Starting phenix.real_space_refine on Tue Mar 12 19:20:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e33_27855/03_2024/8e33_27855_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e33_27855/03_2024/8e33_27855.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e33_27855/03_2024/8e33_27855_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e33_27855/03_2024/8e33_27855_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e33_27855/03_2024/8e33_27855_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e33_27855/03_2024/8e33_27855.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e33_27855/03_2024/8e33_27855.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e33_27855/03_2024/8e33_27855_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e33_27855/03_2024/8e33_27855_neut_trim_updated.pdb" } resolution = 2.23 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= -0.027 sd= 1.021 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 34612 2.51 5 N 13688 2.21 5 O 22593 1.98 5 F 1 1.80 5 H 41830 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K GLU 100": "OE1" <-> "OE2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "M ASP 145": "OD1" <-> "OD2" Residue "N ASP 39": "OD1" <-> "OD2" Residue "O ASP 49": "OD1" <-> "OD2" Residue "O GLU 91": "OE1" <-> "OE2" Residue "O GLU 129": "OE1" <-> "OE2" Residue "P GLU 59": "OE1" <-> "OE2" Residue "Q GLU 36": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 115769 Number of models: 1 Model: "" Number of chains: 11 Chain: "I" Number of atoms: 93326 Number of conformers: 2 Conformer: "A" 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 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: 100661 Chain: "J" Number of atoms: 3810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 3810 Classifications: {'RNA': 118} Modifications used: {'3*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 48} Link IDs: {'rna2p': 13, 'rna3p': 104} Chain: "K" Number of atoms: 4237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 4237 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "L" Number of atoms: 2182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2182 Classifications: {'peptide': 144} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "M" Number of atoms: 3170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3170 Classifications: {'peptide': 201} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "N" Number of atoms: 3182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3182 Classifications: {'peptide': 209} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "O" Number of atoms: 2291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2291 Classifications: {'peptide': 142} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "P" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1775 Classifications: {'peptide': 110} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "Q" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 898 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "R" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 794 Classifications: {'peptide': 46} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "I" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 104 Unusual residues: {'UDU': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" P A U I2506 " occ=0.50 ... (58 atoms not shown) pdb=" H6 B U I2506 " occ=0.50 residue: pdb=" P A C I2507 " occ=0.50 ... (60 atoms not shown) pdb=" H6 B C I2507 " occ=0.50 Time building chain proxies: 64.70, per 1000 atoms: 0.56 Number of scatterers: 115769 At special positions: 0 Unit cell: (229.656, 222.221, 190.003, 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 22593 8.00 N 13688 7.00 C 34612 6.00 H 41830 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: 81.99 Conformation dependent library (CDL) restraints added in 2.6 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 12 sheets defined 29.9% alpha, 15.2% beta 925 base pairs and 1589 stacking pairs defined. Time for finding SS restraints: 57.41 Creating SS restraints... Processing helix chain 'K' and resid 30 through 35 removed outlier: 3.718A pdb=" N LEU K 34 " --> pdb=" O PHE K 30 " (cutoff:3.500A) removed outlier: 5.629A 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 Proline residue: K 136 - end of helix Processing helix chain 'K' and resid 207 through 215 removed outlier: 3.837A pdb=" N ALA K 211 " --> pdb=" O LYS K 207 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 226 removed outlier: 6.935A pdb=" N MET K 225 " --> pdb=" O ARG K 221 " (cutoff:3.500A) removed outlier: 5.343A 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: 5.721A pdb=" N SER L 42 " --> pdb=" O GLN L 38 " (cutoff:3.500A) 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: 7.017A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 5.162A 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: 3.716A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 