Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 13:32:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc7_20298/04_2023/6pc7_20298_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc7_20298/04_2023/6pc7_20298.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc7_20298/04_2023/6pc7_20298_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc7_20298/04_2023/6pc7_20298_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc7_20298/04_2023/6pc7_20298_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc7_20298/04_2023/6pc7_20298.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc7_20298/04_2023/6pc7_20298.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc7_20298/04_2023/6pc7_20298_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pc7_20298/04_2023/6pc7_20298_neut_updated.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= -0.018 sd= 1.319 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: 6 Type Number sf(0) Gaussians P 3015 5.49 5 S 22 5.16 5 C 33516 2.51 5 N 13321 2.21 5 O 22271 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K ARG 52": "NH1" <-> "NH2" Residue "K ARG 63": "NH1" <-> "NH2" Residue "K ARG 80": "NH1" <-> "NH2" Residue "K ARG 133": "NH1" <-> "NH2" Residue "K ARG 167": "NH1" <-> "NH2" Residue "K ARG 177": "NH1" <-> "NH2" Residue "K ARG 189": "NH1" <-> "NH2" Residue "K ARG 203": "NH1" <-> "NH2" Residue "K ARG 212": "NH1" <-> "NH2" Residue "K ARG 221": "NH1" <-> "NH2" Residue "K ARG 258": "NH1" <-> "NH2" Residue "K ARG 269": "NH1" <-> "NH2" Residue "K ARG 270": "NH1" <-> "NH2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L GLU 86": "OE1" <-> "OE2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M ARG 21": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M ARG 49": "NH1" <-> "NH2" Residue "M ARG 61": "NH1" <-> "NH2" Residue "M ARG 88": "NH1" <-> "NH2" Residue "M ARG 102": "NH1" <-> "NH2" Residue "M ARG 162": "NH1" <-> "NH2" Residue "M ARG 170": "NH1" <-> "NH2" Residue "N ARG 13": "NH1" <-> "NH2" Residue "N ARG 33": "NH1" <-> "NH2" Residue "N ARG 59": "NH1" <-> "NH2" Residue "N ARG 77": "NH1" <-> "NH2" Residue "N GLU 81": "OE1" <-> "OE2" Residue "N ARG 83": "NH1" <-> "NH2" Residue "N GLU 168": "OE1" <-> "OE2" Residue "N ARG 169": "NH1" <-> "NH2" Residue "N ARG 184": "NH1" <-> "NH2" Residue "O GLU 9": "OE1" <-> "OE2" Residue "O ARG 13": "NH1" <-> "NH2" Residue "O ARG 37": "NH1" <-> "NH2" Residue "O PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "O GLU 102": "OE1" <-> "OE2" Residue "O ARG 120": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 72146 Number of models: 1 Model: "" Number of chains: 8 Chain: "I" Number of atoms: 62206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2897, 62206 Classifications: {'RNA': 2897} Modifications used: {'rna2p': 7, 'rna2p_pur': 280, 'rna2p_pyr': 151, 'rna3p': 14, 'rna3p_pur': 1384, 'rna3p_pyr': 1061} Link IDs: {'rna2p': 438, 'rna3p': 2458} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 13 Chain: "J" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2529 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 48} Link IDs: {'rna2p': 13, 'rna3p': 104} Chain: "K" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2083 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "L" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "M" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "N" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1542 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain breaks: 1 Chain: "O" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "I" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'O7V': 1} Classifications: {'undetermined': 1} Time building chain proxies: 28.59, per 1000 atoms: 0.40 Number of scatterers: 72146 At special positions: 0 Unit cell: (228.611, 221.984, 190.509, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 22 16.00 P 3015 15.00 F 1 9.00 O 22271 8.00 N 13321 7.00 C 33516 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 33.33 Conformation dependent library (CDL) restraints added in 2.1 seconds 