Starting phenix.real_space_refine (version: dev) on Wed Dec 14 17:55:20 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pch_20300/12_2022/6pch_20300_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pch_20300/12_2022/6pch_20300.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pch_20300/12_2022/6pch_20300_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pch_20300/12_2022/6pch_20300_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pch_20300/12_2022/6pch_20300_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pch_20300/12_2022/6pch_20300.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pch_20300/12_2022/6pch_20300.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pch_20300/12_2022/6pch_20300_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pch_20300/12_2022/6pch_20300_neut_updated.pdb" } resolution = 2.9 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= -0.017 sd= 1.289 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 Convert atoms to be neutral 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 ASP 229": "OD1" <-> "OD2" Residue "K ARG 258": "NH1" <-> "NH2" Residue "K ASP 264": "OD1" <-> "OD2" 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 ARG 126": "NH1" <-> "NH2" Residue "M ARG 21": "NH1" <-> "NH2" Residue "M TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 144": "OE1" <-> "OE2" 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 86": "OE1" <-> "OE2" 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 ASP 71": "OD1" <-> "OD2" Residue "O TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "O PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 120": "NH1" <-> "NH2" Residue "O ASP 141": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 72134 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: 8 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: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'O8D': 1} Classifications: {'undetermined': 1} Time building chain proxies: 33.60, per 1000 atoms: 0.47 Number of scatterers: 72134 At special positions: 0 Unit cell: (228.611, 221.984, 188.852, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 P 3015 15.00 O 22270 8.00 N 13319 7.00 C 33508 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: 33.18 Conformation dependent library (CDL) restraints added in 2.2 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: 27 helices and 13 sheets defined 19.0% alpha, 13.1% beta 793 base pairs and 1610 stacking pairs defined. Time for finding SS restraints: 35.60 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 132 through 134 No H-bonds generated for 'chain 'K' and resid 132 through 134' Processing helix chain 'K' and resid 198 through 202 removed outlier: 3.718A pdb=" N MET K 201 " --> pdb=" O ALA K 198 " (cutoff:3.500A) Processing helix chain 'K' and resid 208 through 213 removed outlier: 3.560A pdb=" N ARG K 212 " --> pdb=" O ALA K 208 " (cutoff:3.500A) Processing helix chain 'K' and resid 226 through 229 No H-bonds generated for 'chain 'K' and resid 226 through 229' Processing helix chain 'L' and resid 3 through 5 No H-bonds generated for 'chain 'L' and resid 3 through 5' Processing helix chain 'L' and resid 23 through 25 No H-bonds generated for 'chain 'L' and resid 23 through 25' 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 85 removed outlier: 4.838A pdb=" N ALA L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 97 removed outlier: 3.536A pdb=" N LYS L 96 " --> pdb=" O LEU L 92 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA L 97 " --> pdb=" O ASN L 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 92 through 97' Processing helix chain 'L' and resid 129 through 138 removed outlier: 3.531A pdb=" N ALA L 134 " --> pdb=" O GLY L 130 " (cutoff:3.500A) 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 37 Processing helix chain 'M' and resid 98 through 114 removed outlier: 3.536A pdb=" N LYS M 106 " --> pdb=" O ARG M 102 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU M 111 " --> pdb=" O SER M 107 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL M 113 " --> pdb=" O LEU M 109 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG M 114 " --> pdb=" O SER M 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 141 removed outlier: 3.834A pdb=" N LYS M 137 " --> pdb=" O LEU M 133 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS M 139 " --> pdb=" O ALA M 135 " (cutoff:3.500A) Processing helix chain 'M' and resid 155 through 160 removed outlier: 3.624A pdb=" N ALA M 160 " --> pdb=" O ASN M 156 " (cutoff:3.500A) Processing