Starting phenix.real_space_refine on Tue Mar 12 18:07:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e45_27880/03_2024/8e45_27880_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e45_27880/03_2024/8e45_27880.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e45_27880/03_2024/8e45_27880_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e45_27880/03_2024/8e45_27880_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e45_27880/03_2024/8e45_27880_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e45_27880/03_2024/8e45_27880.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e45_27880/03_2024/8e45_27880.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e45_27880/03_2024/8e45_27880_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e45_27880/03_2024/8e45_27880_neut_trim_updated.pdb" } resolution = 2.3 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= -0.011 sd= 0.632 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 3017 5.49 5 S 28 5.16 5 C 34596 2.51 5 N 13687 2.21 5 O 22589 1.98 5 F 1 1.80 5 H 41831 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K ASP 187": "OD1" <-> "OD2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "M ASP 154": "OD1" <-> "OD2" Residue "N ASP 43": "OD1" <-> "OD2" Residue "N ASP 108": "OD1" <-> "OD2" Residue "N ASP 200": "OD1" <-> "OD2" Residue "O GLU 98": "OE1" <-> "OE2" Residue "P ASP 67": "OD1" <-> "OD2" Residue "Q GLU 36": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 115749 Number of models: 1 Model: "" Number of chains: 11 Chain: "I" Number of atoms: 93329 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2897, 93265 Classifications: {'RNA': 2897} Modifications used: {'3*END': 1, 'rna2p': 6, 'rna2p_pur': 279, 'rna2p_pyr': 151, 'rna3p': 15, 'rna3p_pur': 1385, 'rna3p_pyr': 1061} Link IDs: {'rna2p': 436, 'rna3p': 2460} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 8 Conformer: "B" Number of residues, atoms: 2897, 93265 Classifications: {'RNA': 2897} Modifications used: {'3*END': 1, 'rna2p': 6, 'rna2p_pur': 280, 'rna2p_pyr': 151, 'rna3p': 15, 'rna3p_pur': 1384, 'rna3p_pyr': 1061} Link IDs: {'rna2p': 437, 'rna3p': 2459} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 8 bond proxies already assigned to first conformer: 100657 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: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 81 Unusual residues: {'UI6': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" P A A I2062 " occ=0.50 ... (64 atoms not shown) pdb=" H2 B A I2062 " occ=0.50 residue: pdb=" P A C I2063 " occ=0.50 ... (60 atoms not shown) pdb=" H6 B C I2063 " occ=0.50 Time building chain proxies: 64.81, per 1000 atoms: 0.56 Number of scatterers: 115749 At special positions: 0 Unit cell: (232.05, 223.65, 191.1, 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 3017 15.00 F 1 9.00 O 22589 8.00 N 13687 7.00 C 34596 6.00 H 41831 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: 71.19 Conformation dependent library (CDL) restraints added in 2.1 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 29.7% alpha, 15.4% beta 806 base pairs and 1612 stacking pairs defined. Time for finding SS restraints: 55.72 Creating SS restraints... Processing helix chain 'K' and resid 10 through 16 removed outlier: 3.691A pdb=" N ARG K 14 " --> pdb=" O SER K 10 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N HIS K 15 " --> pdb=" O PRO K 11 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N VAL K 16 " --> pdb=" O GLY K 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 10 through 16' Processing helix chain 'K' and resid 30 through 35 removed outlier: 3.962A pdb=" N LEU K 34 " --> pdb=" O PHE K 30 " (cutoff:3.500A) removed outlier: 5.758A 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: 3.767A 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: 3.915A pdb=" N ALA K 211 " --> pdb=" O LYS K 207 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG K 214 " --> pdb=" O ALA K 210 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY K 215 " --> pdb=" O ALA K 211 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 226 removed outlier: 7.415A pdb=" N MET K 225 " --> pdb=" O ARG K 221 " (cutoff:3.500A) removed outlier: 5.592A 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 'L' and resid 37 through 42 removed outlier: 3.711A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N SER L 42 " --> pdb=" O GLN L 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 37 through 42' Processing helix chain 'L' and resid 56 through 62 Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 68 through 75 removed outlier: 7.054A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 5.311A 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 85 removed outlier: 3.884A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 85' Processing helix chain 'L' and resid 91 through 99 Processing helix chain 'L' and resid 128 through 139 Processing helix chain 'M' and resid 15 through 20 Processing helix chain 'M' and resid 24 through 40 removed outlier: 3.537A pdb=" N ALA M 39 " --> pdb=" O TYR M 35 " (cutoff:3.500A) removed outlier: 3.764A 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 Processing helix chain 'M' and resid 154 through 163 removed outlier: 4.624A pdb=" N ASN M 163 " --> pdb=" O LEU M 159 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 