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1706 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 13 sheets defined 17.6% alpha, 14.3% beta 901 base pairs and 1651 stacking pairs defined. Time for finding SS restraints: 35.37 Creating SS restraints... Processing helix chain 'K' and resid 31 through 33 No H-bonds generated for 'chain 'K' and resid 31 through 33' Processing helix chain 'K' and resid 198 through 200 No H-bonds generated for 'chain 'K' and resid 198 through 200' Processing helix chain 'K' and resid 208 through 213 Processing helix chain 'L' and resid 57 through 60 No H-bonds generated for 'chain 'L' and resid 57 through 60' Processing helix chain 'L' and resid 79 through 81 No H-bonds generated for 'chain 'L' and resid 79 through 81' Processing helix chain 'L' and resid 92 through 95 No H-bonds generated for 'chain 'L' and resid 92 through 95' Processing helix chain 'L' and resid 129 through 137 Processing helix chain 'M' and resid 16 through 19 No H-bonds generated for 'chain 'M' and resid 16 through 19' Processing helix chain 'M' and resid 25 through 38 removed outlier: 3.611A pdb=" N GLN M 30 " --> pdb=" O ALA M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 114 removed outlier: 3.731A pdb=" N SER M 110 " --> pdb=" O LYS M 106 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU M 111 " --> pdb=" O SER M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 140 Processing helix chain 'M' and resid 155 through 160 Processing helix chain 'M' and resid 177 through 182 Processing helix chain 'M' and resid 190 through 200 Processing helix chain 'N' and resid 62 through 71 Processing helix chain 'N' and resid 98 through 101 Processing helix chain 'N' and resid 121 through 124 No H-bonds generated for 'chain 'N' and resid 121 through 124' Processing helix chain 'O' and resid 25 through 37 removed outlier: 3.994A pdb=" N GLU O 31 " --> pdb=" O ARG O 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 59 through 61 No H-bonds generated for 'chain 'O' and resid 59 through 61' Processing helix chain 'O' and resid 68 through 71 No H-bonds generated for 'chain 'O' and resid 68 through 71' Processing helix chain 'O' and resid 89 through 108 Proline residue: O 97 - end of helix removed outlier: 4.432A pdb=" N VAL O 100 " --> pdb=" O ARG O 96 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE O 101 " --> pdb=" O PRO O 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 121 removed outlier: 3.547A pdb=" N PHE O 119 " --> pdb=" O GLY O 115 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG O 120 " --> pdb=" O ARG O 116 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS O 121 " --> pdb=" O ALA O 117 " (cutoff:3.500A) Processing helix chain 'O' and resid 133 through 135 No H-bonds generated for 'chain 'O' and resid 133 through 135' Processing sheet with id= A, first strand: chain 'K' and resid 3 through 5 Processing sheet with id= B, first strand: chain 'K' and resid 34 through 36 Processing sheet with id= C, first strand: chain 'K' and resid 101 through 105 removed outlier: 3.753A pdb=" N ARG K 80 " --> pdb=" O LEU K 93 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU K 95 " --> pdb=" O VAL K 78 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N VAL K 78 " --> pdb=" O LEU K 95 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'K' and resid 129 through 131 removed outlier: 3.511A pdb=" N LEU K 130 " --> pdb=" O ALA K 190 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'K' and resid 181 through 185 removed outlier: 3.782A pdb=" N ALA K 166 " --> pdb=" O THR K 173 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ARG K 175 " --> pdb=" O ILE K 164 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ILE K 164 " --> pdb=" O ARG K 175 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'L' and resid 74 through 76 removed outlier: 6.642A pdb=" N PHE L 107 " --> pdb=" O ALA L 75 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'L' and resid 121 through 123 removed outlier: 6.568A pdb=" N LYS L 141 " --> pdb=" O VAL L 122 