helix chain 'M' and resid 177 through 182 Processing helix chain 'M' and resid 190 through 200 removed outlier: 3.655A pdb=" N LYS M 194 " --> pdb=" O ALA M 190 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 68 Processing helix chain 'N' and resid 98 through 102 Processing helix chain 'O' and resid 25 through 37 removed outlier: 4.144A 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 66 through 71 removed outlier: 4.414A pdb=" N ARG O 69 " --> pdb=" O GLY O 66 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP O 71 " --> pdb=" O LYS O 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 95 removed outlier: 3.590A pdb=" N ALA O 94 " --> pdb=" O GLU O 90 " (cutoff:3.500A) Processing helix chain 'O' and resid 97 through 106 removed outlier: 3.586A pdb=" N GLU O 102 " --> pdb=" O ARG O 99 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL O 105 " --> pdb=" O GLU O 102 " (cutoff:3.500A) Processing helix chain 'O' and resid 115 through 121 removed outlier: 3.508A pdb=" N PHE O 119 " --> pdb=" O GLY O 115 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ARG O 120 " --> pdb=" O ARG O 116 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS O 121 " --> pdb=" O ALA O 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 115 through 121' 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 101 through 105 removed outlier: 3.568A pdb=" N ARG K 102 " --> pdb=" O VAL K 94 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE K 104 " --> pdb=" O ALA K 92 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG K 80 " --> pdb=" O LEU K 93 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU K 95 " --> pdb=" O VAL K 78 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N VAL K 78 " --> pdb=" O LEU K 95 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'K' and resid 129 through 131 removed outlier: 3.788A pdb=" N LEU K 130 " --> pdb=" O ALA K 190 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'K' and resid 181 through 185 removed outlier: 3.575A pdb=" N ALA K 166 " --> pdb=" O THR K 173 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ARG K 175 " --> pdb=" O ILE K 164 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ILE K 164 " --> pdb=" O ARG K 175 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'L' and resid 74 through 76 removed outlier: 6.544A pdb=" N PHE L 107 " --> pdb=" O ALA L 75 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'L' and resid 89 through 91 removed outlier: 6.522A pdb=" N THR L 121 " --> pdb=" O VAL L 90 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS L 141 " --> pdb=" O VAL L 122 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'M' and resid 2 through 4 Processing sheet with id= H, first strand: chain 'M' and resid 118 through 121 removed outlier: 6.401A pdb=" N VAL M 186 " --> pdb=" O ILE M 119 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL M 121 " --> pdb=" O VAL M 186 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N MET M 188 " --> pdb=" O VAL M 121 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR M 150 " --> pdb=" O ARG M 170 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 169 through 171 removed outlier: 4.780A pdb=" N THR N 112 " --> pdb=" O ASP N 200 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ASP N 200 " --> pdb=" O THR N 112 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL N 26 " --> pdb=" O VAL N 9 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N MET N 11 " --> pdb=" O VAL N 24 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL N 24 " --> pdb=" O MET N 11 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ARG N 13 " --> pdb=" O ILE N 22 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ILE N 22 " --> pdb=" O ARG N 13 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP N 181 " --> pdb=" O LEU N 186 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG N 179 " --> pdb=" O LEU N 188 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N LYS N 190 " --> pdb=" O VAL N 177 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL N 177 " --> pdb=" O LYS N 190 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 47 through 50 Processing sheet with id= K, first strand: chain 'N' and resid 117 through 119 removed outlier: 3.546A pdb=" N GLY N 117 " --> pdb=" O MET N 165 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'O' and resid 15 through 19 removed outlier: 6.480A pdb=" N TYR O 53 " --> pdb=" O TYR O 16 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N VAL O 18 " --> pdb=" O TYR O 53 " (cutoff:3.500A) removed outlier: 6.323A 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 76 117 hydrogen bonds defined for protein. 