3.739A 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 removed outlier: 3.551A pdb=" N GLY L 139 " --> pdb=" O ILE L 135 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 20 Processing helix chain 'M' and resid 24 through 41 removed outlier: 3.634A pdb=" N ARG M 40 " --> pdb=" O ALA M 36 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N GLN M 41 " --> pdb=" O ALA M 37 " (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 165 removed outlier: 4.481A pdb=" N ASN M 163 " --> pdb=" O LEU M 159 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LEU M 164 " --> pdb=" O ALA M 160 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N HIS M 165 " --> pdb=" O ALA M 161 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 184 removed outlier: 3.569A pdb=" N ILE M 181 " --> pdb=" O PRO M 177 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ASP M 184 " --> pdb=" O LEU M 180 " (cutoff:3.500A) Processing helix chain 'M' and resid 189 through 201 Processing helix chain 'N' and resid 56 through 61 removed outlier: 5.790A pdb=" N THR N 61 " --> pdb=" O ALA N 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 72 removed outlier: 3.533A pdb=" N ALA N 71 " --> pdb=" O HIS N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 103 removed outlier: 4.641A pdb=" N ALA N 102 " --> pdb=" O VAL N 98 " (cutoff:3.500A) removed outlier: 5.348A 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: 3.842A pdb=" N GLU O 31 " --> pdb=" O ARG O 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 88 through 96 Processing helix chain 'O' and resid 97 through 110 removed outlier: 4.101A pdb=" N ILE O 101 " --> pdb=" O PRO O 97 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET O 108 " --> pdb=" O ALA O 104 " (cutoff:3.500A) Proline residue: O 110 - end of helix Processing helix chain 'O' and resid 112 through 122 removed outlier: 3.919A pdb=" N LYS O 121 " --> pdb=" O ALA O 117 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU O 122 " --> pdb=" O MET O 118 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 72 removed outlier: 4.459A pdb=" N LYS O 72 " --> pdb=" O ASN O 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 67 through 72' Processing helix chain 'P' and resid 13 through 25 removed outlier: 3.994A pdb=" N VAL P 20 " --> pdb=" O LYS P 16 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU P 23 " --> pdb=" O LEU P 19 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE P 24 " --> pdb=" O VAL P 20 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 39 Processing helix chain 'P' and resid 41 through 61 removed outlier: 3.768A pdb=" N VAL P 45 " --> pdb=" O LYS P 41 " (cutoff:3.500A) Processing helix chain 'P' and resid 65 through 70 removed outlier: 3.553A pdb=" N LEU P 69 " --> pdb=" O ASP P 65 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N LYS P 70 " --> pdb=" O ILE P 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 65 through 70' Processing helix chain 'Q' and resid 9 through 19 removed outlier: 4.845A 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 25 removed outlier: 4.106A pdb=" N THR R 24 " --> pdb=" O ALA R 20 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N LYS R 25 " --> pdb=" O ARG R 21 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 38 Processing sheet with id= 1, first strand: chain 'K' and resid 2 through 6 removed outlier: 5.493A pdb=" N VAL K 16 " --> pdb=" O CYS K 6 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'K' and resid 80 through 83 removed outlier: 3.640A pdb=" N ARG K 80 " --> pdb=" O LEU K 93 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU K 93 " --> pdb=" O GLU K 79 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASP K 114 " --> pdb=" O VAL K 78 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLY K 127 " --> pdb=" O GLN K 115 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLN K 117 " --> pdb=" O GLY K 127 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'K' and resid 162 through 165 removed outlier: 6.734A pdb=" N THR K 173 " --> pdb=" O VAL K 165 " (cutoff:3.500A) removed outlier: 4.080A 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: 4.129A pdb=" N GLU K 100 " --> pdb=" O TYR K 96 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'M' and resid 2 through 6 removed outlier: 4.791A pdb=" N SER M 10 " --> pdb=" O LEU M 5 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'M' and resid 117 through 120 Processing sheet with id= 7, first strand: chain 'N' and resid 3 through 6 Processing sheet with id= 8, first strand: chain 'N' and resid 10 through 16 removed outlier: 3.533A pdb=" N GLY N 10 " --> pdb=" O VAL N 26 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL N 20 " --> pdb=" O THR N 16 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'N' and resid 79 through 84 removed outlier: 5.985A pdb=" N ARG N 46 " --> pdb=" O LEU N 84 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLN N 49 " --> pdb=" O THR N 35 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLN N 94 " --> pdb=" O VAL N 34 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'N' and resid 105 through 108 removed outlier: 5.860A pdb=" N LYS N 105 " --> pdb=" O VAL N 177 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL N 177 " --> pdb=" O LYS N 105 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'O' and resid 52 through 57 removed outlier: 4.856A 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 8 263 hydrogen bonds defined for protein. 