Starting phenix.real_space_refine on Fri Jan 19 21:13:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e32_27854/01_2024/8e32_27854_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e32_27854/01_2024/8e32_27854.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e32_27854/01_2024/8e32_27854_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e32_27854/01_2024/8e32_27854_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e32_27854/01_2024/8e32_27854_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e32_27854/01_2024/8e32_27854.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e32_27854/01_2024/8e32_27854.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e32_27854/01_2024/8e32_27854_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e32_27854/01_2024/8e32_27854_neut_trim_updated.pdb" } resolution = 2.35 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= -0.014 sd= 0.785 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: 7 Type Number sf(0) Gaussians P 3019 5.49 5 S 28 5.16 5 C 34675 2.51 5 N 13708 2.21 5 O 22616 1.98 5 F 1 1.80 5 H 41852 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K GLU 35": "OE1" <-> "OE2" Residue "K GLU 82": "OE1" <-> "OE2" Residue "K GLU 185": "OE1" <-> "OE2" Residue "K ASP 187": "OD1" <-> "OD2" Residue "L GLU 10": "OE1" <-> "OE2" Residue "L GLU 136": "OE1" <-> "OE2" Residue "L GLU 143": "OE1" <-> "OE2" Residue "M ASP 22": "OD1" <-> "OD2" Residue "M ASP 116": "OD1" <-> "OD2" Residue "M ASP 145": "OD1" <-> "OD2" Residue "M ASP 171": "OD1" <-> "OD2" Residue "M ASP 191": "OD1" <-> "OD2" Residue "N ASP 18": "OD1" <-> "OD2" Residue "N GLU 64": "OE1" <-> "OE2" Residue "O ASP 14": "OD1" <-> "OD2" Residue "O GLU 43": "OE1" <-> "OE2" Residue "O ASP 71": "OD1" <-> "OD2" Residue "O GLU 98": "OE1" <-> "OE2" Residue "O GLU 129": "OE1" <-> "OE2" Residue "P ASP 22": "OD1" <-> "OD2" Residue "P ASP 67": "OD1" <-> "OD2" Residue "Q GLU 36": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 115899 Number of models: 1 Model: "" Number of chains: 11 Chain: "I" Number of atoms: 93393 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2898, 93298 Classifications: {'RNA': 2898} Modifications used: {'3*END': 1, 'rna2p': 7, 'rna2p_pur': 280, 'rna2p_pyr': 151, 'rna3p': 14, 'rna3p_pur': 1385, 'rna3p_pyr': 1061} Link IDs: {'rna2p': 438, 'rna3p': 2459} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 8 Conformer: "B" Number of residues, atoms: 2898, 93298 Classifications: {'RNA': 2898} Modifications used: {'3*END': 1, 'rna2p': 7, 'rna2p_pur': 280, 'rna2p_pyr': 151, 'rna3p': 14, 'rna3p_pur': 1385, 'rna3p_pyr': 1061} Link IDs: {'rna2p': 438, 'rna3p': 2459} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 8 bond proxies already assigned to first conformer: 100661 Chain: "J" Number of atoms: 3810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 3810 Classifications: {'RNA': 118} Modifications used: {'3*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 48} Link IDs: {'rna2p': 13, 'rna3p': 104} Chain: "K" Number of atoms: 4237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 4237 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "L" Number of atoms: 2182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2182 Classifications: {'peptide': 144} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "M" Number of atoms: 3170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3170 Classifications: {'peptide': 201} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "N" Number of atoms: 3182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3182 Classifications: {'peptide': 209} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "O" Number of atoms: 2291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2291 Classifications: {'peptide': 142} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "P" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1775 Classifications: {'peptide': 110} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "Q" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 898 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "R" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 794 Classifications: {'peptide': 46} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "I" Number of atoms: 167 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3, 104 Unusual residues: {'UCX': 1, 'UDF': 1} Classifications: {'undetermined': 2, 'water': 1} Link IDs: {None: 2} Conformer: "B" Number of residues, atoms: 3, 104 Unusual residues: {'UCX': 1, 'UDF': 1} Classifications: {'undetermined': 2, 'water': 1} Link IDs: {None: 2} bond proxies already assigned to first conformer: 42 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" P A G I2505 " occ=0.50 ... (66 atoms not shown) pdb=" H22B G I2505 " occ=0.50 residue: pdb=" P A U I2506 " occ=0.50 ... (58 atoms not shown) pdb=" H6 B U I2506 " occ=0.50 residue: pdb=" P A C I2507 " occ=0.50 ... (60 atoms not shown) pdb=" H6 B C I2507 " occ=0.50 residue: pdb=" C1 AUDF I3002 " occ=0.50 ... (124 atoms not shown) pdb=" O9 BUDF I3002 " occ=0.50 Time building chain proxies: 67.45, per 1000 atoms: 0.58 Number of scatterers: 115899 At special positions: 0 Unit cell: (232.085, 224.105, 192.185, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 28 16.00 P 3019 15.00 F 1 9.00 O 22616 8.00 N 13708 7.00 C 34675 6.00 H 41852 1.