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'M' and resid 118 through 121 removed outlier: 6.146A pdb=" N VAL M 186 " --> pdb=" O ILE M 119 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL M 121 " --> pdb=" O VAL M 186 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N MET M 188 " --> pdb=" O VAL M 121 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP M 168 " --> pdb=" O VAL M 146 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 169 through 172 removed outlier: 4.921A pdb=" N THR N 112 " --> pdb=" O ASP N 200 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ASP N 200 " --> pdb=" O THR N 112 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL N 26 " --> pdb=" O VAL N 9 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N MET N 11 " --> pdb=" O VAL N 24 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL N 24 " --> pdb=" O MET N 11 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ARG N 13 " --> pdb=" O ILE N 22 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ILE N 22 " --> pdb=" O ARG N 13 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N PHE N 15 " --> pdb=" O VAL N 20 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL N 20 " --> pdb=" O PHE N 15 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL N 189 " --> pdb=" O THR N 25 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP N 181 " --> pdb=" O LEU N 186 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LYS N 190 " --> pdb=" O VAL N 177 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL N 177 " --> pdb=" O LYS N 190 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 80 through 83 removed outlier: 6.205A pdb=" N THR N 51 " --> pdb=" O VAL N 34 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N VAL N 34 " --> pdb=" O THR N 51 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'N' and resid 115 through 119 removed outlier: 6.090A pdb=" N MET N 165 " --> pdb=" O LYS N 116 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N PHE N 118 " --> pdb=" O GLY N 163 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N GLY N 163 " --> pdb=" O PHE N 118 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'O' and resid 15 through 19 removed outlier: 6.699A pdb=" N TYR O 53 " --> pdb=" O TYR O 16 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N VAL O 18 " --> pdb=" O TYR O 53 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE O 55 " --> pdb=" O VAL O 18 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'O' and resid 73 through 76 removed outlier: 3.515A pdb=" N HIS O 76 " --> pdb=" O LYS O 85 " (cutoff:3.500A) 131 hydrogen bonds defined for protein. 372 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2259 hydrogen bonds 3678 hydrogen bond angles 0 basepair planarities 901 basepair parallelities 1651 stacking parallelities Total time for adding SS restraints: 141.44 Time building geometry restraints manager: 36.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5153 1.31 - 1.43: 40218 1.43 - 1.56: 28559 1.56 - 1.68: 6048 1.68 - 1.81: 42 Bond restraints: 80020 Sorted by residual: bond pdb=" C4 5MU I 747 " pdb=" C5 5MU I 747 " ideal model delta sigma weight residual 1.802 1.409 0.393 2.00e-02 2.50e+03 3.87e+02 bond pdb=" C4 5MU I1939 " pdb=" C5 5MU I1939 " ideal model delta sigma weight residual 1.802 1.410 0.392 2.00e-02 2.50e+03 3.83e+02 bond pdb=" N1 5MU I1939 " pdb=" C6 5MU I1939 " ideal model delta sigma weight residual 1.635 1.366 0.269 2.00e-02 2.50e+03 1.81e+02 bond pdb=" N1 5MU I 747 " pdb=" C6 5MU I 747 " ideal model delta sigma weight residual 1.635 1.367 0.268 2.00e-02 2.50e+03 1.79e+02 bond pdb=" C15 O7V I3001 " pdb=" C16 O7V I3001 " ideal model delta sigma weight residual 1.601 1.348 0.253 2.00e-02 2.50e+03 1.60e+02 ... (remaining 80015 not shown) Histogram of bond angle deviations from ideal: 99.95 - 106.93: 17925 106.93 - 113.90: 50587 113.90 - 120.88: 32158 120.88 - 127.85: 17425 127.85 - 134.82: 5103 Bond angle restraints: 123198 Sorted by residual: angle pdb=" N30 O7V I3001 " pdb=" C31 O7V I3001 " pdb=" N40 O7V I3001 " ideal model delta sigma weight