Starting phenix.real_space_refine on Sun Feb 18 10:04:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pct_20307/02_2024/6pct_20307_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pct_20307/02_2024/6pct_20307.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pct_20307/02_2024/6pct_20307_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pct_20307/02_2024/6pct_20307_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pct_20307/02_2024/6pct_20307_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pct_20307/02_2024/6pct_20307.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pct_20307/02_2024/6pct_20307.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pct_20307/02_2024/6pct_20307_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pct_20307/02_2024/6pct_20307_neut_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.017 sd= 1.376 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: 5 Type Number sf(0) Gaussians P 3015 5.49 5 S 22 5.16 5 C 33554 2.51 5 N 13326 2.21 5 O 22281 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K GLU 23": "OE1" <-> "OE2" Residue "K GLU 35": "OE1" <-> "OE2" 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 TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 167": "NH1" <-> "NH2" Residue "K TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 264": "OD1" <-> "OD2" Residue "K ARG 269": "NH1" <-> "NH2" Residue "K ARG 270": "NH1" <-> "NH2" Residue "L GLU 10": "OE1" <-> "OE2" 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 GLU 51": "OE1" <-> "OE2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ASP 81": "OD1" <-> "OD2" 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 GLU 122": "OE1" <-> "OE2" Residue "M GLU 127": "OE1" <-> "OE2" Residue "M GLU 144": "OE1" <-> "OE2" Residue "M ARG 162": "NH1" <-> "NH2" Residue "M ASP 168": "OD1" <-> "OD2" 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 ARG 83": "NH1" <-> "NH2" Residue "N ARG 169": "NH1" <-> "NH2" Residue "N ARG 184": "NH1" <-> "NH2" Residue "O ARG 13": "NH1" <-> "NH2" Residue "O ARG 37": "NH1" <-> "NH2" Residue "O ASP 71": "OD1" <-> "OD2" Residue "O PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "O ARG 120": "NH1" <-> "NH2" Residue "O TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 72198 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': 6, 'rna2p_pur': 280, 'rna2p_pyr': 151, 'rna3p': 15, 'rna3p_pur': 1384, 'rna3p_pyr': 1061} Link IDs: {'rna2p': 437, 'rna3p': 2459} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 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: 104 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 52 Unusual residues: {'O8V': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 52 Unusual residues: {'O8V': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C02AO8V I3001 " occ=0.50 ... (102 atoms not shown) pdb=" O52BO8V I3001 " occ=0.50 Time building chain proxies: 28.91, per 1000 atoms: 0.40 Number of scatterers: 72198 At special positions: 0 Unit cell: (228.611, 222.813, 190.509, 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 22281 8.00 N 13326 7.00 C 33554 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: 32.89 Conformation dependent library (CDL) restraints added in 1.4 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: 28 helices and 14 sheets defined 19.9% alpha, 13.7% beta 889 base pairs and 1638 stacking pairs defined. Time for finding SS restraints: 37.87 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 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 'K' and resid 226 through 229 No H-bonds generated for 'chain 'K' and resid 226 through 229' 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 71 through 73 No H-bonds generated for 'chain 'L' and resid 71 through 73' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.734A pdb=" N ALA L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 98 removed outlier: 3.928A pdb=" N LYS L 96 " --> pdb=" O LEU L 92 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA L 97 " --> pdb=" O ASN L 93 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA L 98 " --> pdb=" O THR L 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 92 through 98' 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 39 removed outlier: 3.647A pdb=" N ALA M 34 " --> pdb=" O GLN M 30 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA M 39 " --> pdb=" O TYR M 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 114 removed outlier: 3.620A pdb=" N SER M 110 " --> pdb=" O LYS M 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 140 Processing helix chain 'M' and resid 155 through 161 removed outlier: 3.672A 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 Processing helix chain 'N' and resid 57 through 59 No H-bonds generated for 'chain 'N' and resid 57 through 59' Processing helix chain 'N' and resid 62 through 69 Processing helix chain 'N' and resid 