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 76.76 Conformation dependent library (CDL) restraints added in 2.2 seconds 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2114 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 35 helices and 13 sheets defined 29.5% alpha, 15.6% beta 748 base pairs and 1610 stacking pairs defined. Time for finding SS restraints: 58.64 Creating SS restraints... Processing helix chain 'K' and resid 12 through 17 removed outlier: 5.198A pdb=" N VAL K 16 " --> pdb=" O GLY K 12 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL K 17 " --> pdb=" O ARG K 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 12 through 17' Processing helix chain 'K' and resid 30 through 35 removed outlier: 3.835A pdb=" N LEU K 34 " --> pdb=" O PHE K 30 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N GLU K 35 " --> pdb=" O ALA K 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 30 through 35' Processing helix chain 'K' and resid 131 through 136 removed outlier: 4.049A pdb=" N ILE K 135 " --> pdb=" O PRO K 131 " (cutoff:3.500A) Proline residue: K 136 - end of helix No H-bonds generated for 'chain 'K' and resid 131 through 136' Processing helix chain 'K' and resid 207 through 215 removed outlier: 3.889A pdb=" N ALA K 211 " --> pdb=" O LYS K 207 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG K 214 " --> pdb=" O ALA K 210 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY K 215 " --> pdb=" O ALA K 211 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 226 removed outlier: 7.168A pdb=" N MET K 225 " --> pdb=" O ARG K 221 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N ASN K 226 " --> pdb=" O GLY K 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 221 through 226' Processing helix chain 'K' and resid 263 through 268 removed outlier: 6.711A pdb=" N ILE K 267 " --> pdb=" O THR K 263 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N VAL K 268 " --> pdb=" O ASP K 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 263 through 268' Processing helix chain 'K' and resid 197 through 202 removed outlier: 4.097A pdb=" N MET K 201 " --> pdb=" O ALA K 198 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 62 removed outlier: 3.615A pdb=" N LEU L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 68 through 75 removed outlier: 6.994A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 68 through 75' Processing helix chain 'L' and resid 78 through 83 removed outlier: 3.954A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 83' Processing helix chain 'L' and resid 91 through 99 Processing helix chain 'L' and resid 128 through 139 removed outlier: 3.700A pdb=" N GLY L 139 " --> pdb=" O ILE L 135 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 20 Processing helix chain 'M' and resid 24 through 40 removed outlier: 3.584A pdb=" N ALA M 39 " --> pdb=" O TYR M 35 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG M 40 " --> pdb=" O ALA M 36 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 116 Processing helix chain 'M' and resid 130 through 142 removed outlier: 3.527A pdb=" N MET M 141 " --> pdb=" O LYS M 137 " (cutoff:3.500A) Processing helix chain 'M' and resid 154 through 163 removed outlier: 4.571A pdb=" N ASN M 163 " --> pdb=" O LEU M 159 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 183 removed outlier: 3.726A pdb=" N ILE M 181 " --> pdb=" O PRO M 177 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE M 183 " --> pdb=" O SER M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 189 through 201 removed outlier: 3.743A pdb=" N LYS M 194 " --> pdb=" O ALA M 190 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN M 195 " --> pdb=" O ASP M 191 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 61 removed outlier: 5.739A pdb=" N THR N 61 " --> pdb=" O ALA N 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 72 removed outlier: 3.511A pdb=" N HIS N 67 " --> pdb=" O PRO N 63 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA N 71 " --> pdb=" O HIS N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 120 through 125 Processing helix chain 'N' and resid 97 through 103 removed outlier: 4.542A pdb=" N LEU N 100 " --> pdb=" O SER N 97 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE N 101 " --> pdb=" O VAL N 98 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA N 102 " --> pdb=" O GLU N 99 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ASP N 103 " --> pdb=" O LEU N 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 97 through 103' Processing helix chain 'N' and resid 39 through 44 Processing helix chain 'O' and resid 24 through 38 removed outlier: 4.426A