183 removed outlier: 3.514A pdb=" N LEU M 180 " --> pdb=" O ASP M 176 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE M 181 " --> pdb=" O PRO M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 189 through 201 Processing helix chain 'N' and resid 56 through 61 removed outlier: 5.643A pdb=" N THR N 61 " --> pdb=" O ALA N 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 72 removed outlier: 3.698A pdb=" N ALA N 71 " --> pdb=" O HIS N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 103 removed outlier: 4.402A pdb=" N ALA N 102 " --> pdb=" O VAL N 98 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ASP N 103 " --> pdb=" O GLU N 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 98 through 103' Processing helix chain 'N' and resid 120 through 125 Processing helix chain 'N' and resid 39 through 44 Processing helix chain 'O' and resid 24 through 38 removed outlier: 4.197A pdb=" N GLU O 31 " --> pdb=" O ARG O 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 72 Processing helix chain 'O' and resid 88 through 96 Processing helix chain 'O' and resid 97 through 110 removed outlier: 4.102A pdb=" N ILE O 101 " --> pdb=" O PRO O 97 " (cutoff:3.500A) removed outlier: 3.706A 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: 4.119A pdb=" N LYS O 121 " --> pdb=" O ALA O 117 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU O 122 " --> pdb=" O MET O 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 25 removed outlier: 3.621A pdb=" N LEU P 19 " --> pdb=" O GLN P 15 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL P 20 " --> pdb=" O LYS P 16 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU P 23 " --> pdb=" O LEU P 19 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE P 24 " --> pdb=" O VAL P 20 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG P 25 " --> pdb=" O ALA P 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 40 removed outlier: 3.608A pdb=" N ASP P 34 " --> pdb=" O SER P 30 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR P 38 " --> pdb=" O ASP P 34 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR P 39 " --> pdb=" O ILE P 35 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ASN P 40 " --> pdb=" O LEU P 36 " (cutoff:3.500A) Processing helix chain 'P' and resid 41 through 61 removed outlier: 3.852A pdb=" N VAL P 45 " --> pdb=" O LYS P 41 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU P 46 " --> pdb=" O LYS P 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 19 removed outlier: 4.925A 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: 4.417A 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 2 through 5 Processing sheet with id= 2, first strand: chain 'K' and resid 80 through 83 removed outlier: 3.703A pdb=" N ARG K 80 " --> pdb=" O LEU K 93 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU K 93 " --> pdb=" O GLU K 79 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ASP K 114 " --> pdb=" O VAL K 78 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N GLY K 127 " --> pdb=" O GLN K 115 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N GLN K 117 " --> pdb=" O GLY K 127 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'K' and resid 138 through 142 removed outlier: 4.393A pdb=" N SER K 139 " --> pdb=" O ILE K 164 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN K 163 " --> pdb=" O ARG K 175 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N THR K 173 " --> pdb=" O VAL K 165 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU K 180 " --> pdb=" O LEU K 176 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'K' and resid 91 through 96 removed outlier: 4.108A pdb=" N GLU K 100 " --> pdb=" O TYR K 96 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'M' and resid 1 through 6 removed outlier: 4.097A pdb=" N MET M 1 " --> pdb=" O VAL M 14 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N SER M 10 " --> pdb=" O LEU M 5 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'M' and resid 44 through 47 removed outlier: 7.021A pdb=" N ARG M 44 " --> pdb=" O PRO M 89 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ALA M 87 " --> pdb=" O GLN M 46 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'M' and resid 117 through 120 removed outlier: 5.718A pdb=" N ARG M 117 " --> pdb=" O ASP M 184 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP M 168 " --> pdb=" O VAL M 146 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'N' and resid 3 through 7 removed outlier: 7.228A pdb=" N ASP N 200 " --> pdb=" O THR N 112 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N THR N 112 " --> pdb=" O ASP N 200 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU N 168 " --> pdb=" O SER N 113 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'N' and resid 10 through 16 removed outlier: 3.740A pdb=" N GLY N 10 " --> pdb=" O VAL N 26 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL N 20 " --> pdb=" O THR N 16 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG N 179 " --> pdb=" O LEU N 188 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'N' and resid 79 through 84 removed outlier: 6.001A pdb=" N ARG N 46 " --> pdb=" O LEU N 84 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLN N 49 " --> pdb=" O THR N 35 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLN N 94 " --> pdb=" O VAL N 34 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'O' and resid 52 through 57 removed outlier: 5.043A pdb=" N ASP O 19 " --> pdb=" O LEU O 140 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'P' and resid 2 through 8 removed outlier: 6.980A pdb=" N VAL P 106 " --> pdb=" O THR P 72 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'Q' and resid 28 through 31 removed outlier: 6.570A pdb=" N SER Q 29 " --> pdb=" O LYS Q 37 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LYS Q 37 " --> pdb=" O SER Q 29 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ASP Q 31 " --> pdb=" O GLY Q 35 " (cutoff:3.500A) 259 hydrogen bonds defined for protein. 