98 through 101 Processing helix chain 'N' and resid 121 through 125 Processing helix chain 'O' and resid 8 through 10 No H-bonds generated for 'chain 'O' and resid 8 through 10' Processing helix chain 'O' and resid 25 through 37 removed outlier: 3.930A pdb=" N GLU O 31 " --> pdb=" O ARG O 27 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU O 32 " --> pdb=" O LEU O 28 " (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: 4.179A pdb=" N VAL O 100 " --> pdb=" O ARG O 96 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE O 101 " --> pdb=" O PRO O 97 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA O 104 " --> pdb=" O VAL O 100 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 121 removed outlier: 3.638A pdb=" N PHE O 119 " --> pdb=" O GLY O 115 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG O 120 " --> pdb=" O ARG O 116 " (cutoff:3.500A) removed outlier: 3.663A 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 removed outlier: 3.649A pdb=" N VAL K 4 " --> pdb=" O LYS K 18 " (cutoff:3.500A) 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: 3.588A pdb=" N ARG K 80 " --> pdb=" O LEU K 93 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU K 95 " --> pdb=" O VAL K 78 " (cutoff:3.500A) removed outlier: 5.699A 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 Processing sheet with id= E, first strand: chain 'K' and resid 181 through 185 removed outlier: 3.636A pdb=" N ALA K 166 " --> pdb=" O THR K 173 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG K 175 " --> pdb=" O ILE K 164 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ILE K 164 " --> pdb=" O ARG K 175 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'L' and resid 121 through 123 removed outlier: 6.573A 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: 6.277A pdb=" N VAL M 186 " --> pdb=" O ILE M 119 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N VAL M 121 " --> pdb=" O VAL M 186 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N MET M 188 " --> pdb=" O VAL M 121 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP M 168 " --> pdb=" O VAL M 146 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 4 through 7 removed outlier: 7.317A pdb=" N ASP N 200 " --> pdb=" O THR N 112 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N THR N 112 " --> pdb=" O ASP N 200 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 186 through 190 removed outlier: 3.552A pdb=" N VAL N 189 " --> pdb=" O THR N 25 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY N 10 " --> pdb=" O VAL N 26 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLU N 28 " --> pdb=" O LYS N 8 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LYS N 8 " --> pdb=" O GLU N 28 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'N' and resid 80 through 83 removed outlier: 6.271A pdb=" N THR N 51 " --> pdb=" O VAL N 34 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N VAL N 34 " --> pdb=" O THR N 51 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'N' and resid 115 through 119 removed outlier: 5.707A pdb=" N MET N 165 " --> pdb=" O LYS N 116 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N PHE N 118 " --> pdb=" O GLY N 163 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLY N 163 " --> pdb=" O PHE N 118 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'O' and resid 15 through 19 removed outlier: 6.492A pdb=" N TYR O 53 " --> pdb=" O TYR O 16 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N VAL O 18 " --> pdb=" O TYR O 53 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE O 55 " --> pdb=" O VAL O 18 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'O' and resid 73 through 77 132 hydrogen bonds defined for protein. 378 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2215 hydrogen bonds 3592 hydrogen bond angles 0 basepair planarities 889 basepair parallelities 1638 stacking parallelities Total time for adding SS restraints: 131.71 Time building geometry restraints manager: 35.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 5645 1.31 - 1.43: 39780 1.43 - 1.56: 28560 1.56 - 1.68: 6049 1.68 - 1.80: 42 Bond restraints: 80076 Sorted by residual: bond pdb=" C4 5MU I 747 " pdb=" C5 5MU I 747 " ideal model delta sigma weight residual 1.802 1.411 0.391 2.00e-02 2.50e+03 3.81e+02 bond pdb=" C4 5MU I1939 " pdb=" C5 5MU I1939 " ideal model delta sigma weight residual 1.802 1.412 0.390 2.00e-02 2.50e+03 3.80e+02 bond pdb=" N1 5MU I1939 " pdb=" C6 5MU I1939 " ideal model delta sigma weight residual 1.635 1.365 0.270 2.00e-02 2.50e+03 1.83e+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=" C5 5MU I 747 " pdb=" C6 5MU I 747 " ideal model delta sigma weight residual 1.155 1.347 -0.192 2.00e-02 2.50e+03 9.20e+01 ... (remaining 80071 not shown) Histogram of bond angle deviations from ideal: 99.40 - 106.49: 17853 106.49 - 113.59: 48303 113.59 - 120.68: 33108 120.68 - 