pdb=" N GLU O 31 " --> pdb=" O ARG O 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 88 through 96 Processing helix chain 'O' and resid 97 through 110 removed outlier: 4.196A pdb=" N ILE O 101 " --> pdb=" O PRO O 97 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET O 108 " --> pdb=" O ALA O 104 " (cutoff:3.500A) Proline residue: O 110 - end of helix Processing helix chain 'O' and resid 112 through 122 removed outlier: 3.646A pdb=" N ARG O 120 " --> pdb=" O ARG O 116 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS O 121 " --> pdb=" O ALA O 117 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU O 122 " --> pdb=" O MET O 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 25 removed outlier: 3.673A pdb=" N LEU P 19 " --> pdb=" O GLN P 15 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL P 20 " --> pdb=" O LYS P 16 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU P 23 " --> pdb=" O LEU P 19 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE P 24 " --> pdb=" O VAL P 20 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG P 25 " --> pdb=" O ALA P 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 40 removed outlier: 3.622A pdb=" N ASP P 34 " --> pdb=" O SER P 30 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR P 39 " --> pdb=" O ILE P 35 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ASN P 40 " --> pdb=" O LEU P 36 " (cutoff:3.500A) Processing helix chain 'P' and resid 41 through 61 removed outlier: 3.902A pdb=" N VAL P 45 " --> pdb=" O LYS P 41 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU P 46 " --> pdb=" O LYS P 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 19 removed outlier: 5.027A pdb=" N HIS Q 19 " --> pdb=" O MET Q 15 " (cutoff:3.500A) Processing helix chain 'R' and resid 8 through 16 Processing helix chain 'R' and resid 17 through 24 removed outlier: 4.363A pdb=" N THR R 24 " --> pdb=" O ALA R 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 38 Processing sheet with id= 1, first strand: chain 'K' and resid 80 through 83 removed outlier: 3.803A pdb=" N ARG K 80 " --> pdb=" O LEU K 93 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU K 93 " --> pdb=" O GLU K 79 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ASP K 114 " --> pdb=" O VAL K 78 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY K 127 " --> pdb=" O GLN K 115 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLN K 117 " --> pdb=" O GLY K 127 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'K' and resid 138 through 142 removed outlier: 4.231A pdb=" N SER K 139 " --> pdb=" O ILE K 164 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN K 163 " --> pdb=" O ARG K 175 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR K 173 " --> pdb=" O VAL K 165 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU K 180 " --> pdb=" O LEU K 176 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'K' and resid 91 through 96 removed outlier: 4.176A pdb=" N GLU K 100 " --> pdb=" O TYR K 96 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'M' and resid 1 through 6 removed outlier: 3.849A pdb=" N MET M 1 " --> pdb=" O VAL M 14 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N SER M 10 " --> pdb=" O LEU M 5 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'M' and resid 44 through 47 No H-bonds generated for sheet with id= 5 Processing sheet with id= 6, first strand: chain 'M' and resid 117 through 120 removed outlier: 5.740A pdb=" N ARG M 117 " --> pdb=" O ASP M 184 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS M 185 " --> pdb=" O ASP M 145 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP M 168 " --> pdb=" O VAL M 146 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'N' and resid 3 through 7 removed outlier: 7.314A pdb=" N ASP N 200 " --> pdb=" O THR N 112 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N THR N 112 " --> pdb=" O ASP N 200 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU N 168 " --> pdb=" O SER N 113 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'N' and resid 10 through 16 removed outlier: 3.800A pdb=" N GLY N 10 " --> pdb=" O VAL N 26 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL N 20 " --> pdb=" O THR N 16 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG N 179 " --> pdb=" O LEU N 188 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'N' and resid 32 through 35 removed outlier: 6.658A pdb=" N GLN N 49 " --> pdb=" O THR N 35 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ARG N 46 " --> pdb=" O LEU N 84 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU N 84 " --> pdb=" O ARG N 46 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'O' and resid 52 through 57 removed outlier: 4.910A pdb=" N ASP O 19 " --> pdb=" O LEU O 140 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'O' and resid 74 through 78 removed outlier: 7.360A pdb=" N GLY O 83 " --> pdb=" O THR O 78 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'P' and resid 2 through 8 removed outlier: 4.666A pdb=" N THR P 100 " --> pdb=" O GLY P 79 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS P 73 " --> pdb=" O VAL P 106 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'Q' and resid 28 through 31 removed outlier: 6.688A pdb=" N SER Q 29 " --> pdb=" O LYS Q 37 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LYS Q 37 " --> pdb=" O SER Q 29 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ASP Q 31 " --> pdb=" O GLY Q 35 " (cutoff:3.500A) 251 hydrogen bonds defined for protein. 