774 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2321 hydrogen bonds 3646 hydrogen bond angles 0 basepair planarities 925 basepair parallelities 1590 stacking parallelities Total time for adding SS restraints: 139.46 Time building geometry restraints manager: 86.27 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: 41828 1.03 - 1.23: 633 1.23 - 1.42: 43495 1.42 - 1.62: 37660 1.62 - 1.81: 54 Bond restraints: 123670 Sorted by residual: bond pdb=" C4 5MU I 747 " pdb=" C5 5MU I 747 " ideal model delta sigma weight residual 1.802 1.411 0.391 2.00e-02 2.50e+03 3.82e+02 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 3.78e+02 bond pdb=" C31 UDU I3001 " pdb=" C32 UDU I3001 " ideal model delta sigma weight residual 1.621 1.352 0.269 2.00e-02 2.50e+03 1.81e+02 bond pdb=" N1 5MU I1939 " pdb=" C6 5MU I1939 " ideal model delta sigma weight residual 1.635 1.367 0.268 2.00e-02 2.50e+03 1.80e+02 bond pdb=" N1 5MU I 747 " pdb=" C6 5MU I 747 " ideal model delta sigma weight residual 1.635 1.368 0.267 2.00e-02 2.50e+03 1.78e+02 ... (remaining 123665 not shown) Histogram of bond angle deviations from ideal: 75.51 - 87.37: 3 87.37 - 99.24: 0 99.24 - 111.10: 113996 111.10 - 122.96: 87215 122.96 - 134.83: 20245 Bond angle restraints: 221459 Sorted by residual: angle pdb=" C31 UDU I3001 " pdb=" C32 UDU I3001 " pdb=" C37 UDU I3001 " ideal model delta sigma weight residual 85.78 128.36 -42.58 3.00e+00 1.11e-01 2.01e+02 angle pdb=" C65 UDU I3001 " pdb=" C29 UDU I3001 " pdb=" N9 UDU I3001 " ideal model delta sigma weight residual 80.83 123.41 -42.58 3.00e+00 1.11e-01 2.01e+02 angle pdb=" C43 UDU I3001 " pdb=" C54 UDU I3001 " pdb=" C53 UDU I3001 " ideal model delta sigma weight residual 85.77 125.28 -39.51 3.00e+00 1.11e-01 1.73e+02 angle pdb=" C27 UDU I3001 " pdb=" C29 UDU I3001 " pdb=" C65 UDU I3001 " ideal model delta sigma weight residual 165.02 127.48 37.54 3.00e+00 1.11e-01 1.57e+02 angle pdb=" C5'A U I2506 " pdb=" C4'A U I2506 " pdb=" H4'A U I2506 " ideal model delta sigma weight residual 109.00 75.51 33.49 3.00e+00 1.11e-01 1.25e+02 ... (remaining 221454 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 54156 35.99 - 71.99: 7261 71.99 - 107.98: 806 107.98 - 143.98: 21 143.98 - 179.97: 9 Dihedral angle restraints: 62253 sinusoidal: 58603 harmonic: 3650 Sorted by residual: dihedral pdb=" O4' U I1340 " pdb=" C1' U I1340 " pdb=" N1 U I1340 " pdb=" C2 U I1340 " ideal model delta sinusoidal sigma weight residual -128.00 51.97 -179.97 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C I 323 " pdb=" C1' C I 323 " pdb=" N1 C I 323 " pdb=" C2 C I 323 " ideal model delta sinusoidal sigma weight residual -128.00 44.75 -172.75 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" O4' U I1313 " pdb=" C1' U I1313 " pdb=" N1 U I1313 " pdb=" C2 U I1313 " ideal model delta sinusoidal sigma weight residual 200.00 92.04 107.96 1 1.50e+01 4.44e-03 5.58e+01 ... (remaining 62250 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.898: 16432 0.898 - 1.796: 0 1.796 - 2.694: 0 2.694 - 3.592: 0 3.592 - 4.490: 1 Chirality restraints: 16433 Sorted by residual: chirality pdb=" C2' G7M I2069 " pdb=" C3' G7M I2069 " pdb=" O2' G7M I2069 " pdb=" C1' G7M I2069 " both_signs ideal model delta sigma weight residual False -2.75 1.74 -4.49 2.00e-01 2.50e+01 5.04e+02 chirality pdb=" C4'A U I2506 " pdb=" C5'A U I2506 " pdb=" O4'A U I2506 " pdb=" C3'A U I2506 " both_signs ideal model delta sigma weight residual False -2.50 -1.69 -0.81 2.00e-01 2.50e+01 1.64e+01 chirality pdb=" C2 UDU I3001 " pdb=" C3 UDU I3001 " pdb=" C5 UDU I3001 " pdb=" N5 UDU I3001 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.38 2.00e-01 2.50e+01 3.68e+00 ... (remaining 16430 not shown) Planarity restraints: 8171 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC I2498 " 0.024 2.00e-02 2.50e+03 5.97e-01 8.01e+03 pdb=" C4' OMC I2498 " 0.462 2.00e-02 2.50e+03 pdb=" O4' OMC I2498 " 0.765 2.00e-02 2.50e+03 pdb=" C3' OMC I2498 " -0.586 2.00e-02 2.50e+03 pdb=" O3' OMC I2498 " -0.568 2.00e-02 2.50e+03 pdb=" C2' OMC I2498 " -0.235 2.00e-02 2.50e+03 pdb=" O2' OMC I2498 " 0.875 2.00e-02 2.50e+03 pdb=" C1' OMC I2498 " 0.200 2.00e-02 2.50e+03 pdb=" N1 OMC I2498 " -0.937 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I2445 " -0.026 2.00e-02 2.50e+03 5.92e-01 7.87e+03 pdb=" C4' 2MG I2445 " -0.455 2.00e-02 2.50e+03 pdb=" O4' 2MG I2445 " -0.734 2.00e-02 2.50e+03 pdb=" C3' 2MG I2445 " 0.589 