127.78: 18824 127.78 - 134.87: 5187 Bond angle restraints: 123275 Sorted by residual: angle pdb=" C1' 6MZ I1618 " pdb=" N9 6MZ I1618 " pdb=" C8 6MZ I1618 " ideal model delta sigma weight residual 91.39 126.40 -35.01 3.00e+00 1.11e-01 1.36e+02 angle pdb=" C1' 6MZ I1618 " pdb=" N9 6MZ I1618 " pdb=" C4 6MZ I1618 " ideal model delta sigma weight residual 154.15 126.21 27.94 3.00e+00 1.11e-01 8.67e+01 angle pdb=" N ASP K 229 " pdb=" CA ASP K 229 " pdb=" C ASP K 229 " ideal model delta sigma weight residual 111.36 121.09 -9.73 1.09e+00 8.42e-01 7.98e+01 angle pdb=" C1' 1MG I 745 " pdb=" N9 1MG I 745 " pdb=" C8 1MG I 745 " ideal model delta sigma weight residual 100.16 126.67 -26.51 3.00e+00 1.11e-01 7.81e+01 angle pdb=" N THR M 84 " pdb=" CA THR M 84 " pdb=" C THR M 84 " ideal model delta sigma weight residual 111.71 102.47 9.24 1.15e+00 7.56e-01 6.46e+01 ... (remaining 123270 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 44275 35.93 - 71.86: 6539 71.86 - 107.79: 785 107.79 - 143.72: 8 143.72 - 179.65: 7 Dihedral angle restraints: 51614 sinusoidal: 48934 harmonic: 2680 Sorted by residual: dihedral pdb=" O4' U I1340 " pdb=" C1' U I1340 " pdb=" N1 U I1340 " pdb=" C2 U I1340 " ideal model delta sinusoidal sigma weight residual -128.00 51.65 -179.65 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C I 323 " pdb=" C1' C I 323 " pdb=" N1 C I 323 " pdb=" C2 C I 323 " ideal model delta sinusoidal sigma weight residual -128.00 47.38 -175.38 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' U I1313 " pdb=" C1' U I1313 " pdb=" N1 U I1313 " pdb=" C2 U I1313 " ideal model delta sinusoidal sigma weight residual 200.00 85.90 114.10 1 1.50e+01 4.44e-03 6.01e+01 ... (remaining 51611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 15884 0.062 - 0.125: 233 0.125 - 0.187: 12 0.187 - 0.250: 3 0.250 - 0.312: 2 Chirality restraints: 16134 Sorted by residual: 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 2.20 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CA SER M 80 " pdb=" N SER M 80 " pdb=" C SER M 80 " pdb=" CB SER M 80 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA VAL N 155 " pdb=" N VAL N 155 " pdb=" C VAL N 155 " pdb=" CB VAL N 155 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 16131 not shown) Planarity restraints: 4355 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMG I2251 " 0.039 2.00e-02 2.50e+03 5.89e-01 7.82e+03 pdb=" C4' OMG I2251 " 0.441 2.00e-02 2.50e+03 pdb=" O4' OMG I2251 " 0.680 2.00e-02 2.50e+03 pdb=" C3' OMG I2251 " -0.598 2.00e-02 2.50e+03 pdb=" O3' OMG I2251 " -0.589 2.00e-02 2.50e+03 pdb=" C2' OMG I2251 " -0.206 2.00e-02 2.50e+03 pdb=" O2' OMG I2251 " 0.923 2.00e-02 2.50e+03 pdb=" C1' OMG I2251 " 0.217 2.00e-02 2.50e+03 pdb=" N9 OMG I2251 " -0.907 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 1MG I 745 " -0.035 2.00e-02 2.50e+03 5.88e-01 7.78e+03 pdb=" C4' 1MG I 745 " -0.445 2.00e-02 2.50e+03 pdb=" O4' 1MG I 745 " -0.687 2.00e-02 2.50e+03 pdb=" C3' 1MG I 745 " 0.593 2.00e-02 2.50e+03 pdb=" O3' 1MG I 745 " 0.583 2.00e-02 2.50e+03 pdb=" C2' 1MG I 745 " 0.210 2.00e-02 2.50e+03 pdb=" O2' 1MG I 745 " -0.912 2.00e-02 2.50e+03 pdb=" C1' 1MG I 745 " -0.216 2.00e-02 2.50e+03 pdb=" N9 1MG I 745 " 0.910 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I2445 " -0.029 2.00e-02 2.50e+03 5.84e-01 7.67e+03 pdb=" C4' 2MG I2445 " -0.450 2.00e-02 2.50e+03 pdb=" O4' 2MG I2445 " -0.692 2.00e-02 2.50e+03 pdb=" C3' 2MG I2445 " 0.588 2.00e-02 2.50e+03 pdb=" O3' 2MG I2445 " 0.572 2.00e-02 2.50e+03 pdb=" C2' 2MG I2445 " 0.218 2.00e-02 2.50e+03 pdb=" O2' 2MG I2445 " -0.897 2.00e-02 2.50e+03 pdb=" C1' 2MG I2445 " -0.214 2.00e-02 2.50e+03 pdb=" N9 2MG I2445 " 0.903 2.00e-02 2.50e+03 ... (remaining 4352 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 371 2.49 - 3.09: 46793 3.09 - 3.70: 140916 3.70 - 4.30: 212310 4.30 - 4.90: 273872 Nonbonded interactions: 674262 Sorted by model distance: nonbonded pdb=" O2* PSU I1911 " pdb=" OP1 A I1912 " model vdw 1.891 3.040 nonbonded pdb=" OP2 G I1799 " pdb=" NH2 ARG K 270 " model vdw 1.955 2.520 nonbonded pdb=" OP1 G I2642 " pdb=" OG1 THR O 78 " model vdw 1.965 2.440 nonbonded pdb=" O MET K 225 " pdb=" O ASN K 226 " model vdw 1.966 3.040 nonbonded pdb=" O2' G I1826 " pdb=" OP2 U I1971 " model vdw 1.986 2.440 ... (remaining 674257 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.750 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: 49.910 Check model and map are aligned: 0.810 Set scattering table: 0.520 Process input model: 273.490 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 348.