Starting phenix.real_space_refine on Sat Dec 9 14:07:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e45_27880/12_2023/8e45_27880_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e45_27880/12_2023/8e45_27880.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e45_27880/12_2023/8e45_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_27880/12_2023/8e45_27880_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e45_27880/12_2023/8e45_27880_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e45_27880/12_2023/8e45_27880.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e45_27880/12_2023/8e45_27880.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e45_27880/12_2023/8e45_27880_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e45_27880/12_2023/8e45_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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 64.58, 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: 76.11 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 29.7% alpha, 15.4% beta 806 base pairs and 1612 stacking pairs defined. Time for finding SS restraints: 57.15 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: 130.02 Time building geometry restraints manager: 80.21 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: 52906 35.75 - 71.49: 5248 71.49 - 107.24: 779 107.24 - 142.98: 11 142.98 - 178.73: 9 Dihedral angle restraints: 58953 sinusoidal: 55303 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 58950 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: 11.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.840 Extract box with map and model: 61.860 Check model and map are aligned: 1.260 Set scattering table: 0.740 Process input model: 422.150 Find NCS groups from input model: 1.360 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: 0.020 Load rotamer database and sin/cos tables:10.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 510.780 ------------------------------------------------------------------------------- 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 : 0.392 33.905 125625 Z= 0.192 Chirality : 0.026 0.721 16439 Planarity : 0.022 0.601 4632 Dihedral : 22.100 178.727 48183 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 : 3.144 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 189 average time/residue: 3.1426 time to fit residues: 747.6423 Evaluate side-chains 188 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 181 time to evaluate : 3.377 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 2 average time/residue: 1.0835 time to fit residues: 6.0987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0670 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: 4.4126 ------------------------------------------------------------------------------- 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: 0.8988 moved from start: 0.1233 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= 0.290 Angle : 0.602 19.788 125625 Z= 0.335 Chirality : 0.039 0.707 16439 Planarity : 0.007 0.135 4632 Dihedral : 22.068 179.235 45943 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.42 % Favored : 94.41 % Rotamer: Outliers : 1.70 % Allowed : 13.80 % Favored : 84.50 % 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: 0.02 (0.25), residues: 1163 helix: 1.38 (0.35), residues: 259 sheet: 0.90 (0.40), residues: 178 loop : -0.75 (0.23), residues: 726 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 0.009 0.001 PHE K 240 TYR 0.009 0.001 TYR P 38 ARG 0.007 0.000 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: 16 poor density : 192 time to evaluate : 3.214 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 201 average time/residue: 3.1084 time to fit residues: 785.6867 Evaluate side-chains 185 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 177 time to evaluate : 3.076 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 3 average time/residue: 0.8934 time to fit residues: 7.0211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 313 optimal weight: 0.5980 chunk 256 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 377 optimal weight: 0.7980 chunk 407 optimal weight: 4.9990 chunk 336 optimal weight: 6.9990 chunk 374 optimal weight: 0.3980 chunk 128 optimal weight: 5.9990 chunk 302 optimal weight: 4.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- 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: 0.8964 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 81818 Z= 0.167 Angle : 0.560 20.120 125625 Z= 0.316 Chirality : 0.035 0.728 16439 Planarity : 0.006 0.128 4632 Dihedral : 22.074 179.429 45943 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.73 % Favored : 95.01 % Rotamer: Outliers : 0.96 % Allowed : 14.76 % Favored : 84.29 % 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: -0.06 (0.25), residues: 1163 helix: 1.40 (0.34), residues: 259 sheet: 0.79 (0.40), residues: 172 loop : -0.81 (0.22), residues: 732 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 0.010 0.001 PHE K 240 TYR 0.007 0.001 TYR P 38 ARG 0.005 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 189 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 180 time to evaluate : 3.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 187 average time/residue: 3.2213 time to fit residues: 756.2723 Evaluate side-chains 187 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 179 time to evaluate : 3.161 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 3 average time/residue: 1.0192 time to fit residues: 7.8395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 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: 6.9990 chunk 401 optimal weight: 7.9990 chunk 197 optimal weight: 5.9990 chunk 359 optimal weight: 6.9990 chunk 108 optimal weight: 40.