738 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1786 hydrogen bonds 2774 hydrogen bond angles 0 basepair planarities 748 basepair parallelities 1611 stacking parallelities Total time for adding SS restraints: 134.40 Time building geometry restraints manager: 81.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 41850 1.03 - 1.23: 632 1.23 - 1.42: 40675 1.42 - 1.61: 40598 1.61 - 1.81: 55 Bond restraints: 123810 Sorted by residual: bond pdb=" C4 5MU I1939 " pdb=" C5 5MU I1939 " ideal model delta sigma weight residual 1.802 1.412 0.390 2.00e-02 2.50e+03 3.80e+02 bond pdb=" C4 5MU I 747 " pdb=" C5 5MU I 747 " ideal model delta sigma weight residual 1.802 1.412 0.390 2.00e-02 2.50e+03 3.80e+02 bond pdb=" N1 5MU I1939 " pdb=" C6 5MU I1939 " ideal model delta sigma weight residual 1.635 1.366 0.269 2.00e-02 2.50e+03 1.81e+02 bond pdb=" N1 5MU I 747 " pdb=" C6 5MU I 747 " ideal model delta sigma weight residual 1.635 1.369 0.266 2.00e-02 2.50e+03 1.77e+02 bond pdb=" C2 UCX I3001 " pdb=" C3 UCX I3001 " ideal model delta sigma weight residual 1.611 1.351 0.260 2.00e-02 2.50e+03 1.69e+02 ... (remaining 123805 not shown) Histogram of bond angle deviations from ideal: 58.84 - 82.76: 6 82.76 - 106.68: 17980 106.68 - 130.59: 202801 130.59 - 154.51: 892 154.51 - 178.43: 3 Bond angle restraints: 221682 Sorted by residual: angle pdb=" C LYS N 114 " pdb=" N GLY N 115 " pdb=" H GLY N 115 " ideal model delta sigma weight residual 124.45 68.37 56.07 3.00e+00 1.11e-01 3.49e+02 angle pdb=" CA GLY N 115 " pdb=" N GLY N 115 " pdb=" H GLY N 115 " ideal model delta sigma weight residual 114.15 58.84 55.31 3.00e+00 1.11e-01 3.40e+02 angle pdb=" N10BUDF I3002 " pdb=" N9 BUDF I3002 " pdb=" N8 BUDF I3002 " ideal model delta sigma weight residual 119.78 172.54 -52.76 3.00e+00 1.11e-01 3.09e+02 angle pdb=" N10AUDF I3002 " pdb=" N9 AUDF I3002 " pdb=" N8 AUDF I3002 " ideal model delta sigma weight residual 119.78 172.03 -52.25 3.00e+00 1.11e-01 3.03e+02 angle pdb=" O3' A I2031 " pdb=" C3' A I2031 " pdb=" H3' A I2031 " ideal model delta sigma weight residual 109.00 68.69 40.31 3.00e+00 1.11e-01 1.81e+02 ... (remaining 221677 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 53083 35.91 - 71.82: 5184 71.82 - 107.73: 789 107.73 - 143.63: 18 143.63 - 179.54: 12 Dihedral angle restraints: 59086 sinusoidal: 55436 harmonic: 3650 Sorted by residual: dihedral pdb=" C4* PSU I1911 " pdb=" C3* PSU I1911 " pdb=" C2* PSU I1911 " pdb=" C1* PSU I1911 " ideal model delta sinusoidal sigma weight residual -35.00 31.15 -66.15 1 8.00e+00 1.56e-02 8.93e+01 dihedral pdb=" O4' U I1340 " pdb=" C1' U I1340 " pdb=" N1 U I1340 " pdb=" C2 U I1340 " ideal model delta sinusoidal sigma weight residual 232.00 52.83 179.17 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C I 323 " pdb=" C1' C I 323 " pdb=" N1 C I 323 " pdb=" C2 C I 323 " ideal model delta sinusoidal sigma weight residual -128.00 44.66 -172.66 1 1.70e+01 3.46e-03 6.62e+01 ... (remaining 59083 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.392: 16448 0.392 - 0.784: 2 0.784 - 1.177: 0 1.177 - 1.569: 0 1.569 - 1.961: 1 Chirality restraints: 16451 Sorted by residual: chirality pdb=" P B C I2507 " pdb=" OP1B C I2507 " pdb=" OP2B C I2507 " pdb=" O5'B C I2507 " both_signs ideal model delta sigma weight residual True 2.41 0.45 1.96 2.00e-01 2.50e+01 9.61e+01 chirality pdb=" C3' A I2031 " pdb=" C4' A I2031 " pdb=" O3' A I2031 " pdb=" C2' A I2031 " both_signs ideal model delta sigma weight residual False -2.74 -2.14 -0.60 2.00e-01 2.50e+01 9.09e+00 chirality pdb=" C18BUDF I3002 " pdb=" C19BUDF I3002 " pdb=" C20BUDF I3002 " pdb=" N5 BUDF I3002 " both_signs ideal model delta sigma weight residual False 2.62 2.23 0.39 2.00e-01 2.50e+01 3.86e+00 ... (remaining 16448 not shown) Planarity restraints: 8186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC I2498 " 0.035 2.00e-02 2.50e+03 6.03e-01 8.18e+03 pdb=" C4' OMC I2498 " 0.457 2.00e-02 2.50e+03 pdb=" O4' OMC I2498 " 0.754 2.00e-02 2.50e+03 pdb=" C3' OMC I2498 " -0.592 2.00e-02 2.50e+03 pdb=" O3' OMC I2498 " -0.587 2.00e-02 2.50e+03 pdb=" C2' OMC I2498 " -0.222 2.00e-02 2.50e+03 pdb=" O2' OMC I2498 " 0.900 2.00e-02 2.50e+03 pdb=" C1' OMC I2498 " 0.202 2.00e-02 2.50e+03 pdb=" N1 OMC I2498 " -0.947 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I2445 " -0.026 2.00e-02 2.50e+03 5.79e-01 7.54e+03 pdb=" C4' 2MG I2445 " -0.444 2.00e-02 2.50e+03 pdb=" O4' 2MG I2445 " -0.669 2.00e-02 2.50e+03 pdb=" C3' 2MG I2445 " 