768 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1937 hydrogen bonds 3022 hydrogen bond angles 0 basepair planarities 806 basepair parallelities 1613 stacking parallelities Total time for adding SS restraints: 141.26 Time building geometry restraints manager: 75.25 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: 41829 1.03 - 1.23: 628 1.23 - 1.42: 43187 1.42 - 1.62: 37951 1.62 - 1.81: 54 Bond restraints: 123649 Sorted by residual: bond pdb=" C4 5MU I1939 " pdb=" C5 5MU I1939 " ideal model delta sigma weight residual 1.802 1.413 0.389 2.00e-02 2.50e+03 3.79e+02 bond pdb=" C4 5MU I 747 " pdb=" C5 5MU I 747 " ideal model delta sigma weight residual 1.802 1.413 0.389 2.00e-02 2.50e+03 3.79e+02 bond pdb=" N1 5MU I1939 " pdb=" C6 5MU I1939 " ideal model delta sigma weight residual 1.635 1.368 0.267 2.00e-02 2.50e+03 1.79e+02 bond pdb=" N1 5MU I 747 " pdb=" C6 5MU I 747 " ideal model delta sigma weight residual 1.635 1.370 0.265 2.00e-02 2.50e+03 1.76e+02 bond pdb=" C5 5MU I 747 " pdb=" C6 5MU I 747 " ideal model delta sigma weight residual 1.155 1.349 -0.194 2.00e-02 2.50e+03 9.43e+01 ... (remaining 123644 not shown) Histogram of bond angle deviations from ideal: 58.79 - 74.04: 5 74.04 - 89.28: 12 89.28 - 104.53: 13414 104.53 - 119.77: 158435 119.77 - 135.02: 49572 Bond angle restraints: 221438 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 68.38 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 58.79 55.35 3.00e+00 1.11e-01 3.40e+02 angle pdb=" O3' U I2613 " pdb=" C3' U I2613 " pdb=" H3' U I2613 " ideal model delta sigma weight residual 109.00 68.12 40.88 3.00e+00 1.11e-01 1.86e+02 angle pdb=" O3' A I2614 " pdb=" C3' A I2614 " pdb=" H3' A I2614 " ideal model delta sigma weight residual 109.00 68.73 40.27 3.00e+00 1.11e-01 1.80e+02 angle pdb=" O3'A C I2063 " pdb=" C3'A C I2063 " pdb=" H3'A C I2063 " ideal model delta sigma weight residual 109.00 74.03 34.97 3.00e+00 1.11e-01 1.36e+02 ... (remaining 221433 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.75: 54682 35.75 - 71.49: 6753 71.49 - 107.24: 779 107.24 - 142.98: 11 142.98 - 178.73: 9 Dihedral angle restraints: 62234 sinusoidal: 58584 harmonic: 3650 Sorted by residual: dihedral pdb=" CA THR N 151 " pdb=" C THR N 151 " pdb=" N PRO N 152 " pdb=" CA PRO N 152 " ideal model delta harmonic sigma weight residual -180.00 -135.79 -44.21 0 5.00e+00 4.00e-02 7.82e+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 53.27 178.73 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 43.80 -171.80 1 1.70e+01 3.46e-03 6.61e+01 ... (remaining 62231 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 16426 0.144 - 0.289: 4 0.289 - 0.433: 3 0.433 - 0.577: 2 0.577 - 0.721: 4 Chirality restraints: 16439 Sorted by residual: chirality pdb=" C3' A I2058 " pdb=" C4' A I2058 " pdb=" O3' A I2058 " pdb=" C2' A I2058 " both_signs ideal model delta sigma weight residual False -2.48 -1.76 -0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" C3'A C I2063 " pdb=" C4'A C I2063 " pdb=" O3'A C I2063 " pdb=" C2'A C I2063 " both_signs ideal model delta sigma weight residual False -2.48 -1.77 -0.71 2.00e-01 2.50e+01 1.25e+01 chirality pdb=" C4'A C I2063 " pdb=" C5'A C I2063 " pdb=" O4'A C I2063 " pdb=" C3'A C I2063 " both_signs ideal model delta sigma weight residual False -2.50 -1.80 -0.70 2.00e-01 2.50e+01 1.22e+01 ... (remaining 16436 not shown) Planarity restraints: 8161 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC I2498 " 0.031 2.00e-02 2.50e+03 6.01e-01 8.14e+03 pdb=" C4' OMC I2498 " 0.458 2.00e-02 2.50e+03 pdb=" O4' OMC I2498 " 0.762 2.00e-02 2.50e+03 pdb=" C3' OMC I2498 " -0.591 2.00e-02 2.50e+03 pdb=" O3' OMC I2498 " -0.580 2.00e-02 2.50e+03 pdb=" C2' OMC I2498 " -0.228 2.00e-02 2.50e+03 pdb=" O2' OMC I2498 " 0.891 2.00e-02 2.50e+03 pdb=" C1' OMC I2498 " 0.201 2.00e-02 2.50e+03 pdb=" N1 OMC I2498 " -0.945 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I2445 " -0.030 2.00e-02 2.50e+03 5.84e-01 7.66e+03 pdb=" C4' 2MG I2445 " -0.446 2.00e-02 2.50e+03 pdb=" O4' 2MG I2445 " -0.680 2.00e-02 2.50e+03 pdb=" C3' 2MG I2445 " 0.590 2.00e-02 2.50e+03 pdb=" O3' 2MG I2445 " 0.576 2.00e-02 2.50e+03 pdb=" C2' 2MG I2445 " 0.213 2.00e-02 2.50e+03 pdb=" O2' 2MG I2445 " -0.904 2.00e-02 2.50e+03 pdb=" C1' 2MG I2445 " -0.220 2.00e-02 2.50e+03 pdb=" N9 2MG I2445 " 0.902 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG I2251 " 0.039 2.00e-02 2.50e+03 5.68e-01 7.25e+03 pdb=" C4' OMG I2251 " 0.429 2.00e-02 2.50e+03 pdb=" O4' OMG I2251 " 0.606 2.00e-02 2.50e+03 pdb=" C3' OMG I2251 " -0.595 2.00e-02 2.50e+03 pdb=" O3' OMG I2251 " -0.570 2.00e-02 2.50e+03 pdb=" C2' OMG I2251 " -0.203 2.00e-02 2.50e+03 