294 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1962 hydrogen bonds 3204 hydrogen bond angles 0 basepair planarities 793 basepair parallelities 1610 stacking parallelities Total time for adding SS restraints: 145.62 Time building geometry restraints manager: 35.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 4062 1.28 - 1.41: 27849 1.41 - 1.54: 41988 1.54 - 1.68: 6065 1.68 - 1.81: 42 Bond restraints: 80006 Sorted by residual: bond pdb=" C4 5MU I 747 " pdb=" C5 5MU I 747 " ideal model delta sigma weight residual 1.805 1.411 0.394 2.00e-02 2.50e+03 3.89e+02 bond pdb=" C4 5MU I1939 " pdb=" C5 5MU I1939 " ideal model delta sigma weight residual 1.805 1.412 0.393 2.00e-02 2.50e+03 3.86e+02 bond pdb=" N1 5MU I1939 " pdb=" C6 5MU I1939 " ideal model delta sigma weight residual 1.638 1.366 0.272 2.00e-02 2.50e+03 1.86e+02 bond pdb=" N1 5MU I 747 " pdb=" C6 5MU I 747 " ideal model delta sigma weight residual 1.638 1.368 0.270 2.00e-02 2.50e+03 1.82e+02 bond pdb=" C5 5MU I 747 " pdb=" C6 5MU I 747 " ideal model delta sigma weight residual 1.150 1.349 -0.199 2.00e-02 2.50e+03 9.88e+01 ... (remaining 80001 not shown) Histogram of bond angle deviations from ideal: 99.96 - 106.96: 17923 106.96 - 113.96: 51097 113.96 - 120.96: 32327 120.96 - 127.96: 16919 127.96 - 134.97: 4912 Bond angle restraints: 123178 Sorted by residual: angle pdb=" C1' 1MG I 745 " pdb=" N9 1MG I 745 " pdb=" C4 1MG I 745 " ideal model delta sigma weight residual 103.27 126.35 -23.08 3.00e+00 1.11e-01 5.92e+01 angle pdb=" C1' 2MA I2503 " pdb=" N9 2MA I2503 " pdb=" C4 2MA I2503 " ideal model delta sigma weight residual 103.49 126.07 -22.58 3.00e+00 1.11e-01 5.67e+01 angle pdb=" C1' OMG I2251 " pdb=" N9 OMG I2251 " pdb=" C8 OMG I2251 " ideal model delta sigma weight residual 106.81 125.69 -18.88 3.00e+00 1.11e-01 3.96e+01 angle pdb=" C1' 2MA I2503 " pdb=" N9 2MA I2503 " pdb=" C8 2MA I2503 " ideal model delta sigma weight residual 144.94 126.50 18.44 3.00e+00 1.11e-01 3.78e+01 angle pdb=" C1' 2MG I2445 " pdb=" N9 2MG I2445 " pdb=" C4 2MG I2445 " ideal model delta sigma weight residual 109.53 126.78 -17.25 3.00e+00 1.11e-01 3.30e+01 ... (remaining 123173 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.70: 39495 35.70 - 71.41: 1079 71.41 - 107.11: 100 107.11 - 142.81: 5 142.81 - 178.52: 6 Dihedral angle restraints: 40685 sinusoidal: 38005 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 90.64 56.36 1 8.00e+00 1.56e-02 6.69e+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 58.45 173.55 1 1.70e+01 3.46e-03 6.62e+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 63.24 168.76 1 1.70e+01 3.46e-03 6.58e+01 ... (remaining 40682 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 16043 0.086 - 0.171: 107 0.171 - 0.257: 0 0.257 - 0.342: 0 0.342 - 0.428: 2 Chirality restraints: 16152 Sorted by residual: chirality pdb=" CA PRO K 227 " pdb=" N PRO K 227 " pdb=" C PRO K 227 " pdb=" CB PRO K 227 " both_signs ideal model delta sigma weight residual False 2.72 2.29 0.43 2.00e-01 2.50e+01 4.58e+00 chirality pdb=" CB VAL K 228 " pdb=" CA VAL K 228 " pdb=" CG1 VAL K 228 " pdb=" CG2 VAL K 228 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" C3' G I 271 " pdb=" C4' G I 271 " pdb=" O3' G I 271 " pdb=" C2' G I 271 " both_signs ideal model delta sigma weight residual False -2.74 -2.59 -0.15 2.00e-01 2.50e+01 5.96e-01 ... (remaining 16149 not shown) Planarity restraints: 4337 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I2445 " -0.033 2.00e-02 2.50e+03 6.01e-01 8.13e+03 pdb=" C4' 2MG I2445 " -0.461 2.00e-02 2.50e+03 pdb=" O4' 2MG I2445 " -0.751 2.00e-02 2.50e+03 pdb=" C3' 2MG I2445 " 0.589 2.00e-02 2.50e+03 pdb=" O3' 2MG I2445 " 0.584 2.00e-02 2.50e+03 pdb=" C2' 2MG I2445 " 0.224 2.00e-02 2.50e+03 pdb=" O2' 2MG I2445 " -0.897 2.00e-02 2.50e+03 pdb=" C1' 2MG I2445 " -0.199 2.00e-02 2.50e+03 pdb=" N9 2MG I2445 " 0.944 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG I2251 " 0.033 2.00e-02 2.50e+03 5.84e-01 7.67e+03 pdb=" C4' OMG I2251 " 0.443 2.00e-02 2.50e+03 pdb=" O4' OMG I2251 " 0.685 2.00e-02 2.50e+03 pdb=" C3' OMG I2251 " -0.594 2.00e-02 2.50e+03 pdb=" O3' OMG I2251 " -0.574 2.00e-02 2.50e+03 pdb=" C2' OMG I2251 " -0.216 2.00e-02 2.50e+03 pdb=" O2' OMG I2251 " 0.904 2.00e-02 2.50e+03 pdb=" C1' OMG I2251 " 0.218 2.00e-02 2.50e+03 pdb=" N9 OMG I2251 " -0.899 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I1835 " -0.042 2.00e-02 2.50e+03 5.81e-01 7.60e+03 