2.00e-02 2.50e+03 pdb=" O3' 2MG I2445 " 0.568 2.00e-02 2.50e+03 pdb=" C2' 2MG I2445 " 0.226 2.00e-02 2.50e+03 pdb=" O2' 2MG I2445 " -0.885 2.00e-02 2.50e+03 pdb=" C1' 2MG I2445 " -0.207 2.00e-02 2.50e+03 pdb=" N9 2MG I2445 " 0.925 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG I2251 " 0.042 2.00e-02 2.50e+03 5.69e-01 7.28e+03 pdb=" C4' OMG I2251 " 0.431 2.00e-02 2.50e+03 pdb=" O4' OMG I2251 " 0.605 2.00e-02 2.50e+03 pdb=" C3' OMG I2251 " -0.596 2.00e-02 2.50e+03 pdb=" O3' OMG I2251 " -0.575 2.00e-02 2.50e+03 pdb=" C2' OMG I2251 " -0.203 2.00e-02 2.50e+03 pdb=" O2' OMG I2251 " 0.919 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 8168 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 4148 2.16 - 2.77: 149796 2.77 - 3.38: 292296 3.38 - 3.99: 449783 3.99 - 4.60: 633285 Nonbonded interactions: 1529308 Sorted by model distance: nonbonded pdb=" H1 G I 818 " pdb=" OP2 U I1188 " model vdw 1.553 1.850 nonbonded pdb=" H1 G I2029 " pdb=" OP2 A I2033 " model vdw 1.562 1.850 nonbonded pdb=" H ILE L 77 " pdb=" O LYS L 109 " model vdw 1.563 1.850 nonbonded pdb=" H1 G I2688 " pdb=" OP2 U I2720 " model vdw 1.564 1.850 nonbonded pdb=" OP2 U I1779 " pdb=" H61 A I1784 " model vdw 1.569 1.850 ... (remaining 1529303 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.910 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: 28.020 Check model and map are aligned: 1.190 Set scattering table: 0.750 Process input model: 438.210 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.290 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: 0.010 Load rotamer database and sin/cos tables:9.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 484.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.391 81840 Z= 0.375 Angle : 0.487 42.585 125647 Z= 0.218 Chirality : 0.043 4.490 16433 Planarity : 0.022 0.597 4643 Dihedral : 23.563 179.969 50586 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.53 % Allowed : 19.43 % Favored : 80.04 % 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: 0.48 (0.25), residues: 1163 helix: 1.49 (0.35), residues: 254 sheet: 0.49 (0.38), residues: 201 loop : -0.12 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP K 248 HIS 0.003 0.001 HIS K 230 PHE 0.004 0.000 PHE K 240 TYR 0.007 0.001 TYR P 38 ARG 0.003 0.000 ARG P 88 *********************** 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 211 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 206 time to evaluate : 2.978 Fit side-chains REVERT: M 1 MET cc_start: 0.8140 (tmt) cc_final: 0.7623 (ppp) outliers start: 5 outliers final: 4 residues processed: 211 average time/residue: 3.0041 time to fit residues: 801.6442 Evaluate side-chains 203 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 199 time to evaluate : 3.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 168 ASP Chi-restraints excluded: chain Q residue 57 LYS Chi-restraints excluded: chain R residue 15 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 350 optimal weight: 0.0970 chunk 314 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 chunk 107 optimal weight: 30.0000 chunk 212 optimal weight: 50.0000 chunk 168 optimal weight: 5.9990 chunk 325 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 242 optimal weight: 4.9990 chunk 376 optimal weight: 2.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN L 104 GLN M 136 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 81840 Z= 0.339 Angle : 0.608 18.663 125647 Z= 0.324 Chirality : 0.038 0.832 16433 Planarity : 0.007 0.137 4643 Dihedral : 23.433 178.840 48354 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.70 % Allowed : 17.62 % Favored : 80.68 % 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: 0.22 (0.25), residues: 1163 helix: 1.22 (0.33), residues: 266 sheet: 0.36 (0.36), residues: 194 loop : -0.29 (0.24), residues: 703 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 M 183 TYR 0.013 0.001 TYR P 38 ARG 0.004 0.000 ARG O 99 *********************** 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 215 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 199 time to evaluate : 3.049 Fit side-chains REVERT: N 94 GLN cc_start: 0.9039 (tt0) cc_final: 0.8822 (tt0) REVERT: O 108 MET cc_start: 0.9316 (mtt) cc_final: 0.8852 (mtt) outliers start: 16 outliers final: 9 residues processed: 208 average time/residue: 3.0578 time to fit residues: 808.9299 Evaluate side-chains 211 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 202 time to evaluate : 3.