residual 50.79 114.46 -63.67 3.00e+00 1.11e-01 4.50e+02 angle pdb=" C13 O7V I3001 " pdb=" C15 O7V I3001 " pdb=" C16 O7V I3001 " ideal model delta sigma weight residual 85.81 125.34 -39.53 3.00e+00 1.11e-01 1.74e+02 angle pdb=" C1' 6MZ I1618 " pdb=" N9 6MZ I1618 " pdb=" C8 6MZ I1618 " ideal model delta sigma weight residual 91.39 126.51 -35.12 3.00e+00 1.11e-01 1.37e+02 angle pdb=" C32 O7V I3001 " pdb=" C31 O7V I3001 " pdb=" N30 O7V I3001 " ideal model delta sigma weight residual 155.49 122.51 32.98 3.00e+00 1.11e-01 1.21e+02 angle pdb=" C19 O7V I3001 " pdb=" C20 O7V I3001 " pdb=" C21 O7V I3001 " ideal model delta sigma weight residual 154.30 124.62 29.68 3.00e+00 1.11e-01 9.78e+01 ... (remaining 123193 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 39501 35.72 - 71.43: 1124 71.43 - 107.15: 122 107.15 - 142.86: 13 142.86 - 178.58: 5 Dihedral angle restraints: 40765 sinusoidal: 38085 harmonic: 2680 Sorted by residual: dihedral pdb=" C5* PSU I1911 " pdb=" C4* PSU I1911 " pdb=" C3* PSU I1911 " pdb=" O3* PSU I1911 " ideal model delta sinusoidal sigma weight residual 147.00 77.72 69.28 1 8.00e+00 1.56e-02 9.69e+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 232.00 59.53 172.47 1 1.70e+01 3.46e-03 6.61e+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 61.43 170.57 1 1.70e+01 3.46e-03 6.60e+01 ... (remaining 40762 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 16084 0.107 - 0.213: 36 0.213 - 0.320: 2 0.320 - 0.427: 1 0.427 - 0.534: 1 Chirality restraints: 16124 Sorted by residual: chirality pdb=" CA MET K 225 " pdb=" N MET K 225 " pdb=" C MET K 225 " pdb=" CB MET K 225 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.12e+00 chirality pdb=" CA ASP K 229 " pdb=" N ASP K 229 " pdb=" C ASP K 229 " pdb=" CB ASP K 229 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" C3* PSU I1911 " pdb=" C4* PSU I1911 " pdb=" O3* PSU I1911 " pdb=" C2* PSU I1911 " both_signs ideal model delta sigma weight residual False -2.74 -2.43 -0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 16121 not shown) Planarity restraints: 4344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 1MG I 745 " -0.044 2.00e-02 2.50e+03 5.92e-01 7.88e+03 pdb=" C4' 1MG I 745 " -0.445 2.00e-02 2.50e+03 pdb=" O4' 1MG I 745 " -0.672 2.00e-02 2.50e+03 pdb=" C3' 1MG I 745 " 0.595 2.00e-02 2.50e+03 pdb=" O3' 1MG I 745 " 0.600 2.00e-02 2.50e+03 pdb=" C2' 1MG I 745 " 0.201 2.00e-02 2.50e+03 pdb=" O2' 1MG I 745 " -0.931 2.00e-02 2.50e+03 pdb=" C1' 1MG I 745 " -0.217 2.00e-02 2.50e+03 pdb=" N9 1MG I 745 " 0.913 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 6MZ I1618 " -0.876 2.00e-02 2.50e+03 5.88e-01 7.79e+03 pdb=" C4' 6MZ I1618 " 0.220 2.00e-02 2.50e+03 pdb=" O4' 6MZ I1618 " 0.690 2.00e-02 2.50e+03 pdb=" C3' 6MZ I1618 " -0.206 2.00e-02 2.50e+03 pdb=" O3' 6MZ I1618 " 0.915 2.00e-02 2.50e+03 pdb=" C2' 6MZ I1618 " -0.614 2.00e-02 2.50e+03 pdb=" O2' 6MZ I1618 " -0.605 2.00e-02 2.50e+03 pdb=" C1' 6MZ I1618 " 0.447 2.00e-02 2.50e+03 pdb=" N9 6MZ I1618 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I2445 " -0.023 2.00e-02 2.50e+03 5.82e-01 7.62e+03 pdb=" C4' 2MG I2445 " -0.449 2.00e-02 2.50e+03 pdb=" O4' 2MG I2445 " -0.704 2.00e-02 2.50e+03 pdb=" C3' 2MG I2445 " 0.589 2.00e-02 2.50e+03 pdb=" O3' 2MG I2445 " 0.561 2.00e-02 2.50e+03 pdb=" C2' 2MG I2445 " 0.225 2.00e-02 2.50e+03 pdb=" O2' 2MG I2445 " -0.885 2.00e-02 2.50e+03 pdb=" C1' 2MG I2445 " -0.215 2.00e-02 2.50e+03 pdb=" N9 2MG I2445 " 0.901 2.00e-02 2.50e+03 ... (remaining 4341 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 451 2.54 - 3.13: 51323 3.13 - 3.72: 144541 3.72 - 4.31: 209130 4.31 - 4.90: 268753 Nonbonded interactions: 674198 Sorted by model distance: nonbonded pdb=" O2' A I2052 " pdb=" O GLN N 148 " model vdw 1.954 2.440 nonbonded pdb=" O2' A I1084 " pdb=" O2' U I1105 " model vdw 1.955 2.440 nonbonded pdb=" OP1 A I 730 " pdb=" O2' U I1775 " model vdw 1.968 2.440 nonbonded pdb=" O2' G I1715 " pdb=" O6 G I1743 " model vdw 1.984 2.440 nonbonded pdb=" O2' G I1826 " pdb=" OP2 U I1971 " model vdw 1.992 2.440 ... (remaining 674193 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=1.00 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: 14.810 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: 0.080 Extract box with map and model: 47.540 Check model and map are aligned: 0.810 Set scattering table: 0.470 Process input model: 284.480 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.170 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:11.