pdb=" C4' 2MG I1835 " -0.438 2.00e-02 2.50e+03 pdb=" O4' 2MG I1835 " -0.643 2.00e-02 2.50e+03 pdb=" C3' 2MG I1835 " 0.596 2.00e-02 2.50e+03 pdb=" O3' 2MG I1835 " 0.587 2.00e-02 2.50e+03 pdb=" C2' 2MG I1835 " 0.202 2.00e-02 2.50e+03 pdb=" O2' 2MG I1835 " -0.924 2.00e-02 2.50e+03 pdb=" C1' 2MG I1835 " -0.224 2.00e-02 2.50e+03 pdb=" N9 2MG I1835 " 0.887 2.00e-02 2.50e+03 ... (remaining 4334 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 182 2.34 - 2.98: 32732 2.98 - 3.62: 124124 3.62 - 4.26: 221679 4.26 - 4.90: 289588 Nonbonded interactions: 668305 Sorted by model distance: nonbonded pdb=" O MET K 225 " pdb=" O ASN K 226 " model vdw 1.702 3.040 nonbonded pdb=" O2' G I2576 " pdb=" OP2 C I2579 " model vdw 1.913 2.440 nonbonded pdb=" O2' 2MA I2503 " pdb=" OP2 G I2505 " model vdw 1.951 2.440 nonbonded pdb=" O2' G I1715 " pdb=" O6 G I1743 " model vdw 1.963 2.440 nonbonded pdb=" O2' A I1084 " pdb=" O2' U I1105 " model vdw 1.972 2.440 ... (remaining 668300 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3015 5.49 5 S 22 5.16 5 C 33508 2.51 5 N 13319 2.21 5 O 22270 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.850 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: 0.050 Extract box with map and model: 46.360 Check model and map are aligned: 0.850 Convert atoms to be neutral: 0.490 Process input model: 294.330 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Set scattering table: 0.040 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:10.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 364.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.394 80006 Z= 0.309 Angle : 0.376 23.083 123178 Z= 0.191 Chirality : 0.023 0.428 16152 Planarity : 0.023 0.601 4337 Dihedral : 12.690 178.519 38979 Min Nonbonded Distance : 1.702 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.88 % Favored : 92.02 % Rotamer Outliers : 2.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -4.23 (0.23), residues: 952 helix: -4.18 (0.22), residues: 162 sheet: -2.43 (0.37), residues: 167 loop : -2.66 (0.21), residues: 623 *********************** 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 248 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 231 time to evaluate : 2.323 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 241 average time/residue: 1.7009 time to fit residues: 530.8874 Evaluate side-chains 165 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 156 time to evaluate : 2.254 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 5 residues processed: 4 average time/residue: 0.5164 time to fit residues: 5.6274 ------------------------------------------------------------------------------- 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: 10.0000 chunk 299 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 201 optimal weight: 10.0000 chunk 159 optimal weight: 10.0000 chunk 309 optimal weight: 0.8980 chunk 119 optimal weight: 10.0000 chunk 188 optimal weight: 10.0000 chunk 230 optimal weight: 10.0000 chunk 358 optimal weight: 6.9990 overall best weight: 7.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 46 ASN K 86 ASN K 115 GLN K 200 HIS K 239 ASN L 4 ASN L 99 ASN ** M 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 32 ASN N 49 GLN N 67 HIS N 94 GLN N 126 ASN O 86 GLN O 130 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.078 80006 Z= 0.454 Angle : 0.844 14.701 123178 Z= 0.425 Chirality : 0.042 0.295 16152 Planarity : 0.008 0.134 4337 Dihedral : 13.946 176.345 37180 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.30 % Favored : 91.60 % Rotamer Outliers : 7.88 % 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: -3.10 (0.24), residues: 952 helix: -2.91 (0.30), residues: 175 sheet: -1.67 (0.40), residues: 149 loop : -1.98 (0.22), residues: 628 *********************** 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 240 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 180 time to evaluate : 2.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 30 residues processed: 213 average time/residue: 1.5360 time to fit residues: 434.0092 Evaluate side-chains 183 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 153 time to evaluate : 2.247 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 20 residues processed: 11 average time/residue: 0.7220 time to fit residues: 14.8451 ------------------------------------------------------------------------------- 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: 8.9990 chunk 111 optimal weight: 10.0000 chunk 298 optimal weight: 10.0000 chunk 244 optimal weight: 0.7980 chunk 98 optimal weight: 7.9990 chunk 359 optimal weight: 3.9990 chunk 388 optimal weight: 5.9990 chunk 320 optimal weight: 2.9990 chunk 356 optimal weight: 0.8980 chunk 122 optimal weight: 10.0000 chunk 288 optimal weight: 10.