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.391 80076 Z= 0.330 Angle : 0.426 35.007 123275 Z= 0.216 Chirality : 0.025 0.312 16134 Planarity : 0.030 0.589 4355 Dihedral : 23.648 179.647 49908 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.30 % Favored : 93.59 % Rotamer: Outliers : 2.50 % Allowed : 13.14 % Favored : 84.36 % Cbeta Deviations : 0.23 % 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: -3.70 (0.22), residues: 952 helix: -2.94 (0.30), residues: 149 sheet: -2.30 (0.33), residues: 163 loop : -2.51 (0.21), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 78 HIS 0.011 0.001 HIS K 230 PHE 0.004 0.001 PHE N 15 TYR 0.005 0.001 TYR L 58 ARG 0.004 0.000 ARG M 79 *********************** 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 226 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 207 time to evaluate : 2.230 Fit side-chains revert: symmetry clash REVERT: L 99 ASN cc_start: 0.6219 (t0) cc_final: 0.6002 (m-40) REVERT: M 13 THR cc_start: 0.7918 (m) cc_final: 0.7077 (m) REVERT: N 126 ASN cc_start: 0.8699 (m110) cc_final: 0.8395 (m110) REVERT: O 1 MET cc_start: 0.6542 (ptm) cc_final: 0.6231 (ptp) REVERT: O 86 GLN cc_start: 0.7477 (OUTLIER) cc_final: 0.7154 (pt0) outliers start: 19 outliers final: 8 residues processed: 221 average time/residue: 1.6693 time to fit residues: 479.7256 Evaluate side-chains 151 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 142 time to evaluate : 2.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 165 HIS Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 197 THR Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 86 GLN 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: 7.9990 chunk 159 optimal weight: 8.9990 chunk 309 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 chunk 188 optimal weight: 10.0000 chunk 230 optimal weight: 10.0000 chunk 358 optimal weight: 4.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 58 HIS K 143 ASN K 226 ASN ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 GLN M 92 HIS M 115 GLN M 195 GLN N 32 ASN O 67 ASN O 86 GLN O 128 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.087 80076 Z= 0.546 Angle : 0.853 22.527 123275 Z= 0.440 Chirality : 0.045 0.312 16134 Planarity : 0.009 0.144 4355 Dihedral : 23.697 175.583 48123 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.09 % Favored : 93.70 % Rotamer: Outliers : 5.52 % Allowed : 18.66 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -2.31 (0.25), residues: 952 helix: -1.39 (0.36), residues: 172 sheet: -1.48 (0.36), residues: 166 loop : -1.64 (0.23), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 78 HIS 0.007 0.002 HIS K 243 PHE 0.012 0.002 PHE N 101 TYR 0.013 0.002 TYR K 83 ARG 0.007 0.001 ARG K 87 *********************** 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 205 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 163 time to evaluate : 2.073 Fit side-chains REVERT: K 5 LYS cc_start: 0.7188 (tttm) cc_final: 0.6712 (tttm) REVERT: L 99 ASN cc_start: 0.6990 (t0) cc_final: 0.6611 (m-40) REVERT: M 108 ILE cc_start: 0.8905 (mt) cc_final: 0.8673 (mt) REVERT: N 88 GLU cc_start: 0.7293 (mp0) cc_final: 0.7091 (mt-10) REVERT: O 1 MET cc_start: 0.6764 (ptm) cc_final: 0.6446 (ptp) outliers start: 42 outliers final: 23 residues processed: 191 average time/residue: 1.5359 time to fit residues: 391.2393 Evaluate side-chains 171 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 148 time to evaluate : 2.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 35 GLU Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 257 THR Chi-restraints excluded: chain K residue 265 LYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 145 ASP Chi-restraints excluded: chain M residue 165 HIS Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain N residue 9 VAL Chi-restraints excluded: chain N residue 110 THR Chi-restraints excluded: chain N residue 178 VAL Chi-restraints excluded: chain N residue 197 THR Chi-restraints excluded: chain N residue 207 VAL Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 131 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 199 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 298 optimal weight: 6.9990 chunk 244 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 359 optimal weight: 0.7980 chunk 388 optimal weight: 1.9990 chunk 320 optimal weight: 0.9990 chunk 356 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 288 optimal weight: 8.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 239 ASN L 54 GLN ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 115 GLN M 195 GLN O 128 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 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 : 0.003 0.031 80076 Z= 0.171 Angle : 0.616 18.722 123275 Z= 0.344 Chirality : 0.031 0.251 16134 Planarity : 0.008 0.127 4355 Dihedral : 23.622 173.131 48118 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.04 % Favored : 94.75 % Rotamer: Outliers : 3.02 % Allowed : 21.02 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -1.47 (0.26), residues: 952 helix: -0.31 (0.37), residues: 168 sheet: -1.17 (0.34), residues: 195 loop : -1.09 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 78 HIS 