Starting phenix.real_space_refine on Fri Feb 16 04:36:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g57_29735/02_2024/8g57_29735.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g57_29735/02_2024/8g57_29735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g57_29735/02_2024/8g57_29735.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g57_29735/02_2024/8g57_29735.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g57_29735/02_2024/8g57_29735.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g57_29735/02_2024/8g57_29735.pdb" } resolution = 3.07 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= 0.001 sd= 0.395 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 300 5.49 5 S 22 5.16 5 C 8104 2.51 5 N 2706 2.21 5 O 3270 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K ASP 201": "OD1" <-> "OD2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14402 Number of models: 1 Model: "" Number of chains: 11 Chain: "K" Number of atoms: 2037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2037 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 252} Chain breaks: 2 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'TRP:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 54 Chain: "A" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 867 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 666 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 83} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 846 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 105} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 740 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 667 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 874 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 112} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "H" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 739 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 3093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 3093 Classifications: {'DNA': 150} Link IDs: {'rna3p': 149} Chain: "J" Number of atoms: 3057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 3057 Classifications: {'DNA': 150} Link IDs: {'rna3p': 149} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N LEU B 22 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU B 22 " occ=0.00 residue: pdb=" N ARG B 23 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG B 23 " occ=0.00 residue: pdb=" N LYS C 13 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS C 13 " occ=0.00 residue: pdb=" N ALA C 14 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA C 14 " occ=0.00 residue: pdb=" N ARG G 11 " occ=0.00 ... (3 atoms not shown) pdb=" CB ARG G 11 " occ=0.00 residue: pdb=" N ALA G 12 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA G 12 " occ=0.00 Time building chain proxies: 8.06, per 1000 atoms: 0.56 Number of scatterers: 14402 At special positions: 0 Unit cell: (113.4, 141.48, 128.52, 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 22 16.00 P 300 15.00 O 3270 8.00 N 2706 7.00 C 8104 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: 6.98 Conformation dependent library (CDL) restraints added in 1.8 seconds 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1988 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 11 sheets defined 60.0% alpha, 4.7% beta 149 base pairs and 258 stacking pairs defined. Time for finding SS restraints: 6.56 Creating SS restraints... Processing helix chain 'K' and resid 27 through 43 removed outlier: 3.828A pdb=" N GLU K 31 " --> pdb=" O PRO K 27 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG K 32 " --> pdb=" O GLU K 28 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS K 33 " --> pdb=" O GLU K 29 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TRP K 42 " --> pdb=" O ALA K 38 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN K 43 " --> pdb=" O ARG K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 60 removed outlier: 4.395A pdb=" N ALA K 58 " --> pdb=" O ILE K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 76 Processing helix chain 'K' and resid 82 through 87 Processing helix chain 'K' and resid 92 through 105 removed outlier: 3.579A pdb=" N GLN K 100 " --> pdb=" O MET K 96 " (cutoff:3.500A) Processing helix chain 'K' and resid 117 through 122 Processing helix chain 'K' and resid 125 through 127 No H-bonds generated for 'chain 'K' and resid 125 through 127' Processing helix chain 'K' and resid 193 through 206 Processing helix chain 'K' and resid 223 through 232 removed outlier: 4.648A pdb=" N LEU K 227 " --> pdb=" O GLY K 223 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR K 229 " --> pdb=" O LEU K 225 