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 360.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 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 0.393 80020 Z= 0.330 Angle : 0.507 63.667 123198 Z= 0.229 Chirality : 0.025 0.534 16124 Planarity : 0.030 0.592 4344 Dihedral : 12.977 178.581 39059 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.20 % Favored : 93.70 % Rotamer Outliers : 2.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -3.93 (0.22), residues: 952 helix: -3.43 (0.24), residues: 176 sheet: -1.86 (0.35), residues: 197 loop : -2.71 (0.21), residues: 579 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 195 time to evaluate : 2.174 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 5 residues processed: 211 average time/residue: 1.7560 time to fit residues: 477.9306 Evaluate side-chains 145 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 140 time to evaluate : 2.293 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 1.6859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 333 optimal weight: 5.9990 chunk 299 optimal weight: 10.0000 chunk 166 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 201 optimal weight: 8.9990 chunk 159 optimal weight: 8.9990 chunk 309 optimal weight: 0.7980 chunk 119 optimal weight: 8.9990 chunk 188 optimal weight: 10.0000 chunk 230 optimal weight: 10.0000 chunk 358 optimal weight: 0.0470 overall best weight: 4.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 58 HIS K 143 ASN K 200 HIS K 239 ASN L 93 ASN M 41 GLN M 156 ASN N 32 ASN N 167 ASN O 80 HIS O 135 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.097 80020 Z= 0.378 Angle : 0.750 22.348 123198 Z= 0.395 Chirality : 0.038 0.281 16124 Planarity : 0.009 0.136 4344 Dihedral : 13.693 179.610 37260 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.51 % Favored : 93.28 % Rotamer Outliers : 5.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.26 (0.24), residues: 952 helix: -1.43 (0.34), residues: 174 sheet: -1.05 (0.37), residues: 176 loop : -1.71 (0.23), residues: 602 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 160 time to evaluate : 2.139 Fit side-chains revert: symmetry clash outliers start: 40 outliers final: 19 residues processed: 185 average time/residue: 1.7797 time to fit residues: 423.3066 Evaluate side-chains 165 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 146 time to evaluate : 2.107 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 14 residues processed: 5 average time/residue: 1.1284 time to fit residues: 9.6765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 199 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 298 optimal weight: 7.9990 chunk 244 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 359 optimal weight: 3.9990 chunk 388 optimal weight: 4.9990 chunk 320 optimal weight: 0.9980 chunk 356 optimal weight: 0.0010 chunk 122 optimal weight: 7.9990 chunk 288 optimal weight: 10.0000 overall best weight: 3.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 93 ASN ** M 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 ASN N 126 ASN N 167 ASN O 135 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.086 80020 Z= 0.261 Angle : 0.644 18.238 123198 Z= 0.351 Chirality : 0.032 0.280 16124 Planarity : 0.008 0.134 4344 Dihedral : 13.828 178.293 37260 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.88 % Favored : 93.91 % Rotamer Outliers : 5.