0.004 0.001 HIS K 200 PHE 0.010 0.001 PHE M 23 TYR 0.013 0.001 TYR K 83 ARG 0.004 0.000 ARG O 13 *********************** 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 187 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 164 time to evaluate : 2.056 Fit side-chains REVERT: K 5 LYS cc_start: 0.7114 (tttm) cc_final: 0.6661 (tttm) REVERT: L 99 ASN cc_start: 0.6839 (t0) cc_final: 0.6535 (m-40) REVERT: M 57 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8463 (tttp) REVERT: M 108 ILE cc_start: 0.8896 (mt) cc_final: 0.8640 (mt) REVERT: N 1 MET cc_start: 0.6870 (ppp) cc_final: 0.6598 (ptm) REVERT: N 88 GLU cc_start: 0.7105 (mp0) cc_final: 0.6888 (mt-10) REVERT: O 1 MET cc_start: 0.6763 (ptm) cc_final: 0.6537 (ptp) outliers start: 23 outliers final: 11 residues processed: 180 average time/residue: 1.4909 time to fit residues: 359.0842 Evaluate side-chains 170 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 158 time to evaluate : 2.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 264 ASP Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 57 LYS Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain M residue 165 HIS Chi-restraints excluded: chain N residue 110 THR Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 106 LYS Chi-restraints excluded: chain O residue 131 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 355 optimal weight: 0.0980 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: 10.0000 chunk 360 optimal weight: 6.9990 chunk 381 optimal weight: 1.9990 chunk 188 optimal weight: 10.0000 chunk 341 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 overall best weight: 5.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 195 GLN N 42 ASN O 128 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 80076 Z= 0.394 Angle : 0.745 19.067 123275 Z= 0.398 Chirality : 0.039 0.293 16134 Planarity : 0.009 0.137 4355 Dihedral : 23.692 175.361 48115 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.20 % Favored : 93.59 % Rotamer: Outliers : 5.26 % Allowed : 19.58 % Favored : 75.16 % 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: -1.37 (0.26), residues: 952 helix: -0.38 (0.37), residues: 178 sheet: -0.82 (0.38), residues: 162 loop : -1.11 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 78 HIS 0.006 0.001 HIS K 200 PHE 0.016 0.002 PHE N 101 TYR 0.010 0.001 TYR O 75 ARG 0.005 0.001 ARG K 214 *********************** 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 192 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 152 time to evaluate : 2.096 Fit side-chains REVERT: K 5 LYS cc_start: 0.7167 (tttm) cc_final: 0.6691 (tttm) REVERT: L 99 ASN cc_start: 0.6944 (t0) cc_final: 0.6709 (m-40) REVERT: M 57 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8539 (tttp) REVERT: M 108 ILE cc_start: 0.8891 (mt) cc_final: 0.8571 (mt) REVERT: M 165 HIS cc_start: 0.7960 (OUTLIER) cc_final: 0.7663 (t-90) REVERT: N 42 ASN cc_start: 0.8254 (t0) cc_final: 0.7961 (t0) REVERT: O 1 MET cc_start: 0.6910 (OUTLIER) cc_final: 0.6616 (ptp) outliers start: 40 outliers final: 20 residues processed: 178 average time/residue: 1.4746 time to fit residues: 357.9766 Evaluate side-chains 177 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 154 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 35 GLU Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 225 MET Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 57 LYS Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 165 HIS Chi-restraints excluded: chain N residue 9 VAL Chi-restraints excluded: chain N residue 110 THR Chi-restraints excluded: chain N residue 178 VAL Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain N residue 207 VAL Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 131 ASN 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: 40.0000 chunk 5 optimal weight: 7.9990 chunk 284 optimal weight: 10.0000 chunk 157 optimal weight: 10.0000 chunk 325 optimal weight: 4.9990 chunk 263 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 194 optimal weight: 7.9990 chunk 342 optimal weight: 7.9990 chunk 96 optimal weight: 7.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 128 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 80076 Z= 0.463 Angle : 0.791 18.759 123275 Z= 0.418 Chirality : 0.043 0.307 16134 Planarity : 0.009 0.138 4355 Dihedral : 23.816 174.535 48115 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.72 % Favored : 93.07 % Rotamer: Outliers : 5.12 % Allowed : 21.94 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -1.40 (0.26), residues: 952 helix: -0.64 (0.36), residues: 183 sheet: -0.73 (0.38), residues: 162 loop : -1.08 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 78 HIS 0.006 0.001 HIS K 200 PHE 0.016 0.002 PHE N 101 TYR 0.011 0.002 TYR K 83 ARG 0.009 0.001 ARG M 117 *********************** 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 190 