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 195 GLN ** N 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 80006 Z= 0.201 Angle : 0.592 13.484 123178 Z= 0.314 Chirality : 0.031 0.253 16152 Planarity : 0.007 0.128 4337 Dihedral : 13.635 176.500 37180 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.41 % Favored : 93.49 % Rotamer Outliers : 7.62 % 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: -2.62 (0.25), residues: 952 helix: -2.25 (0.34), residues: 175 sheet: -1.53 (0.38), residues: 163 loop : -1.69 (0.23), residues: 614 *********************** 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 244 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 186 time to evaluate : 2.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 31 residues processed: 219 average time/residue: 1.5154 time to fit residues: 442.6985 Evaluate side-chains 192 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 161 time to evaluate : 2.265 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 19 residues processed: 12 average time/residue: 0.8137 time to fit residues: 17.2084 ------------------------------------------------------------------------------- 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: 7.9990 chunk 270 optimal weight: 10.0000 chunk 186 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 171 optimal weight: 10.0000 chunk 241 optimal weight: 10.0000 chunk 360 optimal weight: 9.9990 chunk 381 optimal weight: 5.9990 chunk 188 optimal weight: 10.0000 chunk 341 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 195 GLN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 80 HIS O 86 GLN O 128 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.090 80006 Z= 0.458 Angle : 0.825 14.028 123178 Z= 0.417 Chirality : 0.042 0.277 16152 Planarity : 0.008 0.138 4337 Dihedral : 14.571 171.147 37180 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.51 % Favored : 91.39 % Rotamer Outliers : 8.94 % 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: -2.53 (0.24), residues: 952 helix: -2.30 (0.35), residues: 170 sheet: -1.16 (0.39), residues: 156 loop : -1.70 (0.23), residues: 626 *********************** 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 233 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 165 time to evaluate : 2.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 39 residues processed: 206 average time/residue: 1.4955 time to fit residues: 414.5806 Evaluate side-chains 202 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 163 time to evaluate : 2.291 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 24 residues processed: 15 average time/residue: 0.9187 time to fit residues: 23.0183 ------------------------------------------------------------------------------- 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: 2.9990 chunk 216 optimal weight: 40.0000 chunk 5 optimal weight: 8.9990 chunk 284 optimal weight: 10.0000 chunk 157 optimal weight: 10.0000 chunk 325 optimal weight: 0.8980 chunk 263 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 194 optimal weight: 10.0000 chunk 342 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 25 HIS M 195 GLN N 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.075 80006 Z= 0.328 Angle : 0.693 13.884 123178 Z= 0.361 Chirality : 0.037 0.263 16152 Planarity : 0.007 0.132 4337 Dihedral : 14.435 175.154 37180 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.09 % Favored : 91.81 % Rotamer Outliers : 8.28 % 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: -2.37 (0.25), residues: 952 helix: -2.04 (0.36), residues: 164 sheet: -1.19 (0.38), residues: 164 loop : -1.60 (0.23), residues: 624 *********************** 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 222 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 159 time to evaluate : 2.270 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 40 residues processed: 197 average time/residue: 1.4982 time to fit residues: 393.6108 Evaluate side-chains 199 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 159 time to evaluate : 2.302 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 28 residues processed: 12 average time/residue: 0.5318 time to fit residues: 13.7727 ------------------------------------------------------------------------------- 