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS K 230 " --> pdb=" O PRO K 226 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG K 231 " --> pdb=" O LEU K 227 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG K 232 " --> pdb=" O ALA K 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 257 through 270 removed outlier: 4.147A pdb=" N THR K 263 " --> pdb=" O ASP K 259 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG K 264 " --> pdb=" O GLU K 260 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS K 268 " --> pdb=" O ARG K 264 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU K 269 " --> pdb=" O LEU K 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.582A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 74 removed outlier: 3.609A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.619A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.675A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 125 removed outlier: 3.592A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 56 removed outlier: 3.615A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.604A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.584A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.678A 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 49 through 76 removed outlier: 3.966A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.596A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 removed outlier: 3.894A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.569A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.518A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 35 through 46 Processing helix chain 'H' and resid 52 through 80 removed outlier: 3.677A pdb=" N GLU H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.532A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 121 Processing sheet with id=AA1, first strand: chain 'K' and resid 129 through 131 removed outlier: 6.454A pdb=" N VAL K 47 " --> pdb=" O PHE K 109 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N VAL K 111 " --> pdb=" O VAL K 47 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N PHE K 49 " --> pdb=" O VAL K 111 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE K 211 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N SER K 210 " --> pdb=" O VAL K 237 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N VAL K 239 " --> pdb=" O SER K 210 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N THR K 212 " --> pdb=" O VAL K 239 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE K 238 " --> pdb=" O ILE K 254 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 147 through 149 removed outlier: 7.715A pdb=" N LEU K 181 " --> pdb=" O THR K 162 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA4, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA5, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.634A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA7, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA8, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.045A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.556A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.876A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'G' and resid 77 through 78 443 hydrogen bonds defined for protein. 1302 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 381 hydrogen bonds 758 hydrogen bond angles 0 basepair planarities 149 basepair parallelities 258 stacking parallelities Total time for adding SS restraints: 5.37 Time building geometry restraints manager: 7.44 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: 2942 1.33 - 1.45: 4639 1.45 - 1.57: 7049 1.57 - 1.69: 597 1.69 - 1.81: 37 Bond restraints: 15264 Sorted by residual: bond pdb=" CE1 HIS K 249 " pdb=" NE2 HIS K 249 " ideal model delta sigma weight residual 1.321 1.362 -0.041 1.00e-02 1.00e+04 1.68e+01 bond pdb=" CE1 HIS K 246 " pdb=" NE2 HIS K 246 " ideal model delta sigma weight residual 1.321 1.361 -0.040 1.00e-02 1.00e+04 1.63e+01 bond pdb=" C GLU K 202 " pdb=" O GLU K 202 " ideal model delta sigma weight residual 1.237 1.276 -0.040 1.17e-02 7.31e+03 1.15e+01 bond pdb=" C1' DG I 169 " pdb=" N9 DG I 169 " ideal model delta sigma weight residual 1.460 1.397 0.063 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C1' DA J 1 " pdb=" N9 DA J 1 " ideal model delta sigma weight residual 1.460 1.398 0.062 2.00e-02 2.50e+03 9.61e+00 ... (remaining 15259 not shown) Histogram of bond angle deviations from ideal: 98.50 - 105.61: 1526 105.61 - 112.71: 8462 112.71 - 119.82: 5257 119.82 - 126.93: 5881 126.93 - 134.03: 791 Bond angle restraints: 21917 Sorted by residual: angle pdb=" C ALA K 250 " pdb=" CA ALA K 250 " pdb=" CB