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9021 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 81818 Z= 0.390 Angle : 0.656 19.681 125625 Z= 0.357 Chirality : 0.041 0.697 16439 Planarity : 0.007 0.139 4632 Dihedral : 22.134 178.634 45943 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.67 % Favored : 94.07 % Rotamer: Outliers : 2.55 % Allowed : 13.48 % Favored : 83.97 % 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: -0.28 (0.24), residues: 1163 helix: 1.46 (0.35), residues: 247 sheet: 0.67 (0.39), residues: 183 loop : -1.05 (0.22), residues: 733 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 0.011 0.002 TYR P 38 ARG 0.006 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 197 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 173 time to evaluate : 3.114 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 13 residues processed: 183 average time/residue: 3.4026 time to fit residues: 784.3593 Evaluate side-chains 182 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 169 time to evaluate : 3.119 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 5 residues processed: 8 average time/residue: 1.2649 time to fit residues: 19.4960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 334 optimal weight: 3.9990 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: 6.9990 chunk 277 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 204 optimal weight: 4.9990 chunk 360 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 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: 0.9010 moved from start: 0.1588 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= 0.280 Angle : 0.618 19.862 125625 Z= 0.343 Chirality : 0.038 0.702 16439 Planarity : 0.007 0.136 4632 Dihedral : 22.147 178.427 45943 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.33 % Favored : 94.41 % Rotamer: Outliers : 1.17 % Allowed : 14.65 % Favored : 84.18 % 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: -0.33 (0.24), residues: 1163 helix: 1.46 (0.35), residues: 247 sheet: 0.64 (0.39), residues: 183 loop : -1.10 (0.22), residues: 733 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 0.014 0.001 PHE K 240 TYR 0.010 0.001 TYR P 38 ARG 0.010 0.000 ARG O 96 *********************** REFINEMENT MACRO_CYCLE 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 184 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 173 time to evaluate : 3.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 10 residues processed: 179 average time/residue: 3.3469 time to fit residues: 756.6982 Evaluate side-chains 178 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 168 time to evaluate : 3.372 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 5 residues processed: 5 average time/residue: 1.0413 time to fit residues: 11.8226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 134 optimal weight: 6.9990 chunk 361 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 235 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 401 optimal weight: 10.0000 chunk 333 optimal weight: 0.9990 chunk 185 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 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: L 104 GLN M 115 GLN M 195 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9010 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 81818 Z= 0.336 Angle : 0.622 19.783 125625 Z= 0.343 Chirality : 0.040 0.707 16439 Planarity : 0.007 0.137 4632 Dihedral : 22.140 179.137 45943 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.67 % Favored : 94.07 % Rotamer: Outliers : 2.12 % Allowed : 13.91 % Favored : 83.97 % 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: -0.38 (0.24), residues: 1163 helix: 1.48 (0.35), residues: 247 sheet: 0.53 (0.38), residues: 192 loop : -1.16 (0.21), residues: 724 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 0.002 TYR P 38 ARG 0.008 0.000 ARG P 95 *********************** 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 190 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 170 time to evaluate : 3.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 13 residues processed: 182 average time/residue: 3.4121 time to fit residues: 783.9599 Evaluate side-chains 175 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 162 time to evaluate : 3.356 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 9 residues processed: 5 average time/residue: 1.4076 time to fit residues: 13.8154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 293 optimal weight: 10.0000 chunk 227 optimal weight: 5.9990 chunk 338 optimal weight: 2.9990 chunk 224 optimal weight: 4.9990 chunk 399 optimal weight: 3.9990 chunk 250 optimal weight: 4.9990 chunk 243 optimal weight: 4.9990 chunk 184 optimal weight: 10.0000 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: 0.9006 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 81818 Z= 0.287 Angle : 0.607 19.867 125625 Z= 0.338 Chirality : 0.038 0.707 16439 Planarity : 0.007 0.136 4632 Dihedral : 22.145 179.145 45943 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.76 % Favored : 93.98 % Rotamer: Outliers : 1.49 % Allowed : 14.54 % Favored : 83.97 % 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: -0.38 (0.24), residues: 1163 helix: 1.50 (0.35), residues: 247 sheet: 0.54 (0.38), residues: 192 loop : -1.16 (0.21), residues: 724 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 0.015 0.001 PHE K 240 TYR 0.010 0.001 TYR P 38 ARG 0.005 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 176 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 162 time to evaluate : 3.162 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 12 residues processed: 172 average time/residue: 3.3535 time to fit residues: 719.3747 Evaluate side-chains 180 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 168 time to evaluate : 3.145 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 4 average time/residue: 1.0265 time to fit residues: 9.8614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 120 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 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: 0.6980 overall best weight: 4.9388 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 