0.590 2.00e-02 2.50e+03 pdb=" O3' 2MG I2445 " 0.569 2.00e-02 2.50e+03 pdb=" C2' 2MG I2445 " 0.213 2.00e-02 2.50e+03 pdb=" O2' 2MG I2445 " -0.901 2.00e-02 2.50e+03 pdb=" C1' 2MG I2445 " -0.222 2.00e-02 2.50e+03 pdb=" N9 2MG I2445 " 0.890 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG I2251 " 0.040 2.00e-02 2.50e+03 5.63e-01 7.13e+03 pdb=" C4' OMG I2251 " 0.426 2.00e-02 2.50e+03 pdb=" O4' OMG I2251 " 0.590 2.00e-02 2.50e+03 pdb=" C3' OMG I2251 " -0.595 2.00e-02 2.50e+03 pdb=" O3' OMG I2251 " -0.565 2.00e-02 2.50e+03 pdb=" C2' OMG I2251 " -0.204 2.00e-02 2.50e+03 pdb=" O2' OMG I2251 " 0.914 2.00e-02 2.50e+03 pdb=" C1' OMG I2251 " 0.237 2.00e-02 2.50e+03 pdb=" N9 OMG I2251 " -0.844 2.00e-02 2.50e+03 ... (remaining 8183 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 2208 2.07 - 2.70: 120672 2.70 - 3.33: 273908 3.33 - 3.97: 424690 3.97 - 4.60: 623735 Nonbonded interactions: 1445213 Sorted by model distance: nonbonded pdb=" H GLY N 115 " pdb=" HA2 GLY N 115 " model vdw 1.437 1.816 nonbonded pdb=" H1 G I2029 " pdb=" OP2 A I2033 " model vdw 1.596 1.850 nonbonded pdb=" OP2 U I1779 " pdb=" H61 A I1784 " model vdw 1.601 1.850 nonbonded pdb=" H1 G I2688 " pdb=" OP2 U I2720 " model vdw 1.612 1.850 nonbonded pdb=" O ALA K 170 " pdb=" H ALA K 186 " model vdw 1.616 1.850 ... (remaining 1445208 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 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: 7.340 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: 0.900 Extract box with map and model: 35.070 Check model and map are aligned: 1.760 Set scattering table: 0.820 Process input model: 436.680 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.340 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: 0.030 Load rotamer database and sin/cos tables:10.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 494.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9037 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 : 0.006 0.390 81958 Z= 0.394 Angle : 0.515 52.761 125820 Z= 0.220 Chirality : 0.029 1.961 16451 Planarity : 0.022 0.603 4656 Dihedral : 22.206 179.542 48256 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.74 % Allowed : 14.23 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % 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: 0.03 (0.25), residues: 1163 helix: 0.71 (0.35), residues: 257 sheet: 1.17 (0.39), residues: 205 loop : -0.59 (0.24), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 78 HIS 0.002 0.000 HIS O 76 PHE 0.007 0.001 PHE K 240 TYR 0.005 0.001 TYR K 103 ARG 0.007 0.000 ARG P 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 189 time to evaluate : 3.580 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 194 average time/residue: 2.9936 time to fit residues: 732.1116 Evaluate side-chains 183 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 176 time to evaluate : 3.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain Q residue 57 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 350 optimal weight: 2.9990 chunk 314 optimal weight: 5.9990 chunk 174 optimal weight: 7.9990 chunk 107 optimal weight: 50.0000 chunk 212 optimal weight: 50.0000 chunk 168 optimal weight: 6.9990 chunk 325 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 242 optimal weight: 6.9990 chunk 376 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 136 GLN M 195 GLN N 185 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9062 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 81958 Z= 0.330 Angle : 0.635 27.384 125820 Z= 0.344 Chirality : 0.042 1.928 16451 Planarity : 0.007 0.136 4656 Dihedral : 22.099 179.027 46027 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.70 % Allowed : 14.12 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.24), residues: 1163 helix: 0.50 (0.32), residues: 281 sheet: 1.05 (0.39), residues: 191 loop : -0.93 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 78 HIS 0.005 0.001 HIS K 230 PHE 0.010 0.001 PHE K 240 TYR 0.010 0.001 TYR K 103 ARG 0.004 0.001 ARG K 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 173 time to evaluate : 3.206 Fit side-chains REVERT: O 95 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7538 (ttm-80) outliers start: 16 outliers final: 9 residues processed: 185 average time/residue: 2.9640 time to fit residues: 690.4727 Evaluate side-chains 174 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 164 time to evaluate : 3.