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: 10.0000 chunk 343 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 224 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 382 optimal weight: 9.9990 chunk 317 optimal weight: 6.9990 chunk 176 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 200 optimal weight: 8.9990 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 42 ASN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 135 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.101 80006 Z= 0.506 Angle : 0.860 13.920 123178 Z= 0.432 Chirality : 0.045 0.279 16152 Planarity : 0.008 0.140 4337 Dihedral : 14.985 171.214 37180 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.35 % Favored : 90.55 % Rotamer Outliers : 8.80 % 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: -2.56 (0.24), residues: 952 helix: -2.10 (0.35), residues: 164 sheet: -1.32 (0.39), residues: 157 loop : -1.76 (0.23), residues: 631 *********************** 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 227 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 160 time to evaluate : 2.486 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 46 residues processed: 203 average time/residue: 1.4448 time to fit residues: 394.5212 Evaluate side-chains 199 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 153 time to evaluate : 2.243 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 32 residues processed: 14 average time/residue: 0.8263 time to fit residues: 19.8585 ------------------------------------------------------------------------------- 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: 40.0000 chunk 321 optimal weight: 4.9990 chunk 213 optimal weight: 30.0000 chunk 380 optimal weight: 0.9980 chunk 238 optimal weight: 7.9990 chunk 232 optimal weight: 10.0000 chunk 175 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 251 GLN N 42 ASN N 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.082 80006 Z= 0.357 Angle : 0.723 13.847 123178 Z= 0.375 Chirality : 0.038 0.261 16152 Planarity : 0.007 0.134 4337 Dihedral : 14.766 175.106 37180 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.72 % Favored : 91.18 % Rotamer Outliers : 8.15 % 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: -2.36 (0.25), residues: 952 helix: -1.86 (0.37), residues: 165 sheet: -1.22 (0.39), residues: 154 loop : -1.64 (0.23), residues: 633 *********************** 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 224 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 162 time to evaluate : 2.330 Fit side-chains revert: symmetry clash outliers start: 62 outliers final: 43 residues processed: 202 average time/residue: 1.5172 time to fit residues: 410.5938 Evaluate side-chains 197 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 154 time to evaluate : 2.294 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 34 residues processed: 9 average time/residue: 0.5250 time to fit residues: 10.6303 ------------------------------------------------------------------------------- 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: 10.0000 chunk 152 optimal weight: 20.0000 chunk 227 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 242 optimal weight: 10.0000 chunk 259 optimal weight: 9.9990 chunk 188 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 299 optimal weight: 10.0000 overall best weight: 9.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 42 ASN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.106 80006 Z= 0.578 Angle : 0.939 13.902 123178 Z= 0.467 Chirality : 0.049 0.286 16152 Planarity : 0.009 0.143 4337 Dihedral : 15.454 173.183 37180 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.61 % Favored : 89.18 % Rotamer Outliers : 8.80 % 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: -2.63 (0.25), residues: 952 helix: -2.11 (0.36), residues: 164 sheet: -1.42 (0.39), residues: 157 loop : -1.80 (0.23), residues: 631 *********************** 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 227 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 160 time to evaluate : 2.304 Fit side-chains revert: symmetry clash outliers start: 67 outliers final: 46 residues processed: 207 average time/residue: 1.5320 time to fit residues: 425.0322 Evaluate side-chains 204 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 158 time to evaluate : 2.281 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 35 residues processed: 11 average time/residue: 0.7956 time to fit residues: 15.8168 ------------------------------------------------------------------------------- 