ALA K 250 " ideal model delta sigma weight residual 116.53 108.70 7.83 1.47e+00 4.63e-01 2.84e+01 angle pdb=" O ALA K 250 " pdb=" C ALA K 250 " pdb=" N ASP K 251 " ideal model delta sigma weight residual 121.65 125.55 -3.90 8.30e-01 1.45e+00 2.21e+01 angle pdb=" N GLU K 202 " pdb=" CA GLU K 202 " pdb=" C GLU K 202 " ideal model delta sigma weight residual 111.28 106.52 4.76 1.09e+00 8.42e-01 1.91e+01 angle pdb=" C PHE K 24 " pdb=" N ASP K 25 " pdb=" CA ASP K 25 " ideal model delta sigma weight residual 121.80 132.27 -10.47 2.44e+00 1.68e-01 1.84e+01 angle pdb=" N ALA K 207 " pdb=" CA ALA K 207 " pdb=" C ALA K 207 " ideal model delta sigma weight residual 109.96 116.90 -6.94 1.68e+00 3.54e-01 1.71e+01 ... (remaining 21912 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.44: 7009 34.44 - 68.88: 1403 68.88 - 103.32: 10 103.32 - 137.77: 1 137.77 - 172.21: 1 Dihedral angle restraints: 8424 sinusoidal: 5349 harmonic: 3075 Sorted by residual: dihedral pdb=" CA PRO K 287 " pdb=" C PRO K 287 " pdb=" N PRO K 288 " pdb=" CA PRO K 288 " ideal model delta harmonic sigma weight residual -180.00 -157.22 -22.78 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA LEU B 22 " pdb=" C LEU B 22 " pdb=" N ARG B 23 " pdb=" CA ARG B 23 " ideal model delta harmonic sigma weight residual 180.00 158.82 21.18 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" C4' DT J 115 " pdb=" C3' DT J 115 " pdb=" O3' DT J 115 " pdb=" P DC J 116 " ideal model delta sinusoidal sigma weight residual 220.00 47.79 172.21 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 8421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2182 0.053 - 0.106: 287 0.106 - 0.158: 34 0.158 - 0.211: 2 0.211 - 0.264: 3 Chirality restraints: 2508 Sorted by residual: chirality pdb=" CA PRO K 288 " pdb=" N PRO K 288 " pdb=" C PRO K 288 " pdb=" CB PRO K 288 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA GLU K 202 " pdb=" N GLU K 202 " pdb=" C GLU K 202 " pdb=" CB GLU K 202 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA PRO A 38 " pdb=" N PRO A 38 " pdb=" C PRO A 38 " pdb=" CB PRO A 38 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 2505 not shown) Planarity restraints: 1749 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO K 287 " 0.080 5.00e-02 4.00e+02 1.24e-01 2.46e+01 pdb=" N PRO K 288 " -0.215 5.00e-02 4.00e+02 pdb=" CA PRO K 288 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO K 288 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU K 289 " -0.050 5.00e-02 4.00e+02 7.56e-02 9.14e+00 pdb=" N PRO K 290 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO K 290 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO K 290 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 42 " -0.038 5.00e-02 4.00e+02 5.82e-02 5.43e+00 pdb=" N PRO A 43 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 43 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 43 " -0.032 5.00e-02 4.00e+02 ... (remaining 1746 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.33: 12 2.33 - 2.97: 6043 2.97 - 3.61: 21507 3.61 - 4.26: 36856 4.26 - 4.90: 54275 Nonbonded interactions: 118693 Sorted by model distance: nonbonded pdb=" NH2 ARG K 220 " pdb=" O GLY A 12 " model vdw 1.682 2.520 nonbonded pdb=" NE ARG K 220 " pdb=" O THR A 11 " model vdw 1.976 2.520 nonbonded pdb=" OG SER E 57 " pdb=" OE1 GLU E 59 " model vdw 2.113 2.440 nonbonded pdb=" N2 DG I 79 " pdb=" O2 DC J 93 " model vdw 2.189 2.496 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 65 " model vdw 2.237 2.440 ... (remaining 118688 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 36 through 134) selection = (chain 'E' and ((resid 36 through 39 and (name N or name CA or name C or name O \ or name CB )) or resid 40 through 133 or (resid 134 and (name N or name CA or na \ me C or name O or name CB )))) } ncs_group { reference = (chain 'B' and (resid 19 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 102)) selection = (chain 'F' and ((resid 19 through 21 and (name N or name CA or name C or name O \ or name CB )) or resid 22 through 102)) } ncs_group { reference = (chain 'C' and ((resid 11 through 12 and (name N or name CA or name C or name O \ or name CB )) or resid 13 through 120)) selection = (chain 'G' and resid 11 through 120) } ncs_group { reference = (chain 'D' and resid 31 through 125) selection = (chain 'H' and (resid 28 through 121 or (resid 122 and (name N or name CA or nam \ e C or name O or name CB )))) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.610 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 45.100 Find NCS groups from input model: 0.500 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 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 : 0.004 0.063 15264 Z= 0.224 Angle : 0.646 10.470 21917 Z= 0.402 Chirality : 0.037 0.264 2508 Planarity : 0.006 0.124 1749 Dihedral : 25.922 172.206 6436 Min Nonbonded Distance : 1.682 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.86 % Allowed : 3.07 % Favored : 96.07 % Rotamer: Outliers : 0.12 % Allowed : 0.59 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.11 (0.26), residues: 1043 helix: 1.23 (0.22), residues: 599 sheet: -2.10 (0.82), residues: 42 loop : -1.91 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP K 35 HIS 0.003 0.001 HIS K 249 PHE 0.010 0.001 PHE C 25 TYR 0.016 0.001 TYR F 88 ARG 0.007 0.001 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 353 time to evaluate : 1.112 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8265 (tt0) cc_final: 0.7712 (tt0) REVERT: A 107 THR cc_start: 0.9464 (m) cc_final: 0.9212 (m) REVERT: B 27 GLN cc_start: 0.9130 (mm-40) cc_final: 0.8753 (mm-40) REVERT: B 68 ASP cc_start: 0.8574 (m-30) cc_final: 0.8321 (m-30) REVERT: B 77 LYS cc_start: 0.9321 (mmtp) cc_final: 0.9059 (mmtm) REVERT: D 68 ASP cc_start: 0.8570 (t70) cc_final: 0.7924 (t0) REVERT: D 85 LYS cc_start: 0.9349 (mmtm) cc_final: 0.9032 (mmtt) REVERT: E 90 MET cc_start: 0.8600 (mmp) cc_final: 0.8368 (mmm) REVERT: F 45 ARG cc_start: 0.8691 (ttt90) cc_final: 0.8446 (ttt90) REVERT: G 15 LYS cc_start: 0.8853 (mtpt) cc_final: 0.8618 (mtpp) REVERT: G 76 THR cc_start: 0.9131 (p) cc_final: 0.8889 (t) REVERT: G 90 ASP cc_start: 0.8440 (t0) cc_final: 0.8205 (t0) REVERT: H 65 ASP cc_start: 0.8946 (t0) cc_final: 0.8713 (t0) REVERT: H 105 LYS cc_start: 0.7941 (mtmt) cc_final: 0.7701 (mtmt) outliers start: 1 outliers final: 0 residues processed: 354 average time/residue: 0.3647 time to fit residues: 168.8109 Evaluate side-chains 294 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 103 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 119 optimal weight: 5.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 224 ASN ** K 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN B 25 ASN B 93 GLN D 49 HIS F 27 GLN G 73 ASN H 92 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15264 Z= 0.223 Angle : 0.586 13.182 21917 Z= 0.334 Chirality : 0.035 0.246 2508 Planarity : 0.006 0.119 1749 Dihedral : 29.324 172.344 4453 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.67 % Allowed : 3.36 % Favored : 95.97 % Rotamer: Outliers : 1.90 % Allowed : 11.18 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.27), residues: 1043 helix: 1.69 (0.22), residues: 613 sheet: -2.08 (0.91), residues: 36 loop : -1.73 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 35 HIS 0.008 0.001 HIS K 95 PHE 0.023 0.001 PHE K 109 TYR 0.014 0.001 TYR F 51 ARG 0.007 0.001 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 309 time to evaluate : 1.117 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: A 73 GLU cc_start: 0.8222 (tt0) cc_final: 0.7784 (tt0) REVERT: A 76 GLN cc_start: 0.8687 (pp30) cc_final: 0.8263 (pp30) REVERT: B 27 GLN cc_start: 0.9136 (mm-40) cc_final: 0.8826 (mm-40) REVERT: B 77 LYS cc_start: 0.9323 (mmtp) cc_final: 0.9054 (mmtt) REVERT: D 68 ASP cc_start: 0.8597 (t70) cc_final: 0.7986 (t0) REVERT: D 85 LYS cc_start: 0.9347 (mmtm) cc_final: 0.9036 (mmtt) REVERT: E 129 ARG cc_start: 0.8250 (tpp80) cc_final: 0.7995 (tpt-90) REVERT: F 67 ARG cc_start: 0.8597 (ttp-110) cc_final: 0.8314 (ttp80) REVERT: G 15 LYS cc_start: 0.8708 (mtpt) cc_final: 0.8432 (mtpp) REVERT: G 74 LYS cc_start: 0.9450 (mmtt) cc_final: 0.9161 (mmmm) REVERT: G 76 THR cc_start: 0.9078 (p) cc_final: 0.8835 (t) REVERT: G 104 GLN cc_start: 0.8658 (mm110) cc_final: 0.8364 (mm110) REVERT: H 65 ASP cc_start: 0.8917 (t0) cc_final: 0.8694 (t0) REVERT: H 90 GLU cc_start: 0.8403 (mp0) cc_final: 0.7205 (mp0) REVERT: H 102 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7270 (mm-30) outliers start: 16 outliers final: 11 residues processed: 317 average time/residue: 0.3607 time to fit residues: 151.2315 Evaluate side-chains 297 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 286 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 113 GLN Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 255 HIS Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain H residue 43 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 268 HIS F 27 GLN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15264 Z= 0.242 Angle : 0.584 12.552 21917 Z= 0.331 Chirality : 0.036 0.249 2508 Planarity : 0.005 0.121 1749 Dihedral : 29.402 172.563 4453 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.58 % Allowed : 3.26 % Favored : 96.16 % Rotamer: Outliers : 3.09 % Allowed : 13.44 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 (0.27), residues: 1043 helix: 1.96 (0.22), residues: 614 sheet: -1.38 (1.01), residues: 35 loop : -1.63 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 276 HIS 0.005 0.001 HIS E 39 PHE 0.018 0.001 PHE K 124 TYR 0.013 0.001 TYR F 51 ARG 0.008 0.001 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 296 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8208 (tt0) cc_final: 0.7823 (tt0) REVERT: B 27 GLN cc_start: 0.9126 (mm-40) cc_final: 0.8801 (mm-40) REVERT: B 77 LYS cc_start: 0.9312 (mmtp) cc_final: 0.9060 (mmtt) REVERT: C 36 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8773 (mtmm) REVERT: D 68 ASP cc_start: 0.8620 (t70) cc_final: 0.8037 (t0) REVERT: D 85 LYS cc_start: 0.9335 (mmtm) cc_final: 0.9002 (mmtt) REVERT: E 129 ARG cc_start: 0.8278 (tpp80) cc_final: 0.8035 (tpp80) REVERT: F 67 ARG cc_start: 0.8592 (ttp-110) cc_final: 0.8329 (ttp80) REVERT: G 15 LYS cc_start: 0.8637 (mtpt) cc_final: 0.8345 (mtpp) REVERT: G 64 GLU cc_start: 0.8739 (tm-30) cc_final: 0.8522 (tm-30) REVERT: G 72 ASP cc_start: 0.7894 (m-30) cc_final: 0.7658 (m-30) REVERT: G 74 LYS cc_start: 0.9431 (mmtt) cc_final: 0.9148 (mmmm) REVERT: G 76 THR cc_start: 0.9041 (p) cc_final: 0.8781 (t) REVERT: G 89 ASN cc_start: 0.9197 (m-40) cc_final: 0.8778 (m-40) REVERT: H 65 ASP cc_start: 0.8947 (t0) cc_final: 0.8727 (t0) REVERT: H 105 LYS cc_start: 0.8032 (mtmm) cc_final: 0.7772 (mtmm) outliers start: 26 outliers final: 19 residues processed: 308 average time/residue: 0.3428 time to fit residues: 140.6927 Evaluate side-chains 300 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 280 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 204 SER Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 255 HIS Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 77 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 0.2980 chunk 57 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 76 GLN F 27 GLN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15264 Z= 0.300 Angle : 0.603 13.094 21917 Z= 0.341 Chirality : 0.037 0.238 2508 Planarity : 0.005 0.123 1749 Dihedral : 29.587 172.345 4453 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.48 % Allowed : 3.16 % Favored : 96.36 % Rotamer: Outliers : 3.45 % Allowed : 13.32 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.87 (0.27), residues: 1043 helix: 1.97 (0.22), residues: 617 sheet: -1.26 (0.96), residues: 35 loop : -1.62 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 35 HIS 0.003 0.001 HIS E 39 PHE 0.012 0.001 PHE C 25 TYR 0.013 0.001 TYR F 51 ARG 0.008 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 288 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8374 (tt0) cc_final: 0.7970 (tt0) REVERT: B 27 GLN cc_start: 0.9098 (mm-40) cc_final: 0.8752 (mm-40) REVERT: C 36 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8788 (mtmm) REVERT: C 99 ARG cc_start: 0.8389 (ptp-110) cc_final: 0.7992 (ptp-110) REVERT: D 68 ASP cc_start: 0.8659 (t70) cc_final: 0.8099 (t0) REVERT: D 85 LYS cc_start: 0.9329 (mmtm) cc_final: 0.8966 (mmtt) REVERT: E 129 ARG cc_start: 0.8265 (tpp80) cc_final: 0.8040 (tpp80) REVERT: G 15 LYS cc_start: 0.8640 (mtpt) cc_final: 0.8173 (mtpp) REVERT: G 64 GLU cc_start: 0.8814 (tm-30) cc_final: 0.8592 (tm-30) REVERT: G 76 THR cc_start: 0.9028 (p) cc_final: 0.8758 (t) REVERT: G 89 ASN cc_start: 0.9208 (m-40) cc_final: 0.8776 (m-40) REVERT: G 104 GLN cc_start: 0.8803 (mm110) cc_final: 0.8514 (mm110) REVERT: H 65 ASP cc_start: 0.8953 (t0) cc_final: 0.8716 (t0) REVERT: H 105 LYS cc_start: 0.8161 (mtmm) cc_final: 0.7899 (mtmm) outliers start: 29 outliers final: 21 residues processed: 301 average time/residue: 0.3410 time to fit residues: 137.2459 Evaluate side-chains 297 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 275 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 204 SER Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 255 HIS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 0.6980 chunk 1 optimal weight: 0.0370 chunk 95 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 65 optimal weight: 0.1980 chunk 114 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 76 GLN E 125 GLN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15264 Z= 0.165 Angle : 0.573 11.987 21917 Z= 0.321 Chirality : 0.035 0.246 2508 Planarity : 0.005 0.123 1749 Dihedral : 29.482 173.849 4453 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.97 % Favored : 96.64 % Rotamer: Outliers : 2.14 % Allowed : 15.70 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.05 (0.27), residues: 1043 helix: 2.10 (0.21), residues: 623 sheet: -1.22 (0.92), residues: 35 loop : -1.57 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 35 HIS 