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 199 SER Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 95 ARG Chi-restraints excluded: chain Q residue 57 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 209 optimal weight: 20.0000 chunk 116 optimal weight: 10.0000 chunk 313 optimal weight: 2.9990 chunk 256 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 377 optimal weight: 3.9990 chunk 407 optimal weight: 4.9990 chunk 336 optimal weight: 6.9990 chunk 374 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 302 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 185 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9062 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 81958 Z= 0.300 Angle : 0.614 27.271 125820 Z= 0.334 Chirality : 0.040 1.941 16451 Planarity : 0.007 0.138 4656 Dihedral : 22.134 179.723 46022 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.70 % Allowed : 14.01 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.24), residues: 1163 helix: 0.50 (0.32), residues: 284 sheet: 0.94 (0.40), residues: 181 loop : -1.02 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 248 HIS 0.004 0.001 HIS K 230 PHE 0.015 0.001 PHE K 240 TYR 0.009 0.001 TYR K 103 ARG 0.003 0.000 ARG K 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 166 time to evaluate : 3.200 Fit side-chains REVERT: O 95 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7549 (ttm-80) outliers start: 16 outliers final: 9 residues processed: 174 average time/residue: 3.2146 time to fit residues: 707.8004 Evaluate side-chains 171 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 161 time to evaluate : 3.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 95 ARG Chi-restraints excluded: chain Q residue 57 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 373 optimal weight: 3.9990 chunk 283 optimal weight: 6.9990 chunk 195 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 180 optimal weight: 5.9990 chunk 253 optimal weight: 6.9990 chunk 378 optimal weight: 5.9990 chunk 401 optimal weight: 10.0000 chunk 197 optimal weight: 4.9990 chunk 359 optimal weight: 8.9990 chunk 108 optimal weight: 50.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 136 GLN N 126 ASN N 185 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9082 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 81958 Z= 0.368 Angle : 0.658 27.361 125820 Z= 0.354 Chirality : 0.043 1.947 16451 Planarity : 0.007 0.141 4656 Dihedral : 22.194 178.718 46022 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.02 % Allowed : 14.23 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.58 (0.24), residues: 1163 helix: 0.56 (0.32), residues: 271 sheet: 0.80 (0.38), residues: 198 loop : -1.18 (0.22), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 248 HIS 0.006 0.001 HIS K 230 PHE 0.013 0.001 PHE K 240 TYR 0.010 0.001 TYR P 38 ARG 0.006 0.001 ARG P 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 167 time to evaluate : 3.269 Fit side-chains REVERT: O 1 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.7043 (ptm) REVERT: O 95 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7624 (ttm-80) outliers start: 19 outliers final: 11 residues processed: 177 average time/residue: 3.2509 time to fit residues: 728.6102 Evaluate side-chains 179 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 166 time to evaluate : 3.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 199 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 95 ARG Chi-restraints excluded: chain Q residue 57 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 334 optimal weight: 7.9990 chunk 227 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 298 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 chunk 342 optimal weight: 7.9990 chunk 277 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 204 optimal weight: 4.9990 chunk 360 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 136 GLN N 126 ASN N 185 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9078 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 81958 Z= 0.368 Angle : 0.648 27.395 125820 Z= 0.349 Chirality : 0.042 1.943 16451 Planarity : 0.007 0.141 4656 Dihedral : 22.214 179.333 46022 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.80 % Allowed : 14.12 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.66 (0.24), residues: 1163 helix: 0.46 (0.32), residues: 278 sheet: 0.71 (0.38), residues: 188 loop : -1.18 (0.22), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 248 HIS 0.005 0.001 HIS K 230 PHE 0.016 0.001 PHE K 240 TYR 0.010 0.001 TYR P 38 ARG 0.006 0.001 ARG P 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 168 time to evaluate : 3.197 Fit side-chains REVERT: O 1 MET cc_start: 0.7298 (OUTLIER) cc_final: 0.7055 (ptm) outliers start: 17 outliers final: 14 residues processed: 178 average time/residue: 3.2620 time to fit residues: 740.6256 Evaluate side-chains 179 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 164 time to evaluate : 3.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain M residue 199 MET Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 199 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain Q residue 57 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 134 optimal weight: 5.9990 chunk 361 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 235 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 401 optimal weight: 9.9990 chunk 333 optimal weight: 3.9990 chunk 185 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 210 optimal weight: 50.