pdb=" O2' OMG I2251 " 0.916 2.00e-02 2.50e+03 pdb=" C1' OMG I2251 " 0.234 2.00e-02 2.50e+03 pdb=" N9 OMG I2251 " -0.856 2.00e-02 2.50e+03 ... (remaining 8158 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 2252 2.07 - 2.70: 121392 2.70 - 3.33: 276228 3.33 - 3.97: 428549 3.97 - 4.60: 627018 Nonbonded interactions: 1455439 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 I2688 " pdb=" OP2 U I2720 " model vdw 1.589 1.850 nonbonded pdb=" OP2 U I1779 " pdb=" H61 A I1784 " model vdw 1.596 1.850 nonbonded pdb=" H42 C I1607 " pdb=" OP2 G I1622 " model vdw 1.602 1.850 nonbonded pdb=" H1 G I2029 " pdb=" OP2 A I2033 " model vdw 1.603 1.850 ... (remaining 1455434 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=0.00 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: 12.660 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: 0.880 Extract box with map and model: 59.820 Check model and map are aligned: 1.170 Set scattering table: 0.750 Process input model: 423.250 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.270 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: 0.020 Load rotamer database and sin/cos tables:8.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 508.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 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 : 0.005 0.389 81818 Z= 0.302 Angle : 0.382 19.495 125625 Z= 0.190 Chirality : 0.026 0.721 16439 Planarity : 0.022 0.601 4632 Dihedral : 22.953 178.727 50567 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.47 % Favored : 95.36 % Rotamer: Outliers : 0.74 % Allowed : 14.97 % 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: 0.33 (0.25), residues: 1163 helix: 1.63 (0.36), residues: 240 sheet: 1.09 (0.41), residues: 183 loop : -0.49 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP K 248 HIS 0.002 0.000 HIS O 76 PHE 0.004 0.001 PHE K 240 TYR 0.005 0.001 TYR K 103 ARG 0.011 0.000 ARG O 96 *********************** 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 191 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 184 time to evaluate : 3.112 Fit side-chains REVERT: K 163 GLN cc_start: 0.8339 (tt0) cc_final: 0.8011 (tt0) REVERT: K 167 ARG cc_start: 0.8529 (ttm170) cc_final: 0.8292 (ttp-110) outliers start: 7 outliers final: 7 residues processed: 189 average time/residue: 3.1199 time to fit residues: 740.1140 Evaluate side-chains 188 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 181 time to evaluate : 3.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain M residue 165 HIS Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 131 ASN Chi-restraints excluded: chain O residue 142 ILE 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: 5.9990 chunk 314 optimal weight: 7.9990 chunk 174 optimal weight: 7.9990 chunk 107 optimal weight: 40.0000 chunk 212 optimal weight: 50.0000 chunk 168 optimal weight: 6.9990 chunk 325 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 242 optimal weight: 6.9990 chunk 376 optimal weight: 2.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 21 ASN L 104 GLN M 115 GLN M 156 ASN M 195 GLN P 31 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9007 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 81818 Z= 0.369 Angle : 0.645 19.788 125625 Z= 0.356 Chirality : 0.042 0.706 16439 Planarity : 0.007 0.138 4632 Dihedral : 22.909 179.275 48340 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.42 % Favored : 94.33 % Rotamer: Outliers : 2.12 % Allowed : 13.16 % Favored : 84.71 % 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: -0.08 (0.25), residues: 1163 helix: 1.38 (0.35), residues: 253 sheet: 0.86 (0.40), residues: 178 loop : -0.84 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 248 HIS 0.006 0.001 HIS K 230 PHE 0.011 0.001 PHE K 240 TYR 0.010 0.002 TYR P 38 ARG 0.007 0.001 ARG O 96 *********************** 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 208 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 188 time to evaluate : 3.083 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 163 GLN cc_start: 0.8487 (tt0) cc_final: 0.8132 (tt0) REVERT: K 167 ARG cc_start: 0.8600 (ttm170) cc_final: 0.8368 (ttp-110) REVERT: L 13 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8565 (mptp) REVERT: P 59 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7732 (tm-30) outliers start: 20 outliers final: 9 residues processed: 198 average time/residue: 3.2072 time to fit residues: 792.2639 Evaluate side-chains 182 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 171 time to evaluate : 3.