0.004 0.001 HIS E 39 PHE 0.007 0.001 PHE A 67 TYR 0.014 0.001 TYR K 257 ARG 0.008 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 299 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8540 (pm20) cc_final: 0.8307 (pm20) REVERT: A 73 GLU cc_start: 0.8329 (tt0) cc_final: 0.7955 (tt0) REVERT: C 36 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8772 (mtmm) REVERT: C 99 ARG cc_start: 0.8380 (ptp-110) cc_final: 0.8032 (ptp-110) REVERT: D 68 ASP cc_start: 0.8654 (t70) cc_final: 0.8119 (t0) REVERT: D 85 LYS cc_start: 0.9339 (mmtm) cc_final: 0.9041 (mmtt) REVERT: E 129 ARG cc_start: 0.8239 (tpp80) cc_final: 0.8035 (tpp80) REVERT: F 45 ARG cc_start: 0.8517 (ttt90) cc_final: 0.8290 (ttt90) REVERT: G 15 LYS cc_start: 0.8621 (mtpt) cc_final: 0.8152 (mtpp) REVERT: G 61 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8294 (tp30) REVERT: G 64 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8558 (tm-30) REVERT: G 76 THR cc_start: 0.8959 (p) cc_final: 0.8706 (t) REVERT: G 89 ASN cc_start: 0.9125 (m-40) cc_final: 0.8738 (m-40) REVERT: H 44 GLN cc_start: 0.8602 (tt0) cc_final: 0.8371 (tt0) REVERT: H 102 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7357 (mm-30) REVERT: H 105 LYS cc_start: 0.7992 (mtmm) cc_final: 0.7589 (mtmm) outliers start: 18 outliers final: 10 residues processed: 305 average time/residue: 0.3511 time to fit residues: 142.9429 Evaluate side-chains 293 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 282 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 255 HIS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 77 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 31 optimal weight: 0.5980 chunk 127 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 218 GLN ** K 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15264 Z= 0.303 Angle : 0.605 13.610 21917 Z= 0.342 Chirality : 0.037 0.227 2508 Planarity : 0.005 0.102 1749 Dihedral : 29.637 172.659 4453 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.07 % Favored : 96.55 % Rotamer: Outliers : 2.85 % Allowed : 16.17 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.96 (0.27), residues: 1043 helix: 2.02 (0.21), residues: 630 sheet: -1.34 (0.90), residues: 36 loop : -1.66 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP K 35 HIS 0.003 0.001 HIS E 39 PHE 0.010 0.001 PHE C 25 TYR 0.012 0.001 TYR F 51 ARG 0.006 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 281 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8395 (tt0) cc_final: 0.8030 (tt0) REVERT: C 36 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8803 (mtmm) REVERT: C 99 ARG cc_start: 0.8427 (ptp-110) cc_final: 0.8044 (ptp-110) REVERT: D 68 ASP cc_start: 0.8686 (t70) cc_final: 0.8142 (t0) REVERT: D 85 LYS cc_start: 0.9321 (mmtm) cc_final: 0.9024 (mmtt) REVERT: E 129 ARG cc_start: 0.8264 (tpp80) cc_final: 0.8018 (tpp80) REVERT: F 45 ARG cc_start: 0.8522 (ttt90) cc_final: 0.8227 (ttt90) REVERT: G 15 LYS cc_start: 0.8631 (mtpt) cc_final: 0.8250 (mtmm) REVERT: G 64 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8572 (tm-30) REVERT: G 76 THR cc_start: 0.8982 (p) cc_final: 0.8711 (t) REVERT: G 89 ASN cc_start: 0.9210 (m-40) cc_final: 0.8760 (m-40) REVERT: G 104 GLN cc_start: 0.8781 (mm110) cc_final: 0.8510 (mm110) REVERT: H 105 LYS cc_start: 0.8141 (mtmm) cc_final: 0.7791 (mtmm) outliers start: 24 outliers final: 18 residues processed: 292 average time/residue: 0.3406 time to fit residues: 132.5980 Evaluate side-chains 294 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 275 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 197 LEU Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 245 LYS Chi-restraints excluded: chain K residue 249 HIS Chi-restraints excluded: chain K residue 255 HIS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 77 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 93 optimal weight: 0.3980 chunk 107 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 127 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 77 optimal weight: 0.3980 chunk 58 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15264 Z= 0.181 Angle : 0.582 13.584 21917 Z= 0.329 Chirality : 0.035 0.238 2508 Planarity : 0.005 0.108 1749 Dihedral : 29.597 173.125 4453 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.88 % Favored : 96.74 % Rotamer: Outliers : 1.90 % Allowed : 17.36 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.02 (0.27), residues: 1043 helix: 2.08 (0.21), residues: 629 sheet: -1.00 (0.94), residues: 35 loop : -1.67 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 35 HIS 0.003 0.001 HIS E 39 PHE 0.007 0.001 PHE K 24 TYR 0.009 0.001 TYR F 51 ARG 0.006 0.000 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 