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 151 time to evaluate : 2.107 Fit side-chains REVERT: K 5 LYS cc_start: 0.7134 (tttm) cc_final: 0.6671 (tttm) REVERT: M 2 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7745 (tp30) REVERT: M 57 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8593 (tttp) REVERT: M 108 ILE cc_start: 0.8889 (mt) cc_final: 0.8530 (mt) REVERT: N 42 ASN cc_start: 0.8386 (t0) cc_final: 0.8107 (t0) REVERT: O 1 MET cc_start: 0.6953 (OUTLIER) cc_final: 0.6675 (ptp) outliers start: 39 outliers final: 23 residues processed: 175 average time/residue: 1.4532 time to fit residues: 344.3366 Evaluate side-chains 176 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 150 time to evaluate : 2.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 194 GLU Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 225 MET Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain M residue 2 GLU Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 57 LYS Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 165 HIS Chi-restraints excluded: chain N residue 9 VAL Chi-restraints excluded: chain N residue 110 THR Chi-restraints excluded: chain N residue 178 VAL Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain N residue 207 VAL Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 131 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 128 optimal weight: 7.9990 chunk 343 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 224 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 382 optimal weight: 7.9990 chunk 317 optimal weight: 1.9990 chunk 176 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 chunk 200 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 128 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 80076 Z= 0.359 Angle : 0.732 18.648 123275 Z= 0.396 Chirality : 0.039 0.296 16134 Planarity : 0.008 0.136 4355 Dihedral : 23.823 174.058 48115 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.35 % Favored : 92.54 % Rotamer: Outliers : 5.91 % Allowed : 22.21 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -1.29 (0.26), residues: 952 helix: -0.44 (0.36), residues: 182 sheet: -0.74 (0.38), residues: 162 loop : -1.01 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 78 HIS 0.007 0.001 HIS K 200 PHE 0.014 0.002 PHE N 101 TYR 0.011 0.001 TYR K 83 ARG 0.004 0.001 ARG M 88 *********************** 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 195 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 150 time to evaluate : 2.100 Fit side-chains REVERT: K 5 LYS cc_start: 0.7137 (tttm) cc_final: 0.6668 (tttm) REVERT: M 2 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7769 (tp30) REVERT: M 57 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8620 (tttp) REVERT: M 108 ILE cc_start: 0.8889 (mt) cc_final: 0.8538 (mt) REVERT: N 42 ASN cc_start: 0.8355 (t0) cc_final: 0.8094 (t0) REVERT: N 86 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6044 (tt0) REVERT: O 1 MET cc_start: 0.6939 (OUTLIER) cc_final: 0.6686 (ptp) outliers start: 45 outliers final: 29 residues processed: 176 average time/residue: 1.4631 time to fit residues: 349.0481 Evaluate side-chains 188 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 155 time to evaluate : 2.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 35 GLU Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 194 GLU Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 225 MET Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain M residue 2 GLU Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 57 LYS Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 165 HIS Chi-restraints excluded: chain N residue 9 VAL Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain N residue 110 THR Chi-restraints excluded: chain N residue 178 VAL Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain N residue 207 VAL Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 131 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 368 optimal weight: 0.6980 chunk 43 optimal weight: 10.0000 chunk 217 optimal weight: 40.0000 chunk 279 optimal weight: 10.0000 chunk 216 optimal weight: 40.0000 chunk 321 optimal weight: 1.9990 chunk 213 optimal weight: 40.0000 chunk 380 optimal weight: 0.9990 chunk 238 optimal weight: 7.9990 chunk 232 optimal weight: 7.9990 chunk 175 optimal weight: 10.