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.25), residues: 952 helix: -0.84 (0.37), residues: 177 sheet: -0.59 (0.37), residues: 183 loop : -1.30 (0.24), residues: 592 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 162 time to evaluate : 2.170 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 18 residues processed: 186 average time/residue: 1.6756 time to fit residues: 407.5330 Evaluate side-chains 172 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 154 time to evaluate : 2.147 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 14 residues processed: 4 average time/residue: 1.4070 time to fit residues: 9.2755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 355 optimal weight: 5.9990 chunk 270 optimal weight: 8.9990 chunk 186 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 171 optimal weight: 10.0000 chunk 241 optimal weight: 8.9990 chunk 360 optimal weight: 2.9990 chunk 381 optimal weight: 0.7980 chunk 188 optimal weight: 10.0000 chunk 341 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 93 ASN ** M 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 ASN N 167 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.066 80020 Z= 0.408 Angle : 0.751 17.956 123198 Z= 0.399 Chirality : 0.039 0.298 16124 Planarity : 0.009 0.137 4344 Dihedral : 14.219 179.569 37260 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.77 % Favored : 92.02 % Rotamer Outliers : 6.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.25), residues: 952 helix: -0.85 (0.36), residues: 175 sheet: -0.46 (0.37), residues: 172 loop : -1.23 (0.24), residues: 605 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 155 time to evaluate : 2.191 Fit side-chains revert: symmetry clash outliers start: 53 outliers final: 29 residues processed: 184 average time/residue: 1.7038 time to fit residues: 411.8196 Evaluate side-chains 179 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 150 time to evaluate : 2.235 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 21 residues processed: 8 average time/residue: 0.9567 time to fit residues: 13.1869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 317 optimal weight: 0.9980 chunk 216 optimal weight: 50.0000 chunk 5 optimal weight: 6.9990 chunk 284 optimal weight: 8.9990 chunk 157 optimal weight: 10.0000 chunk 325 optimal weight: 1.9990 chunk 263 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 194 optimal weight: 7.9990 chunk 342 optimal weight: 0.3980 chunk 96 optimal weight: 6.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 93 ASN ** M 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 ASN N 167 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.072 80020 Z= 0.284 Angle : 0.685 17.384 123198 Z= 0.374 Chirality : 0.034 0.265 16124 Planarity : 0.008 0.134 4344 Dihedral : 14.185 178.555 37260 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.04 % Favored : 92.75 % Rotamer Outliers : 5.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.26), residues: 952 helix: -0.83 (0.36), residues: 182 sheet: -0.42 (0.37), residues: 172 loop : -1.11 (0.24), residues: 598 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 146 time to evaluate : 2.293 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 30 residues processed: 176 average time/residue: 1.6504 time to fit residues: 384.0893 Evaluate side-chains 172 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 142 time to evaluate : 2.150 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 23 residues processed: 7 average time/residue: 0.5960 time to fit residues: 9.3511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 128 optimal weight: 8.9990 chunk 343 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 224 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 chunk 382 optimal weight: 3.9990 chunk 317 optimal weight: 0.6980 chunk 176 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 126 optimal weight: 8.9990 chunk 200 optimal weight: 5.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 93 ASN L 99 ASN ** M 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 ASN N 167 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.055 80020 Z= 0.360 Angle : 0.708 16.993 123198 Z= 0.381 Chirality : 0.037 0.278 16124 Planarity : 0.008 0.135 4344 Dihedral : 14.192 177.889 37260 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.04 % Favored : 92.75 % Rotamer Outliers : 6.