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 136 GLN N 126 ASN N 185 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9076 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 81958 Z= 0.343 Angle : 0.643 27.364 125820 Z= 0.347 Chirality : 0.042 1.948 16451 Planarity : 0.007 0.140 4656 Dihedral : 22.215 179.350 46022 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.91 % Allowed : 14.01 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.66 (0.24), residues: 1163 helix: 0.48 (0.32), residues: 278 sheet: 0.70 (0.38), residues: 188 loop : -1.19 (0.22), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 248 HIS 0.005 0.001 HIS K 230 PHE 0.016 0.001 PHE K 240 TYR 0.011 0.001 TYR P 38 ARG 0.006 0.000 ARG M 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 164 time to evaluate : 3.209 Fit side-chains REVERT: O 1 MET cc_start: 0.7304 (OUTLIER) cc_final: 0.7038 (ptm) outliers start: 18 outliers final: 16 residues processed: 173 average time/residue: 3.2950 time to fit residues: 722.3949 Evaluate side-chains 181 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 164 time to evaluate : 3.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain M residue 199 MET Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 199 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain Q residue 57 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 387 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 228 optimal weight: 8.9990 chunk 293 optimal weight: 10.0000 chunk 227 optimal weight: 4.9990 chunk 338 optimal weight: 6.9990 chunk 224 optimal weight: 4.9990 chunk 399 optimal weight: 0.9980 chunk 250 optimal weight: 4.9990 chunk 243 optimal weight: 4.9990 chunk 184 optimal weight: 10.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 136 GLN N 126 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9071 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 81958 Z= 0.280 Angle : 0.626 27.274 125820 Z= 0.342 Chirality : 0.040 1.957 16451 Planarity : 0.007 0.139 4656 Dihedral : 22.217 179.302 46022 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.91 % Allowed : 14.23 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.09 % 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: -0.66 (0.24), residues: 1163 helix: 0.49 (0.32), residues: 278 sheet: 0.70 (0.38), residues: 188 loop : -1.19 (0.22), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 248 HIS 0.005 0.001 HIS K 230 PHE 0.016 0.001 PHE K 240 TYR 0.011 0.001 TYR P 38 ARG 0.006 0.000 ARG M 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 164 time to evaluate : 3.257 Fit side-chains REVERT: O 1 MET cc_start: 0.7301 (OUTLIER) cc_final: 0.7057 (ptm) outliers start: 18 outliers final: 17 residues processed: 174 average time/residue: 3.2130 time to fit residues: 699.3225 Evaluate side-chains 182 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 164 time to evaluate : 3.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain M residue 7 ASP Chi-restraints excluded: chain M residue 199 MET Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 199 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain Q residue 57 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 247 optimal weight: 6.9990 chunk 159 optimal weight: 6.9990 chunk 238 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 254 optimal weight: 5.9990 chunk 272 optimal weight: 6.9990 chunk 197 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 314 optimal weight: 0.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 136 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9072 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 81958 Z= 0.308 Angle : 0.632 27.295 125820 Z= 0.343 Chirality : 0.041 1.956 16451 Planarity : 0.007 0.139 4656 Dihedral : 22.216 179.338 46022 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.02 % Allowed : 14.12 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.24), residues: 1163 helix: 0.49 (0.32), residues: 278 sheet: 0.70 (0.38), residues: 188 loop : -1.19 (0.22), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 248 HIS 0.004 0.001 HIS K 230 PHE 0.016 0.001 PHE K 240 TYR 0.011 0.001 TYR P 38 ARG 0.006 0.000 ARG M 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 164 time to evaluate : 3.270 Fit side-chains REVERT: O 1 MET cc_start: 0.7301 (OUTLIER) cc_final: 0.7057 (ptm) outliers start: 19 outliers final: 17 residues processed: 174 average time/residue: 3.1460 time to fit residues: 686.8476 Evaluate side-chains 182 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 164 time to evaluate : 3.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain M residue 7 ASP Chi-restraints excluded: chain M residue 199 MET Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 199 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain Q residue 57 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 363 optimal weight: 4.9990 chunk 383 optimal weight: 6.9990 chunk 349 optimal weight: 0.7980 chunk 372 optimal weight: 3.9990 chunk 224 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 chunk 292 optimal weight: 20.0000 chunk 114 optimal weight: 7.9990 chunk 336 optimal weight: 6.9990 chunk 352 optimal weight: 6.9990 chunk 371 optimal weight: 6.