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain L residue 10 GLU Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain Q residue 57 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 209 optimal weight: 20.0000 chunk 116 optimal weight: 8.9990 chunk 313 optimal weight: 5.9990 chunk 256 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 377 optimal weight: 3.9990 chunk 407 optimal weight: 2.9990 chunk 336 optimal weight: 4.9990 chunk 374 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 302 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN L 104 GLN P 31 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 81840 Z= 0.310 Angle : 0.586 14.245 125647 Z= 0.319 Chirality : 0.036 0.836 16433 Planarity : 0.007 0.135 4643 Dihedral : 23.429 177.697 48350 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.70 % Allowed : 16.99 % Favored : 81.32 % 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: 0.19 (0.25), residues: 1163 helix: 1.27 (0.33), residues: 265 sheet: 0.27 (0.35), residues: 194 loop : -0.32 (0.24), residues: 704 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 0.011 0.001 PHE M 183 TYR 0.018 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 223 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 207 time to evaluate : 2.848 Fit side-chains REVERT: N 74 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7670 (mp0) REVERT: N 183 GLU cc_start: 0.8303 (mp0) cc_final: 0.7933 (mp0) REVERT: O 1 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7634 (pp-130) REVERT: O 12 LYS cc_start: 0.8551 (mmmt) cc_final: 0.8308 (mmmm) REVERT: O 108 MET cc_start: 0.9276 (mtt) cc_final: 0.8889 (mtt) outliers start: 16 outliers final: 14 residues processed: 214 average time/residue: 3.1484 time to fit residues: 859.8894 Evaluate side-chains 210 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 195 time to evaluate : 2.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 168 ASP Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 10 GLU Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain Q residue 57 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 373 optimal weight: 2.9990 chunk 283 optimal weight: 4.9990 chunk 195 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 180 optimal weight: 3.9990 chunk 253 optimal weight: 4.9990 chunk 378 optimal weight: 4.9990 chunk 401 optimal weight: 10.0000 chunk 197 optimal weight: 3.9990 chunk 359 optimal weight: 3.9990 chunk 108 optimal weight: 40.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN L 104 GLN M 136 GLN P 31 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 81840 Z= 0.388 Angle : 0.618 14.701 125647 Z= 0.335 Chirality : 0.039 0.845 16433 Planarity : 0.007 0.140 4643 Dihedral : 23.437 178.254 48350 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.25 % Favored : 94.67 % Rotamer: Outliers : 2.55 % Allowed : 16.14 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.24), residues: 1163 helix: 1.28 (0.33), residues: 259 sheet: 0.02 (0.34), residues: 210 loop : -0.43 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 248 HIS 0.005 0.001 HIS K 230 PHE 0.011 0.001 PHE K 240 TYR 0.020 0.002 TYR P 38 ARG 0.003 0.000 ARG R 3 *********************** 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 235 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 211 time to evaluate : 3.011 Fit side-chains REVERT: M 136 GLN cc_start: 0.8352 (tp40) cc_final: 0.8096 (tp-100) REVERT: N 59 ARG cc_start: 0.9099 (OUTLIER) cc_final: 0.8735 (ttt-90) REVERT: N 74 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7674 (mp0) REVERT: N 94 GLN cc_start: 0.9012 (tt0) cc_final: 0.8805 (tt0) REVERT: N 105 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8277 (mtpp) REVERT: N 183 GLU cc_start: 0.8327 (mp0) cc_final: 0.8003 (mp0) REVERT: O 12 LYS cc_start: 0.8586 (mmmt) cc_final: 0.8343 (mmmm) REVERT: O 81 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8381 (mp) REVERT: O 108 MET cc_start: 0.9314 (mtt) cc_final: 0.8945 (mtt) outliers start: 24 outliers final: 15 residues processed: 225 average time/residue: 3.1017 time to fit residues: 876.6115 Evaluate side-chains 212 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 194 time to evaluate : 3.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 168 ASP Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 10 GLU Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain N residue 59 ARG Chi-restraints excluded: chain N residue 99 GLU Chi-restraints excluded: chain N residue 105 LYS Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 81 ILE 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: 3.9990 chunk 227 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 298 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 342 optimal weight: 7.9990 chunk 277 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 204 optimal weight: 2.9990 chunk 360 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN L 104 GLN P 31 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 81840 Z= 0.307 Angle : 0.600 14.616 125647 Z= 0.329 Chirality : 0.037 0.838 16433 Planarity : 0.007 0.138 4643 Dihedral : 23.457 178.156 48350 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.23 % Allowed : 16.88 % Favored : 80.89 % 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: 0.05 (0.24), residues: 1163 helix: 1.36 (0.33), residues: 259 sheet: 0.05 (0.34), residues: 