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 13 LYS Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 9 GLU Chi-restraints excluded: chain O residue 131 ASN Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 59 GLU 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: 30.0000 chunk 116 optimal weight: 10.9990 chunk 313 optimal weight: 4.9990 chunk 256 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 377 optimal weight: 5.9990 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: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 104 GLN M 115 GLN M 195 GLN P 31 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 81818 Z= 0.291 Angle : 0.593 19.712 125625 Z= 0.328 Chirality : 0.037 0.663 16439 Planarity : 0.007 0.135 4632 Dihedral : 22.913 179.815 48336 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.16 % Favored : 94.58 % Rotamer: Outliers : 1.59 % Allowed : 14.44 % Favored : 83.97 % 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: -0.20 (0.24), residues: 1163 helix: 1.33 (0.34), residues: 259 sheet: 0.76 (0.40), residues: 177 loop : -0.95 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 248 HIS 0.005 0.001 HIS M 165 PHE 0.014 0.001 PHE K 240 TYR 0.009 0.001 TYR P 38 ARG 0.009 0.000 ARG O 96 *********************** 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 191 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 176 time to evaluate : 2.868 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 5 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8432 (ttpp) REVERT: K 163 GLN cc_start: 0.8479 (tt0) cc_final: 0.8161 (tt0) REVERT: K 167 ARG cc_start: 0.8620 (ttm170) cc_final: 0.8376 (ttp-110) REVERT: O 138 GLN cc_start: 0.8127 (mt0) cc_final: 0.7920 (tt0) REVERT: P 95 ARG cc_start: 0.8334 (tpp80) cc_final: 0.7927 (tpp-160) REVERT: R 29 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8571 (mt0) outliers start: 15 outliers final: 8 residues processed: 183 average time/residue: 3.3572 time to fit residues: 763.6112 Evaluate side-chains 182 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 172 time to evaluate : 2.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 5 LYS Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 9 GLU Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 131 ASN Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain Q residue 57 LYS Chi-restraints excluded: chain R residue 29 GLN 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: 5.9990 chunk 378 optimal weight: 5.9990 chunk 401 optimal weight: 10.0000 chunk 197 optimal weight: 5.9990 chunk 359 optimal weight: 4.9990 chunk 108 optimal weight: 40.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 104 GLN M 195 GLN P 31 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9017 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 81818 Z= 0.350 Angle : 0.638 19.736 125625 Z= 0.351 Chirality : 0.040 0.712 16439 Planarity : 0.007 0.138 4632 Dihedral : 22.963 178.700 48336 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.19 % Favored : 93.55 % Rotamer: Outliers : 2.44 % Allowed : 13.27 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.27 % 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: -0.33 (0.24), residues: 1163 helix: 1.35 (0.34), residues: 253 sheet: 0.71 (0.39), residues: 182 loop : -1.09 (0.22), residues: 728 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 0.015 0.001 PHE K 240 TYR 0.010 0.002 TYR P 38 ARG 0.010 0.001 ARG O 96 *********************** 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 195 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 172 time to evaluate : 3.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 163 GLN cc_start: 0.8502 (tt0) cc_final: 0.8201 (tt0) REVERT: K 167 ARG cc_start: 0.8625 (ttm170) cc_final: 0.8390 (ttp-110) REVERT: L 13 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8591 (mptp) REVERT: N 184 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8137 (mtt-85) outliers start: 23 outliers final: 14 residues processed: 186 average time/residue: 3.4008 time to fit residues: 782.8875 Evaluate side-chains 179 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 163 time to evaluate : 3.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 5 LYS Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 252 THR Chi-restraints excluded: chain K residue 264 ASP Chi-restraints excluded: chain L residue 13 LYS Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain M residue 191 ASP Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 184 ARG Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 9 GLU Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 131 ASN Chi-restraints excluded: chain O residue 142 ILE 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: 4.9990 chunk 227 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 298 optimal weight: 6.9990 chunk 165 optimal weight: 5.9990 chunk 342 optimal weight: 8.9990 chunk 277 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 204 optimal weight: 4.9990 chunk 360 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 104 GLN M 115 GLN M 195 GLN P 31 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9017 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 81818 Z= 0.371 Angle : 0.635 19.681 125625 Z= 0.348 Chirality : 0.041 0.699 16439 Planarity : 0.007 0.139 4632 Dihedral : 22.989 179.412 48336 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.76 % Favored : 93.98 % Rotamer: Outliers : 2.65 % Allowed : 13.91 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.18 % 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: -0.44 (0.24), residues: 1163 helix: 1.26 (0.34), residues: 253 sheet: 0.64 (0.39), residues: 182 loop : -1.16 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 248 HIS 0.005 0.001 HIS M 165 PHE 0.015 0.001 PHE K 240 TYR 0.011 0.002 TYR P 38 ARG 0.014 0.001 ARG O 96 *********************** 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 190 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 165 time to evaluate : 3.