285 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8406 (tt0) cc_final: 0.8061 (tt0) REVERT: C 36 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8772 (mtmm) REVERT: C 99 ARG cc_start: 0.8391 (ptp-110) cc_final: 0.8006 (ptp-110) REVERT: D 68 ASP cc_start: 0.8674 (t70) cc_final: 0.8143 (t0) REVERT: D 85 LYS cc_start: 0.9334 (mmtm) cc_final: 0.9030 (mmtt) REVERT: E 129 ARG cc_start: 0.8231 (tpp80) cc_final: 0.8021 (tpp80) REVERT: E 133 GLU cc_start: 0.8347 (mp0) cc_final: 0.8124 (mp0) REVERT: F 45 ARG cc_start: 0.8500 (ttt90) cc_final: 0.8146 (ttt90) REVERT: G 15 LYS cc_start: 0.8623 (mtpt) cc_final: 0.8301 (mtmm) REVERT: G 64 GLU cc_start: 0.8817 (tm-30) cc_final: 0.8570 (tm-30) REVERT: G 76 THR cc_start: 0.8950 (p) cc_final: 0.8676 (t) REVERT: G 89 ASN cc_start: 0.9175 (m-40) cc_final: 0.8717 (m-40) REVERT: G 104 GLN cc_start: 0.8755 (mm110) cc_final: 0.8484 (mm110) REVERT: H 102 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7697 (mm-30) outliers start: 16 outliers final: 14 residues processed: 294 average time/residue: 0.3534 time to fit residues: 138.0836 Evaluate side-chains 295 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 280 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 197 LEU Chi-restraints excluded: chain K residue 204 SER Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 245 LYS Chi-restraints excluded: chain K residue 255 HIS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 77 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 62 optimal weight: 0.3980 chunk 11 optimal weight: 6.9990 chunk 100 optimal weight: 0.2980 chunk 115 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 242 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15264 Z= 0.177 Angle : 0.573 14.704 21917 Z= 0.323 Chirality : 0.035 0.226 2508 Planarity : 0.005 0.108 1749 Dihedral : 29.507 173.998 4453 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.07 % Favored : 96.55 % Rotamer: Outliers : 1.78 % Allowed : 17.72 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.10 (0.27), residues: 1043 helix: 2.11 (0.21), residues: 632 sheet: -0.77 (0.97), residues: 35 loop : -1.63 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 35 HIS 0.003 0.001 HIS K 95 PHE 0.006 0.001 PHE A 67 TYR 0.009 0.001 TYR C 57 ARG 0.007 0.000 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 290 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8392 (tt0) cc_final: 0.8042 (tt0) REVERT: B 84 MET cc_start: 0.8695 (mmm) cc_final: 0.7901 (mmm) REVERT: C 36 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8763 (mtmm) REVERT: C 99 ARG cc_start: 0.8377 (ptp-110) cc_final: 0.7987 (ptp-110) REVERT: D 68 ASP cc_start: 0.8657 (t70) cc_final: 0.8146 (t0) REVERT: D 85 LYS cc_start: 0.9338 (mmtm) cc_final: 0.9040 (mmtt) REVERT: E 133 GLU cc_start: 0.8289 (mp0) cc_final: 0.8060 (mp0) REVERT: G 15 LYS cc_start: 0.8688 (mtpt) cc_final: 0.8298 (mtmm) REVERT: G 61 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8279 (tp30) REVERT: G 64 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8569 (tm-30) REVERT: G 76 THR cc_start: 0.8900 (p) cc_final: 0.8636 (t) REVERT: G 89 ASN cc_start: 0.9114 (m-40) cc_final: 0.8730 (m-40) REVERT: H 102 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7570 (mm-30) outliers start: 15 outliers final: 11 residues processed: 297 average time/residue: 0.3507 time to fit residues: 139.0577 Evaluate side-chains 290 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 278 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 197 LEU Chi-restraints excluded: chain K residue 249 HIS Chi-restraints excluded: chain K residue 255 HIS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 77 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 36 optimal weight: 0.5980 chunk 107 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15264 Z= 0.277 Angle : 0.603 14.465 21917 Z= 0.339 Chirality : 0.037 0.225 2508 Planarity : 0.005 0.108 1749 Dihedral : 29.616 172.976 4453 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.45 % Favored : 96.26 % Rotamer: Outliers : 1.90 % Allowed : 18.31 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.10 (0.27), residues: 1043 helix: 2.07 (0.22), residues: 625 sheet: -0.95 (0.94), residues: 36 loop : -1.47 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 276 HIS 0.005 0.001 HIS K 246 PHE 0.015 0.001 PHE K 124 TYR 0.010 0.001 TYR H 80 ARG 0.006 0.000 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 283 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8482 (tt0) cc_final: 0.8147 (tt0) REVERT: C 36 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8761 (mtmm) REVERT: C 99 ARG cc_start: 0.8425 (ptp-110) cc_final: 0.8045 (ptp-110) REVERT: D 68 ASP cc_start: 0.8660 (t70) cc_final: 0.8215 (t0) REVERT: D 85 LYS cc_start: 0.9338 (mmtm) cc_final: 0.9060 (mmtt) REVERT: E 129 ARG cc_start: 0.8652 (tpp80) cc_final: 0.8165 (tpt90) REVERT: E 133 GLU cc_start: 0.8219 (mp0) cc_final: 0.8004 (mp0) REVERT: G 15 LYS cc_start: 0.8705 (mtpt) cc_final: 0.8322 (mtmm) REVERT: G 64 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8558 (tm-30) REVERT: G 76 THR cc_start: 0.8910 (p) cc_final: 0.8664 (t) REVERT: G 89 ASN cc_start: 0.9186 (m-40) cc_final: 0.8718 (m-40) REVERT: G 104 GLN cc_start: 0.8786 (mm110) cc_final: 0.8525 (mm110) REVERT: H 102 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7638 (mm-30) outliers start: 16 outliers final: 14 residues processed: 293 average time/residue: 0.3514 time to fit residues: 137.4700 Evaluate side-chains 293 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 278 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 197 LEU Chi-restraints excluded: chain K residue 249 HIS Chi-restraints excluded: chain K residue 255 HIS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 77 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 224 ASN ** K 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15264 Z= 0.224 Angle : 0.602 14.370 21917 Z= 0.338 Chirality : 0.036 0.227 2508 Planarity : 0.005 0.104 1749 Dihedral : 29.618 173.111 4453 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.16 % Favored : 96.55 % Rotamer: Outliers : 1.90 % Allowed : 18.91 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.10 (0.27), residues: 1043 helix: 2.08 (0.22), residues: 625 sheet: -0.82 (0.95), residues: 36 loop : -1.48 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 276 HIS 0.006 0.001 HIS K 246 PHE 0.010 0.001 PHE K 49 TYR 0.013 0.001 TYR H 80 ARG 0.010 0.000 ARG D 33 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 279 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8466 (tt0) cc_final: 0.8129 (tt0) REVERT: C 36 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8761 (mtmm) REVERT: C 99 ARG cc_start: 0.8414 (ptp-110) cc_final: 0.8039 (ptp-110) REVERT: D 68 ASP cc_start: 0.8681 (t70) cc_final: 0.8153 (t0) REVERT: D 85 LYS cc_start: 0.9340 (mmtm) cc_final: 0.9062 (mmtt) REVERT: E 120 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8417 (mtm) REVERT: E 129 ARG cc_start: 0.8651 (tpp80) cc_final: 0.8175 (tpt90) REVERT: E 133 GLU cc_start: 0.8224 (mp0) cc_final: 0.8003 (mp0) REVERT: G 15 LYS cc_start: 0.8706 (mtpt) cc_final: 0.8323 (mtmm) REVERT: G 64 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8528 (tm-30) REVERT: G 76 THR cc_start: 0.8905 (p) cc_final: 0.8659 (t) REVERT: G 89 ASN cc_start: 0.9167 (m-40) cc_final: 0.8730 (m-40) REVERT: H 102 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7243 (mm-30) REVERT: H 105 LYS cc_start: 0.8106 (mtmm) cc_final: 0.7752 (mtmm) outliers start: 16 outliers final: 14 residues processed: 289 average time/residue: 0.3383 time to fit residues: 130.6609 Evaluate side-chains 294 residues out of total 894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 278 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 197 LEU Chi-restraints excluded: chain K residue 249 HIS Chi-restraints excluded: chain K residue 255 HIS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 77 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.5980 chunk 15 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 13 optimal weight: 0.0170 chunk 19 optimal weight: 8.9990 chunk 92 optimal weight: 0.0040 chunk 5 optimal weight: 50.0000 chunk 75 optimal weight: 1.9990 overall best weight: 0.6632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 100 GLN ** K 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.094271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.059616 restraints weight = 32747.609| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 2.10 r_work: 0.2617 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15264 Z= 0.188 Angle : 0.592 14.932 21917 Z= 0.332 Chirality : 0.035 0.218 2508 Planarity : 0.005 0.101 1749 Dihedral : 29.582 173.439 4453 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.26 % Favored : 96.45 % Rotamer: Outliers : 1.78 % Allowed : 19.26 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.21 (0.27), residues: 1043 helix: 2.17 (0.22), residues: 621 sheet: -0.32 (0.89), residues: 40 loop : -1.47 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 276 HIS 0.004 0.001 HIS K 246 PHE 0.017 0.001 PHE K 124 TYR 0.013 0.001 TYR K 257 ARG 0.016 0.000 ARG A 8 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3400.85 seconds wall clock time: 61 minutes 45.63 seconds (3705.63 seconds total)