210 loop : -0.46 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 248 HIS 0.005 0.001 HIS K 230 PHE 0.011 0.001 PHE K 240 TYR 0.016 0.001 TYR P 38 ARG 0.003 0.000 ARG O 99 *********************** 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 226 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 205 time to evaluate : 3.038 Fit side-chains REVERT: N 59 ARG cc_start: 0.9102 (OUTLIER) cc_final: 0.8741 (ttt-90) REVERT: N 74 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7669 (mp0) REVERT: N 94 GLN cc_start: 0.9011 (tt0) cc_final: 0.8797 (tt0) REVERT: N 105 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8269 (mtpp) REVERT: N 183 GLU cc_start: 0.8327 (mp0) cc_final: 0.8004 (mp0) REVERT: O 12 LYS cc_start: 0.8590 (mmmt) cc_final: 0.8347 (mmmm) REVERT: O 81 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8363 (mp) REVERT: O 108 MET cc_start: 0.9295 (mtt) cc_final: 0.8930 (mtt) outliers start: 21 outliers final: 16 residues processed: 214 average time/residue: 3.1035 time to fit residues: 843.7444 Evaluate side-chains 221 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 202 time to evaluate : 3.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 168 ASP Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 10 GLU Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain N residue 59 ARG Chi-restraints excluded: chain N residue 99 GLU Chi-restraints excluded: chain N residue 105 LYS Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain Q residue 57 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 134 optimal weight: 4.9990 chunk 361 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 235 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 401 optimal weight: 7.9990 chunk 333 optimal weight: 0.7980 chunk 185 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 210 optimal weight: 50.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 104 GLN M 136 GLN P 31 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 81840 Z= 0.346 Angle : 0.599 14.391 125647 Z= 0.327 Chirality : 0.038 0.846 16433 Planarity : 0.007 0.138 4643 Dihedral : 23.447 177.884 48350 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.50 % Favored : 94.41 % Rotamer: Outliers : 2.23 % Allowed : 16.88 % Favored : 80.89 % 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: -0.00 (0.24), residues: 1163 helix: 1.28 (0.33), residues: 262 sheet: 0.06 (0.34), residues: 210 loop : -0.50 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 248 HIS 0.005 0.001 HIS K 230 PHE 0.012 0.001 PHE K 240 TYR 0.020 0.001 TYR P 38 ARG 0.003 0.000 ARG O 99 *********************** 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 223 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 202 time to evaluate : 3.021 Fit side-chains REVERT: K 199 GLU cc_start: 0.8165 (pm20) cc_final: 0.7765 (pm20) REVERT: N 74 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7671 (mp0) REVERT: N 105 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8272 (mtpp) REVERT: N 183 GLU cc_start: 0.8320 (mp0) cc_final: 0.7994 (mp0) REVERT: O 12 LYS cc_start: 0.8586 (mmmt) cc_final: 0.8340 (mmmm) REVERT: O 81 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.8371 (mp) REVERT: O 108 MET cc_start: 0.9291 (mtt) cc_final: 0.8954 (mtt) outliers start: 21 outliers final: 16 residues processed: 211 average time/residue: 3.0497 time to fit residues: 812.1558 Evaluate side-chains 208 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 190 time to evaluate : 3.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 168 ASP Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 10 GLU Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain N residue 99 GLU Chi-restraints excluded: chain N residue 105 LYS Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain Q residue 57 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 387 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 228 optimal weight: 6.9990 chunk 293 optimal weight: 10.0000 chunk 227 optimal weight: 3.9990 chunk 338 optimal weight: 0.8980 chunk 224 optimal weight: 3.9990 chunk 399 optimal weight: 1.9990 chunk 250 optimal weight: 3.9990 chunk 243 optimal weight: 2.9990 chunk 184 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN L 104 GLN P 31 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 81840 Z= 0.238 Angle : 0.582 14.361 125647 Z= 0.321 Chirality : 0.034 0.838 16433 Planarity : 0.007 0.135 4643 Dihedral : 23.471 177.874 48350 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.93 % Favored : 93.98 % Rotamer: Outliers : 2.23 % Allowed : 17.09 % Favored : 80.68 % 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: -0.04 (0.24), residues: 1163 helix: 1.20 (0.33), residues: 268 sheet: 0.08 (0.34), residues: 210 loop : -0.53 (0.23), residues: 685 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 0.010 0.001 PHE K 240 TYR 0.017 0.001 TYR P 38 ARG 0.005 0.000 ARG O 99 *********************** 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 215 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 194 time to evaluate : 2.944 Fit side-chains REVERT: K 199 GLU cc_start: 0.8163 (pm20) cc_final: 0.7765 (pm20) REVERT: N 59 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.8732 (ttt-90) REVERT: O 12 LYS cc_start: 0.8588 (mmmt) cc_final: 0.8340 (mmmm) REVERT: O 81 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8346 (mp) REVERT: O 108 MET cc_start: 0.9275 (mtt) cc_final: 0.8955 (mtt) outliers start: 21 outliers final: 16 residues processed: 205 average time/residue: 3.0245 time to fit residues: 784.9597 Evaluate side-chains 218 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 200 time to evaluate : 3.