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 163 GLN cc_start: 0.8504 (tt0) cc_final: 0.8214 (tt0) REVERT: K 167 ARG cc_start: 0.8627 (ttm170) cc_final: 0.8391 (ttp-110) REVERT: L 13 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8631 (mptp) REVERT: N 184 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8127 (mtt-85) REVERT: P 59 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7838 (tm-30) REVERT: R 29 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8576 (mt0) outliers start: 25 outliers final: 16 residues processed: 180 average time/residue: 3.4733 time to fit residues: 782.0407 Evaluate side-chains 189 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 169 time to evaluate : 3.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 5 LYS Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 252 THR Chi-restraints excluded: chain K residue 264 ASP Chi-restraints excluded: chain L residue 13 LYS Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain M residue 191 ASP Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 184 ARG Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 9 GLU Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 131 ASN Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 59 GLU Chi-restraints excluded: chain Q residue 57 LYS Chi-restraints excluded: chain R residue 29 GLN 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: 7.9990 chunk 79 optimal weight: 4.9990 chunk 235 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 401 optimal weight: 1.9990 chunk 333 optimal weight: 0.6980 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: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 104 GLN M 195 GLN P 31 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 81818 Z= 0.253 Angle : 0.605 19.897 125625 Z= 0.338 Chirality : 0.037 0.701 16439 Planarity : 0.007 0.136 4632 Dihedral : 22.999 179.287 48336 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.85 % Favored : 93.90 % Rotamer: Outliers : 2.12 % Allowed : 14.54 % Favored : 83.33 % 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: -0.42 (0.24), residues: 1163 helix: 1.30 (0.34), residues: 253 sheet: 0.62 (0.39), residues: 182 loop : -1.16 (0.21), residues: 728 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 0.014 0.001 PHE K 240 TYR 0.010 0.001 TYR P 38 ARG 0.007 0.000 ARG O 96 *********************** 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 189 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 169 time to evaluate : 2.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 163 GLN cc_start: 0.8497 (tt0) cc_final: 0.8160 (tt0) REVERT: K 167 ARG cc_start: 0.8624 (ttm170) cc_final: 0.8384 (ttp-110) REVERT: L 13 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8620 (mptp) REVERT: N 184 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8126 (mtt-85) REVERT: P 59 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7823 (tm-30) REVERT: R 29 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8562 (mt0) outliers start: 20 outliers final: 16 residues processed: 181 average time/residue: 3.3831 time to fit residues: 768.6980 Evaluate side-chains 183 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 163 time to evaluate : 3.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 5 LYS Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 252 THR Chi-restraints excluded: chain K residue 264 ASP Chi-restraints excluded: chain L residue 13 LYS Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain M residue 191 ASP Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 184 ARG Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 9 GLU Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 131 ASN Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 59 GLU Chi-restraints excluded: chain Q residue 57 LYS Chi-restraints excluded: chain R residue 29 GLN 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: 6.9990 chunk 228 optimal weight: 8.9990 chunk 293 optimal weight: 10.0000 chunk 227 optimal weight: 5.9990 chunk 338 optimal weight: 6.9990 chunk 224 optimal weight: 4.9990 chunk 399 optimal weight: 3.9990 chunk 250 optimal weight: 5.9990 chunk 243 optimal weight: 5.9990 chunk 184 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 104 GLN M 195 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9012 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 81818 Z= 0.340 Angle : 0.623 19.718 125625 Z= 0.344 Chirality : 0.040 0.701 16439 Planarity : 0.007 0.137 4632 Dihedral : 22.987 179.360 48336 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.02 % Favored : 93.72 % Rotamer: Outliers : 2.02 % Allowed : 14.76 % Favored : 83.23 % 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: -0.42 (0.24), residues: 1163 helix: 1.34 (0.34), residues: 253 sheet: 0.52 (0.38), residues: 192 loop : -1.16 (0.21), residues: 718 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 0.002 TYR P 38 ARG 0.010 0.000 ARG O 96 *********************** 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 186 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 167 time to evaluate : 3.061 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 72 ASP cc_start: 0.8940 (OUTLIER) cc_final: 0.8689 (m-30) REVERT: K 163 GLN cc_start: 0.8506 (tt0) cc_final: 0.8177 (tt0) REVERT: K 167 ARG cc_start: 0.8630 (ttm170) cc_final: 0.8402 (ttp-110) REVERT: L 13 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8645 (mptp) REVERT: P 59 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7827 (tm-30) REVERT: P 95 ARG cc_start: 0.8297 (tpp80) cc_final: 0.7852 (tpp-160) REVERT: R 29 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8568 (mt0) outliers start: 19 outliers final: 13 residues processed: 178 average time/residue: 3.3791 time to fit residues: 745.5822 Evaluate side-chains 188 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 171 time to evaluate : 3.