81818 Z= 0.322 Angle : 0.614 19.892 125625 Z= 0.340 Chirality : 0.039 0.704 16439 Planarity : 0.007 0.137 4632 Dihedral : 22.156 179.359 45943 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.59 % Favored : 94.15 % Rotamer: Outliers : 1.59 % Allowed : 14.54 % 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: -0.41 (0.24), residues: 1163 helix: 1.39 (0.35), residues: 253 sheet: 0.62 (0.39), residues: 182 loop : -1.18 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 248 HIS 0.004 0.001 HIS K 230 PHE 0.014 0.001 PHE K 240 TYR 0.010 0.002 TYR P 38 ARG 0.010 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 184 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 169 time to evaluate : 3.132 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 13 residues processed: 180 average time/residue: 3.3169 time to fit residues: 748.4206 Evaluate side-chains 176 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 163 time to evaluate : 3.348 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 11 residues processed: 4 average time/residue: 1.0542 time to fit residues: 9.8900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 363 optimal weight: 1.9990 chunk 383 optimal weight: 6.9990 chunk 349 optimal weight: 4.9990 chunk 372 optimal weight: 3.9990 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: 4.9990 chunk 352 optimal weight: 6.9990 chunk 371 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 P 31 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9004 moved from start: 0.1761 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= 0.275 Angle : 0.601 19.947 125625 Z= 0.336 Chirality : 0.038 0.706 16439 Planarity : 0.007 0.136 4632 Dihedral : 22.161 179.303 45943 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.67 % Favored : 94.07 % Rotamer: Outliers : 1.38 % Allowed : 14.76 % 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: -0.40 (0.24), residues: 1163 helix: 1.41 (0.35), residues: 253 sheet: 0.61 (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 0.013 0.001 PHE K 240 TYR 0.010 0.001 TYR P 38 ARG 0.012 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 176 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 163 time to evaluate : 3.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 13 residues processed: 172 average time/residue: 3.4662 time to fit residues: 747.4289 Evaluate side-chains 181 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 168 time to evaluate : 3.114 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 11 residues processed: 4 average time/residue: 1.4178 time to fit residues: 11.4864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 244 optimal weight: 4.9990 chunk 394 optimal weight: 0.8980 chunk 240 optimal weight: 6.9990 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: 2.9990 chunk 34 optimal weight: 10.0000 chunk 254 optimal weight: 6.9990 chunk 201 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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: 0.8996 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 81818 Z= 0.193 Angle : 0.580 20.082 125625 Z= 0.329 Chirality : 0.036 0.705 16439 Planarity : 0.007 0.134 4632 Dihedral : 22.169 179.260 45943 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.50 % Favored : 94.24 % Rotamer: Outliers : 1.38 % Allowed : 14.97 % Favored : 83.65 % 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: -0.38 (0.24), residues: 1163 helix: 1.45 (0.35), residues: 253 sheet: 0.61 (0.39), residues: 182 loop : -1.17 (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 0.013 0.001 PHE K 240 TYR 0.009 0.001 TYR P 38 ARG 0.012 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 182 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 169 time to evaluate : 3.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 12 residues processed: 179 average time/residue: 3.2854 time to fit residues: 733.4194 Evaluate side-chains 174 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 162 time to evaluate : 3.408 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 3 average time/residue: 0.9917 time to fit residues: 7.7443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 261 optimal weight: 6.9990 chunk 350 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 chunk 303 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 91 optimal weight: 6.9990 chunk 329 optimal weight: 4.9990 chunk 138 optimal weight: 7.9990 chunk 338 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.105559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.062881 restraints weight = 244986.447| |-----------------------------------------------------------------------------| r_work (start): 0.2613 rms_B_bonded: 0.51 r_work: 0.2524 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2455 rms_B_bonded: 2.25 restraints_weight: 0.2500 r_work (final): 0.2455 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2484 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2484 r_free = 0.2484 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 = 0.2484 r_free = 0.2484 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 49 | |-----------------------------------------------------------------------------| r_final: 0.2484 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 81818 Z= 0.288 Angle : 0.601 19.885 125625 Z= 0.334 Chirality : 0.038 0.704 16439 Planarity : 0.007 0.135 4632 Dihedral : 22.157 179.597 45943 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.67 % Favored : 94.07 % Rotamer: Outliers : 1.70 % Allowed : 14.76 % Favored : 83.55 % 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: -0.35 (0.24), residues: 1163 helix: 1.47 (0.35), residues: 253 sheet: 0.54 (0.38), residues: 192 loop : -1.14 (0.22), residues: 718 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 0.002 TYR P 38 ARG 0.010 0.000 ARG O 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 33522.50 seconds wall clock time: 575 minutes 47.21 seconds (34547.21 seconds total)