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 168 ASP Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 10 GLU Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain N residue 59 ARG Chi-restraints excluded: chain N residue 99 GLU Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain Q residue 57 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 247 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 238 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 254 optimal weight: 4.9990 chunk 272 optimal weight: 5.9990 chunk 197 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 314 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN L 104 GLN M 136 GLN P 31 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 81840 Z= 0.418 Angle : 0.626 14.203 125647 Z= 0.339 Chirality : 0.040 0.848 16433 Planarity : 0.007 0.142 4643 Dihedral : 23.466 178.314 48350 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.59 % Favored : 94.33 % Rotamer: Outliers : 2.34 % Allowed : 16.77 % Favored : 80.89 % 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: -0.07 (0.24), residues: 1163 helix: 1.26 (0.33), residues: 261 sheet: 0.02 (0.34), residues: 210 loop : -0.55 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 248 HIS 0.005 0.001 HIS K 230 PHE 0.011 0.001 PHE K 240 TYR 0.024 0.002 TYR P 38 ARG 0.003 0.000 ARG K 214 *********************** 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 228 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 206 time to evaluate : 3.053 Fit side-chains REVERT: K 199 GLU cc_start: 0.8174 (pm20) cc_final: 0.7768 (pm20) REVERT: N 59 ARG cc_start: 0.9105 (OUTLIER) cc_final: 0.8731 (ttt-90) REVERT: N 74 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7670 (mp0) REVERT: N 105 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8266 (mtpp) REVERT: O 12 LYS cc_start: 0.8612 (mmmt) cc_final: 0.8340 (mmmm) REVERT: O 81 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8423 (mp) REVERT: O 108 MET cc_start: 0.9299 (mtt) cc_final: 0.8964 (mtt) REVERT: O 138 GLN cc_start: 0.8634 (mt0) cc_final: 0.8405 (mt0) outliers start: 22 outliers final: 17 residues processed: 217 average time/residue: 3.0844 time to fit residues: 845.2525 Evaluate side-chains 226 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 206 time to evaluate : 2.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 168 ASP Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 10 GLU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain N residue 59 ARG Chi-restraints excluded: chain N residue 99 GLU Chi-restraints excluded: chain N residue 105 LYS Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain Q residue 57 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 363 optimal weight: 0.7980 chunk 383 optimal weight: 4.9990 chunk 349 optimal weight: 0.0970 chunk 372 optimal weight: 3.9990 chunk 224 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 292 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 chunk 336 optimal weight: 0.7980 chunk 352 optimal weight: 5.9990 chunk 371 optimal weight: 4.9990 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN L 104 GLN M 136 GLN P 31 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 81840 Z= 0.204 Angle : 0.590 14.454 125647 Z= 0.324 Chirality : 0.034 0.824 16433 Planarity : 0.006 0.132 4643 Dihedral : 23.540 177.991 48350 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.76 % Favored : 94.15 % Rotamer: Outliers : 1.80 % Allowed : 17.62 % Favored : 80.57 % 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: 0.04 (0.24), residues: 1163 helix: 1.36 (0.33), residues: 262 sheet: 0.09 (0.34), residues: 210 loop : -0.49 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 248 HIS 0.004 0.001 HIS K 230 PHE 0.010 0.001 PHE M 183 TYR 0.022 0.001 TYR P 38 ARG 0.004 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 226 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 209 time to evaluate : 3.055 Fit side-chains REVERT: K 199 GLU cc_start: 0.8166 (pm20) cc_final: 0.7766 (pm20) REVERT: N 59 ARG cc_start: 0.9100 (OUTLIER) cc_final: 0.8677 (ttt-90) REVERT: N 74 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7654 (mp0) REVERT: O 12 LYS cc_start: 0.8605 (mmmt) cc_final: 0.8330 (mmmm) REVERT: O 81 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8390 (mp) REVERT: O 108 MET cc_start: 0.9239 (mtt) cc_final: 0.8935 (mtt) outliers start: 17 outliers final: 15 residues processed: 216 average time/residue: 3.1734 time to fit residues: 870.9932 Evaluate side-chains 222 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 205 time to evaluate : 3.