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 5 LYS Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 264 ASP Chi-restraints excluded: chain L residue 13 LYS Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 9 GLU Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 131 ASN Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 59 GLU Chi-restraints excluded: chain Q residue 57 LYS Chi-restraints excluded: chain R residue 29 GLN 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: 6.9990 chunk 78 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 254 optimal weight: 6.9990 chunk 272 optimal weight: 6.9990 chunk 197 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 314 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 104 GLN M 115 GLN M 195 GLN N 42 ASN P 31 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9017 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 81818 Z= 0.352 Angle : 0.631 19.745 125625 Z= 0.346 Chirality : 0.040 0.706 16439 Planarity : 0.007 0.138 4632 Dihedral : 22.993 179.264 48336 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.19 % Favored : 93.55 % Rotamer: Outliers : 2.02 % Allowed : 15.07 % Favored : 82.91 % 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: -0.44 (0.24), residues: 1163 helix: 1.32 (0.35), residues: 253 sheet: 0.53 (0.38), residues: 192 loop : -1.18 (0.21), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 248 HIS 0.005 0.001 HIS K 230 PHE 0.015 0.001 PHE K 240 TYR 0.010 0.002 TYR P 38 ARG 0.011 0.000 ARG O 96 *********************** 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 191 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 172 time to evaluate : 3.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 72 ASP cc_start: 0.8934 (OUTLIER) cc_final: 0.8670 (m-30) REVERT: K 163 GLN cc_start: 0.8510 (tt0) cc_final: 0.8184 (tt0) REVERT: K 167 ARG cc_start: 0.8627 (ttm170) cc_final: 0.8392 (ttp-110) REVERT: L 13 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8646 (mptp) REVERT: P 59 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7828 (tm-30) REVERT: R 29 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8572 (mt0) outliers start: 19 outliers final: 13 residues processed: 182 average time/residue: 3.3171 time to fit residues: 749.0228 Evaluate side-chains 182 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 165 time to evaluate : 3.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 5 LYS Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 252 THR Chi-restraints excluded: chain K residue 264 ASP Chi-restraints excluded: chain L residue 13 LYS Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 9 GLU Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 131 ASN Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 59 GLU Chi-restraints excluded: chain Q residue 57 LYS Chi-restraints excluded: chain R residue 29 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 363 optimal weight: 0.9990 chunk 383 optimal weight: 5.9990 chunk 349 optimal weight: 0.6980 chunk 372 optimal weight: 4.9990 chunk 224 optimal weight: 4.9990 chunk 162 optimal weight: 6.9990 chunk 292 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 336 optimal weight: 5.9990 chunk 352 optimal weight: 8.9990 chunk 371 optimal weight: 4.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 104 GLN M 195 GLN N 42 ASN P 31 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9006 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 81818 Z= 0.217 Angle : 0.597 19.957 125625 Z= 0.336 Chirality : 0.036 0.704 16439 Planarity : 0.007 0.136 4632 Dihedral : 23.005 179.135 48336 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.02 % Favored : 93.72 % Rotamer: Outliers : 2.34 % Allowed : 14.97 % Favored : 82.70 % 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: -0.41 (0.24), residues: 1163 helix: 1.37 (0.35), residues: 253 sheet: 0.52 (0.38), residues: 192 loop : -1.16 (0.21), residues: 718 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 0.014 0.001 PHE K 240 TYR 0.010 0.001 TYR P 38 ARG 0.010 0.000 ARG O 96 *********************** 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 189 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 167 time to evaluate : 3.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 72 ASP cc_start: 0.8920 (OUTLIER) cc_final: 0.8658 (m-30) REVERT: K 163 GLN cc_start: 0.8496 (tt0) cc_final: 0.8171 (tt0) REVERT: K 167 ARG cc_start: 0.8621 (ttm170) cc_final: 0.8378 (ttp-110) REVERT: L 13 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8634 (mptp) REVERT: N 184 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8132 (mtt-85) REVERT: P 59 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7824 (tm-30) REVERT: R 29 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8563 (mt0) outliers start: 22 outliers final: 13 residues processed: 181 average time/residue: 3.2997 time to fit residues: 739.4288 Evaluate side-chains 190 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 172 time to evaluate : 3.