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: 1.9990 chunk 364 optimal weight: 5.9990 chunk 332 optimal weight: 4.9990 chunk 354 optimal weight: 2.9990 chunk 213 optimal weight: 30.0000 chunk 154 optimal weight: 10.0000 chunk 278 optimal weight: 10.0000 chunk 108 optimal weight: 30.0000 chunk 320 optimal weight: 0.9990 chunk 335 optimal weight: 3.9990 chunk 353 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 15 HIS K 153 GLN N 42 ASN N 49 GLN ** N 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 80006 Z= 0.216 Angle : 0.628 13.781 123178 Z= 0.335 Chirality : 0.033 0.254 16152 Planarity : 0.007 0.127 4337 Dihedral : 14.676 179.195 37180 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.09 % Favored : 91.81 % Rotamer Outliers : 6.04 % 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: -2.20 (0.25), residues: 952 helix: -1.60 (0.38), residues: 163 sheet: -1.27 (0.40), residues: 161 loop : -1.52 (0.24), residues: 628 *********************** 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 214 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 168 time to evaluate : 2.355 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 39 residues processed: 203 average time/residue: 1.4929 time to fit residues: 406.8553 Evaluate side-chains 198 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 159 time to evaluate : 2.251 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 31 residues processed: 8 average time/residue: 0.5222 time to fit residues: 9.6363 ------------------------------------------------------------------------------- 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: 10.0000 chunk 375 optimal weight: 0.0470 chunk 228 optimal weight: 10.0000 chunk 177 optimal weight: 10.0000 chunk 260 optimal weight: 10.0000 chunk 393 optimal weight: 0.9980 chunk 362 optimal weight: 5.9990 chunk 313 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 242 optimal weight: 10.0000 chunk 192 optimal weight: 10.0000 overall best weight: 5.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 153 GLN ** M 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 ASN N 49 GLN ** N 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.071 80006 Z= 0.320 Angle : 0.694 13.860 123178 Z= 0.362 Chirality : 0.036 0.256 16152 Planarity : 0.007 0.133 4337 Dihedral : 14.756 176.339 37180 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.14 % Favored : 90.65 % Rotamer Outliers : 5.65 % 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: -2.11 (0.26), residues: 952 helix: -1.51 (0.38), residues: 164 sheet: -1.20 (0.40), residues: 157 loop : -1.47 (0.24), residues: 631 ********************** 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 208 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 165 time to evaluate : 2.303 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 36 residues processed: 198 average time/residue: 1.5012 time to fit residues: 396.9824 Evaluate side-chains 193 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 157 time to evaluate : 2.241 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 31 residues processed: 5 average time/residue: 0.5202 time to fit residues: 6.5772 ------------------------------------------------------------------------------- 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: 10.0000 chunk 333 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 288 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 313 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 chunk 322 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 ASN N 49 GLN ** O 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.145889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.123677 restraints weight = 144506.063| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 0.83 r_work: 0.3635 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3557 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.090 80006 Z= 0.430 Angle : 0.794 13.870 123178 Z= 0.405 Chirality : 0.042 0.269 16152 Planarity : 0.008 0.137 4337 Dihedral : 15.061 173.623 37180 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.77 % Favored : 90.02 % 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: -2.28 (0.25), residues: 952 helix: -1.70 (0.37), residues: 163 sheet: -1.25 (0.40), residues: 146 loop : -1.59 (0.23), residues: 643 =============================================================================== Job complete usr+sys time: 10238.96 seconds wall clock time: 184 minutes 33.78 seconds (11073.78 seconds total)