.26), residues: 1098 helix: 1.88 (0.20), residues: 657 sheet: 1.13 (0.58), residues: 82 loop : -0.22 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 43 HIS 0.009 0.001 HIS H 82 PHE 0.008 0.001 PHE K 326 TYR 0.015 0.001 TYR B 88 ARG 0.007 0.000 ARG L 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2448.83 seconds wall clock time: 44 minutes 59.02 seconds (2699.02 seconds total)