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.26), residues: 952 helix: -0.77 (0.37), residues: 182 sheet: -0.30 (0.38), residues: 167 loop : -1.01 (0.25), residues: 603 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 143 time to evaluate : 2.177 Fit side-chains outliers start: 51 outliers final: 29 residues processed: 176 average time/residue: 1.6371 time to fit residues: 381.1957 Evaluate side-chains 166 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 137 time to evaluate : 2.156 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 22 residues processed: 7 average time/residue: 0.8887 time to fit residues: 11.5150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 368 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 217 optimal weight: 30.0000 chunk 279 optimal weight: 10.0000 chunk 216 optimal weight: 50.0000 chunk 321 optimal weight: 6.9990 chunk 213 optimal weight: 40.0000 chunk 380 optimal weight: 4.9990 chunk 238 optimal weight: 7.9990 chunk 232 optimal weight: 7.9990 chunk 175 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 93 ASN L 99 ASN ** M 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 ASN N 167 ASN O 138 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.099 80020 Z= 0.506 Angle : 0.816 17.148 123198 Z= 0.426 Chirality : 0.043 0.320 16124 Planarity : 0.009 0.141 4344 Dihedral : 14.545 177.335 37260 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.67 % Favored : 92.12 % Rotamer Outliers : 5.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.26), residues: 952 helix: -0.89 (0.37), residues: 177 sheet: -0.64 (0.35), residues: 192 loop : -1.07 (0.25), residues: 583 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 132 time to evaluate : 2.336 Fit side-chains outliers start: 44 outliers final: 28 residues processed: 165 average time/residue: 1.7826 time to fit residues: 388.7424 Evaluate side-chains 151 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 123 time to evaluate : 2.237 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 24 residues processed: 4 average time/residue: 0.9537 time to fit residues: 7.6780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 235 optimal weight: 5.9990 chunk 152 optimal weight: 10.0000 chunk 227 optimal weight: 5.9990 chunk 114 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 242 optimal weight: 4.9990 chunk 259 optimal weight: 6.9990 chunk 188 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 299 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 93 ASN L 99 ASN ** M 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 ASN N 167 ASN O 138 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.097 80020 Z= 0.416 Angle : 0.761 17.115 123198 Z= 0.406 Chirality : 0.040 0.302 16124 Planarity : 0.009 0.139 4344 Dihedral : 14.513 177.079 37260 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.77 % Favored : 92.02 % Rotamer Outliers : 5.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.26), residues: 952 helix: -0.95 (0.37), residues: 181 sheet: -0.52 (0.37), residues: 172 loop : -1.03 (0.24), residues: 599 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 121 time to evaluate : 2.363 Fit side-chains outliers start: 40 outliers final: 27 residues processed: 152 average time/residue: 1.6103 time to fit residues: 324.9548 Evaluate side-chains 153 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 126 time to evaluate : 2.175 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 25 residues processed: 2 average time/residue: 1.1746 time to fit residues: 5.0520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 346 optimal weight: 0.2980 chunk 364 optimal weight: 6.9990 chunk 332 optimal weight: 0.7980 chunk 354 optimal weight: 5.9990 chunk 213 optimal weight: 40.0000 chunk 154 optimal weight: 8.9990 chunk 278 optimal weight: 10.0000 chunk 108 optimal weight: 30.0000 chunk 320 optimal weight: 2.9990 chunk 335 optimal weight: 0.3980 chunk 353 optimal weight: 7.