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 168 ASP Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 10 GLU Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain N residue 59 ARG Chi-restraints excluded: chain N residue 99 GLU Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain Q residue 57 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 244 optimal weight: 3.9990 chunk 394 optimal weight: 0.3980 chunk 240 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 chunk 274 optimal weight: 6.9990 chunk 413 optimal weight: 0.7980 chunk 380 optimal weight: 3.9990 chunk 329 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 254 optimal weight: 4.9990 chunk 201 optimal weight: 3.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 81840 Z= 0.267 Angle : 0.579 13.931 125647 Z= 0.318 Chirality : 0.035 0.842 16433 Planarity : 0.007 0.135 4643 Dihedral : 23.473 177.463 48350 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.76 % Favored : 94.15 % Rotamer: Outliers : 1.91 % Allowed : 17.73 % Favored : 80.36 % 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: -0.02 (0.24), residues: 1163 helix: 1.24 (0.33), residues: 268 sheet: 0.10 (0.34), residues: 210 loop : -0.53 (0.23), residues: 685 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 0.012 0.001 PHE K 240 TYR 0.021 0.001 TYR P 38 ARG 0.002 0.000 ARG L 123 ********************** 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 226 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 208 time to evaluate : 3.413 Fit side-chains REVERT: K 199 GLU cc_start: 0.8175 (pm20) cc_final: 0.7778 (pm20) REVERT: N 59 ARG cc_start: 0.9089 (OUTLIER) cc_final: 0.8716 (ttt-90) REVERT: N 74 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7668 (mp0) REVERT: O 12 LYS cc_start: 0.8598 (mmmt) cc_final: 0.8328 (mmmm) REVERT: O 81 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8363 (mp) REVERT: O 108 MET cc_start: 0.9236 (mtt) cc_final: 0.8933 (mtt) outliers start: 18 outliers final: 14 residues processed: 216 average time/residue: 3.1265 time to fit residues: 850.7019 Evaluate side-chains 223 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 207 time to evaluate : 3.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 38 SER Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 168 ASP Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 10 GLU Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain N residue 59 ARG Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain O residue 10 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain Q residue 57 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 261 optimal weight: 4.9990 chunk 350 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 303 optimal weight: 0.0030 chunk 48 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 329 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 338 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 overall best weight: 2.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN M 136 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 = 0.3391 r_free = 0.3391 target = 0.109125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.064495 restraints weight = 262374.957| |-----------------------------------------------------------------------------| r_work (start): 0.2636 rms_B_bonded: 0.52 r_work: 0.2543 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2474 rms_B_bonded: 2.31 restraints_weight: 0.2500 r_work (final): 0.2474 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2474 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2474 r_free = 0.2474 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2474 r_free = 0.2474 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2474 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 81840 Z= 0.259 Angle : 0.575 13.917 125647 Z= 0.317 Chirality : 0.035 0.842 16433 Planarity : 0.006 0.134 4643 Dihedral : 23.480 177.463 48350 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.85 % Favored : 94.07 % Rotamer: Outliers : 1.70 % Allowed : 17.83 % Favored : 80.47 % 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: -0.02 (0.24), residues: 1163 helix: 1.25 (0.33), residues: 268 sheet: 0.09 (0.34), residues: 210 loop : -0.53 (0.23), residues: 685 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 0.011 0.001 PHE K 240 TYR 0.019 0.001 TYR P 38 ARG 0.004 0.000 ARG M 170 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 35201.04 seconds wall clock time: 605 minutes 1.07 seconds (36301.07 seconds total)