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 136 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9070 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 81958 Z= 0.276 Angle : 0.624 27.254 125820 Z= 0.341 Chirality : 0.040 1.960 16451 Planarity : 0.007 0.139 4656 Dihedral : 22.217 179.332 46022 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.91 % Allowed : 13.91 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.24), residues: 1163 helix: 0.50 (0.32), residues: 278 sheet: 0.70 (0.38), residues: 188 loop : -1.19 (0.22), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 248 HIS 0.004 0.001 HIS K 230 PHE 0.016 0.001 PHE K 240 TYR 0.011 0.001 TYR P 38 ARG 0.005 0.000 ARG M 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 163 time to evaluate : 2.943 Fit side-chains REVERT: O 1 MET cc_start: 0.7300 (OUTLIER) cc_final: 0.7055 (ptm) outliers start: 18 outliers final: 17 residues processed: 173 average time/residue: 3.1418 time to fit residues: 683.4405 Evaluate side-chains 181 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 163 time to evaluate : 3.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain M residue 7 ASP Chi-restraints excluded: chain M residue 199 MET Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 199 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain Q residue 57 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 244 optimal weight: 3.9990 chunk 394 optimal weight: 6.9990 chunk 240 optimal weight: 7.9990 chunk 186 optimal weight: 10.0000 chunk 274 optimal weight: 8.9990 chunk 413 optimal weight: 4.9990 chunk 380 optimal weight: 4.9990 chunk 329 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 254 optimal weight: 5.9990 chunk 201 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 136 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9072 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 81958 Z= 0.329 Angle : 0.635 27.333 125820 Z= 0.343 Chirality : 0.041 1.952 16451 Planarity : 0.007 0.139 4656 Dihedral : 22.215 179.420 46022 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.12 % Allowed : 13.80 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.24), residues: 1163 helix: 0.50 (0.32), residues: 278 sheet: 0.72 (0.38), residues: 193 loop : -1.21 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 248 HIS 0.005 0.001 HIS K 230 PHE 0.017 0.001 PHE K 240 TYR 0.010 0.001 TYR P 38 ARG 0.012 0.000 ARG P 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 163 time to evaluate : 3.573 Fit side-chains REVERT: O 1 MET cc_start: 0.7311 (OUTLIER) cc_final: 0.7066 (ptm) outliers start: 20 outliers final: 17 residues processed: 174 average time/residue: 3.1023 time to fit residues: 675.8722 Evaluate side-chains 180 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 162 time to evaluate : 3.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain M residue 7 ASP Chi-restraints excluded: chain M residue 199 MET Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 199 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain Q residue 57 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 261 optimal weight: 5.9990 chunk 350 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 303 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 329 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 chunk 338 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.108325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.061397 restraints weight = 356676.162| |-----------------------------------------------------------------------------| r_work (start): 0.2581 rms_B_bonded: 0.60 r_work: 0.2481 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2406 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.2406 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2356 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2356 r_free = 0.2356 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2356 r_free = 0.2356 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2356 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 81958 Z= 0.305 Angle : 0.628 27.322 125820 Z= 0.341 Chirality : 0.041 1.952 16451 Planarity : 0.007 0.139 4656 Dihedral : 22.216 179.404 46022 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.91 % Allowed : 14.33 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.24), residues: 1163 helix: 0.51 (0.32), residues: 278 sheet: 0.71 (0.38), residues: 193 loop : -1.21 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 248 HIS 0.005 0.001 HIS K 230 PHE 0.016 0.001 PHE K 240 TYR 0.010 0.001 TYR P 38 ARG 0.012 0.000 ARG P 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 35809.76 seconds wall clock time: 614 minutes 48.39 seconds (36888.39 seconds total)