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 93 ASN L 99 ASN ** M 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 ASN N 167 ASN O 138 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 80020 Z= 0.183 Angle : 0.622 16.555 123198 Z= 0.346 Chirality : 0.031 0.252 16124 Planarity : 0.008 0.128 4344 Dihedral : 14.203 176.011 37260 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.88 % Favored : 93.91 % Rotamer Outliers : 4.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.26), residues: 952 helix: -0.51 (0.39), residues: 183 sheet: -0.31 (0.37), residues: 168 loop : -0.89 (0.25), residues: 601 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 134 time to evaluate : 2.185 Fit side-chains outliers start: 33 outliers final: 25 residues processed: 159 average time/residue: 1.5888 time to fit residues: 338.1059 Evaluate side-chains 156 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 131 time to evaluate : 2.174 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 22 residues processed: 3 average time/residue: 0.5954 time to fit residues: 5.0089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 232 optimal weight: 8.9990 chunk 375 optimal weight: 2.9990 chunk 228 optimal weight: 10.0000 chunk 177 optimal weight: 7.9990 chunk 260 optimal weight: 8.9990 chunk 393 optimal weight: 5.9990 chunk 362 optimal weight: 0.0970 chunk 313 optimal weight: 0.0980 chunk 32 optimal weight: 10.0000 chunk 242 optimal weight: 10.0000 chunk 192 optimal weight: 10.0000 overall best weight: 3.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 93 ASN M 94 GLN ** M 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 ASN N 167 ASN O 138 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 80020 Z= 0.276 Angle : 0.658 16.575 123198 Z= 0.360 Chirality : 0.034 0.250 16124 Planarity : 0.008 0.133 4344 Dihedral : 14.201 176.736 37260 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.72 % Favored : 93.07 % Rotamer Outliers : 3.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.26), residues: 952 helix: -0.50 (0.39), residues: 181 sheet: -0.47 (0.35), residues: 187 loop : -0.85 (0.25), residues: 584 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 131 time to evaluate : 2.171 Fit side-chains outliers start: 28 outliers final: 24 residues processed: 153 average time/residue: 1.6630 time to fit residues: 337.8282 Evaluate side-chains 147 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 123 time to evaluate : 2.171 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 22 residues processed: 2 average time/residue: 0.7024 time to fit residues: 4.3372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 248 optimal weight: 8.9990 chunk 333 optimal weight: 0.0040 chunk 95 optimal weight: 7.9990 chunk 288 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 313 optimal weight: 0.3980 chunk 131 optimal weight: 10.0000 chunk 322 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 chunk 57 optimal weight: 6.9990 overall best weight: 4.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 93 ASN ** M 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 ASN N 167 ASN O 138 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.125468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.098819 restraints weight = 122618.094| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 0.64 r_work: 0.3206 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.061 80020 Z= 0.357 Angle : 0.705 16.508 123198 Z= 0.380 Chirality : 0.037 0.274 16124 Planarity : 0.008 0.136 4344 Dihedral : 14.302 176.813 37260 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.83 % Favored : 92.96 % Rotamer Outliers : 4.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.26), residues: 952 helix: -0.62 (0.38), residues: 182 sheet: -0.39 (0.38), residues: 158 loop : -0.92 (0.24), residues: 612 =============================================================================== Job complete usr+sys time: 11134.78 seconds wall clock time: 200 minutes 16.88 seconds (12016.88 seconds total)