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 5 LYS Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 252 THR Chi-restraints excluded: chain K residue 264 ASP Chi-restraints excluded: chain L residue 13 LYS Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 184 ARG Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 9 GLU Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 131 ASN Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 59 GLU Chi-restraints excluded: chain Q residue 57 LYS Chi-restraints excluded: chain R residue 29 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 244 optimal weight: 5.9990 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: 0.9990 chunk 380 optimal weight: 4.9990 chunk 329 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 254 optimal weight: 6.9990 chunk 201 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: L 104 GLN M 115 GLN M 195 GLN N 42 ASN P 31 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9010 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 81818 Z= 0.305 Angle : 0.612 19.787 125625 Z= 0.339 Chirality : 0.039 0.704 16439 Planarity : 0.007 0.136 4632 Dihedral : 22.997 179.356 48336 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.93 % Favored : 93.81 % Rotamer: Outliers : 1.91 % Allowed : 15.29 % Favored : 82.80 % 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: -0.43 (0.24), residues: 1163 helix: 1.37 (0.35), residues: 253 sheet: 0.59 (0.39), residues: 182 loop : -1.19 (0.21), residues: 728 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 0.014 0.001 PHE K 240 TYR 0.010 0.001 TYR P 38 ARG 0.013 0.000 ARG O 96 ********************** 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 188 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 170 time to evaluate : 3.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 72 ASP cc_start: 0.8925 (OUTLIER) cc_final: 0.8682 (m-30) REVERT: K 163 GLN cc_start: 0.8501 (tt0) cc_final: 0.8177 (tt0) REVERT: K 167 ARG cc_start: 0.8625 (ttm170) cc_final: 0.8382 (ttp-110) REVERT: L 13 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8642 (mptp) REVERT: N 184 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8140 (mtt-85) REVERT: P 59 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7823 (tm-30) REVERT: R 29 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8568 (mt0) outliers start: 18 outliers final: 13 residues processed: 181 average time/residue: 3.3393 time to fit residues: 751.4412 Evaluate side-chains 182 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 164 time to evaluate : 3.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 5 LYS Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 252 THR Chi-restraints excluded: chain K residue 264 ASP Chi-restraints excluded: chain L residue 13 LYS Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 184 ARG Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 9 GLU Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 131 ASN Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain P residue 59 GLU Chi-restraints excluded: chain Q residue 57 LYS Chi-restraints excluded: chain R residue 29 GLN 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: 2.9990 chunk 100 optimal weight: 6.9990 chunk 303 optimal weight: 4.9990 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: 0.7980 chunk 41 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 104 GLN M 115 GLN M 195 GLN N 42 ASN P 31 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.105215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.062621 restraints weight = 243646.409| |-----------------------------------------------------------------------------| r_work (start): 0.2630 rms_B_bonded: 0.51 r_work: 0.2542 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2473 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.2473 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2476 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2476 r_free = 0.2476 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 49 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2476 r_free = 0.2476 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 49 | |-----------------------------------------------------------------------------| r_final: 0.2476 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9026 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 81818 Z= 0.245 Angle : 0.598 19.891 125625 Z= 0.335 Chirality : 0.037 0.704 16439 Planarity : 0.007 0.135 4632 Dihedral : 23.000 179.320 48336 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.93 % Favored : 93.81 % Rotamer: Outliers : 1.91 % Allowed : 15.39 % Favored : 82.70 % 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: -0.42 (0.24), residues: 1163 helix: 1.39 (0.35), residues: 253 sheet: 0.58 (0.39), residues: 182 loop : -1.18 (0.21), residues: 728 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 0.014 0.001 PHE K 240 TYR 0.009 0.001 TYR P 38 ARG 0.008 0.000 ARG O 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 34381.26 seconds wall clock time: 590 minutes 33.17 seconds (35433.17 seconds total)