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 128 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 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 : 0.005 0.050 80076 Z= 0.323 Angle : 0.714 18.554 123275 Z= 0.387 Chirality : 0.037 0.416 16134 Planarity : 0.008 0.135 4355 Dihedral : 23.821 173.573 48115 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.04 % Favored : 92.86 % Rotamer: Outliers : 5.65 % Allowed : 22.47 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -1.19 (0.26), residues: 952 helix: -0.40 (0.37), residues: 184 sheet: -0.69 (0.38), residues: 162 loop : -0.94 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 78 HIS 0.006 0.001 HIS K 200 PHE 0.011 0.002 PHE N 101 TYR 0.011 0.001 TYR K 83 ARG 0.005 0.001 ARG M 88 *********************** 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 197 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 154 time to evaluate : 2.094 Fit side-chains REVERT: K 5 LYS cc_start: 0.7133 (tttm) cc_final: 0.6660 (tttm) REVERT: M 2 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7771 (tp30) REVERT: M 57 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8616 (tttp) REVERT: M 108 ILE cc_start: 0.8859 (mt) cc_final: 0.8517 (mt) REVERT: N 42 ASN cc_start: 0.8347 (t0) cc_final: 0.8073 (t0) REVERT: N 88 GLU cc_start: 0.7307 (mp0) cc_final: 0.7105 (mt-10) REVERT: O 1 MET cc_start: 0.6918 (OUTLIER) cc_final: 0.6663 (ptp) outliers start: 43 outliers final: 28 residues processed: 179 average time/residue: 1.5318 time to fit residues: 367.4612 Evaluate side-chains 177 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 146 time to evaluate : 2.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 35 GLU Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 194 GLU Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 225 MET Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain M residue 2 GLU Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 57 LYS Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 165 HIS Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 9 VAL Chi-restraints excluded: chain N residue 110 THR Chi-restraints excluded: chain N residue 178 VAL Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain N residue 207 VAL Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 131 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 235 optimal weight: 7.9990 chunk 152 optimal weight: 10.0000 chunk 227 optimal weight: 7.9990 chunk 114 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 242 optimal weight: 7.9990 chunk 259 optimal weight: 7.9990 chunk 188 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 299 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 128 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.076 80076 Z= 0.593 Angle : 0.893 18.514 123275 Z= 0.459 Chirality : 0.048 0.328 16134 Planarity : 0.009 0.146 4355 Dihedral : 23.898 176.042 48115 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.77 % Favored : 92.12 % Rotamer: Outliers : 6.44 % Allowed : 22.21 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -1.47 (0.25), residues: 952 helix: -0.75 (0.35), residues: 184 sheet: -0.65 (0.39), residues: 150 loop : -1.15 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP M 78 HIS 0.006 0.002 HIS K 200 PHE 0.016 0.002 PHE N 101 TYR 0.013 0.002 TYR O 75 ARG 0.006 0.001 ARG K 214 *********************** 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 196 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 147 time to evaluate : 2.166 Fit side-chains REVERT: K 5 LYS cc_start: 0.7216 (tttm) cc_final: 0.6726 (tttm) REVERT: K 23 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7392 (mt-10) REVERT: M 108 ILE cc_start: 0.8876 (mt) cc_final: 0.8543 (mt) REVERT: M 165 HIS cc_start: 0.8273 (OUTLIER) cc_final: 0.7894 (t-90) REVERT: N 42 ASN cc_start: 0.8483 (t0) cc_final: 0.8226 (t0) REVERT: O 1 MET cc_start: 0.6947 (OUTLIER) cc_final: 0.6698 (ptp) outliers start: 49 outliers final: 33 residues processed: 178 average time/residue: 1.3857 time to fit residues: 337.4774 Evaluate side-chains 177 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 141 time to evaluate : 2.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 23 GLU Chi-restraints excluded: chain K residue 35 GLU Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 194 GLU Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 225 MET Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 165 HIS Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 9 VAL Chi-restraints excluded: chain N residue 73 VAL Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain N residue 110 THR Chi-restraints excluded: chain N residue 178 VAL Chi-restraints excluded: chain N residue 197 THR Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain N residue 207 VAL Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 131 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 346 optimal weight: 0.9980 chunk 364 optimal weight: 4.9990 chunk 332 optimal weight: 0.9980 chunk 354 optimal weight: 1.9990 chunk 213 optimal weight: 40.0000 chunk 154 optimal weight: 7.9990 chunk 278 optimal weight: 10.0000 chunk 108 optimal weight: 40.0000 chunk 320 optimal weight: 0.9990 chunk 335 optimal weight: 0.0870 chunk 353 optimal weight: 6.9990 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 134 ASN O 128 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 80076 Z= 0.126 Angle : 0.613 17.635 123275 Z= 0.343 Chirality : 0.030 0.253 16134 Planarity : 0.008 0.122 4355 Dihedral : 23.748 173.846 48115 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.02 % Allowed : 25.23 % Favored : 71.75 % 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: -0.86 (0.26), residues: 952 helix: -0.05 (0.38), residues: 182 sheet: -0.49 (0.39), residues: 163 loop : -0.73 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 60 HIS 0.003 0.001 HIS O 47 PHE 0.011 0.001 PHE M 23 TYR 0.010 0.001 TYR K 83 ARG 0.005 0.000 ARG L 132 *********************** 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 181 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 158 time to evaluate : 2.193 Fit side-chains REVERT: M 165 HIS cc_start: 0.7965 (OUTLIER) cc_final: 0.7614 (t-90) REVERT: N 42 ASN cc_start: 0.8286 (t0) cc_final: 0.8045 (t0) REVERT: O 1 MET cc_start: 0.6889 (ptm) cc_final: 0.6678 (ptp) REVERT: O 101 ILE cc_start: 0.8862 (mm) cc_final: 0.8639 (mp) outliers start: 23 outliers final: 13 residues processed: 169 average time/residue: 1.5289 time to fit residues: 347.3500 Evaluate side-chains 156 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 142 time to evaluate : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 35 GLU Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 194 GLU Chi-restraints excluded: chain K residue 225 MET Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 165 HIS Chi-restraints excluded: chain N residue 9 VAL Chi-restraints excluded: chain N residue 197 THR Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 131 ASN 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: 9.9990 chunk 228 optimal weight: 10.0000 chunk 177 optimal weight: 7.9990 chunk 260 optimal weight: 8.9990 chunk 393 optimal weight: 7.9990 chunk 362 optimal weight: 1.9990 chunk 313 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 242 optimal weight: 10.0000 chunk 192 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 128 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.069 80076 Z= 0.543 Angle : 0.840 17.909 123275 Z= 0.435 Chirality : 0.045 0.316 16134 Planarity : 0.009 0.143 4355 Dihedral : 23.792 176.223 48114 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.46 % Favored : 92.44 % Rotamer: Outliers : 2.23 % Allowed : 27.33 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -1.09 (0.26), residues: 952 helix: -0.29 (0.38), residues: 178 sheet: -0.51 (0.39), residues: 160 loop : -0.91 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 78 HIS 0.006 0.002 HIS K 200 PHE 0.016 0.002 PHE N 101 TYR 0.010 0.002 TYR K 83 ARG 0.005 0.001 ARG K 87 ********************** 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 166 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 149 time to evaluate : 2.124 Fit side-chains REVERT: K 5 LYS cc_start: 0.7165 (tttm) cc_final: 0.6685 (tttm) REVERT: M 165 HIS cc_start: 0.8154 (OUTLIER) cc_final: 0.7755 (t-90) REVERT: N 42 ASN cc_start: 0.8485 (t0) cc_final: 0.8238 (t0) REVERT: O 1 MET cc_start: 0.6944 (ptm) cc_final: 0.6712 (ptp) outliers start: 17 outliers final: 14 residues processed: 157 average time/residue: 1.5057 time to fit residues: 317.6621 Evaluate side-chains 160 residues out of total 761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 145 time to evaluate : 2.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 35 GLU Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 194 GLU Chi-restraints excluded: chain K residue 225 MET Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 165 HIS Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 9 VAL Chi-restraints excluded: chain N residue 197 THR Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 131 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 248 optimal weight: 5.9990 chunk 333 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 288 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 313 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 322 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 128 ASN O 136 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.132526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.105072 restraints weight = 168389.777| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 0.58 r_work: 0.3180 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 80076 Z= 0.277 Angle : 0.672 17.480 123275 Z= 0.369 Chirality : 0.035 0.281 16134 Planarity : 0.008 0.132 4355 Dihedral : 23.767 172.566 48114 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.51 % Favored : 93.38 % Rotamer: Outliers : 2.50 % Allowed : 27.07 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.26), residues: 952 helix: -0.10 (0.38), residues: 178 sheet: -0.63 (0.37), residues: 172 loop : -0.81 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP M 78 HIS 0.005 0.001 HIS L 35 PHE 0.010 0.001 PHE N 101 TYR 0.011 0.001 TYR K 83 ARG 0.005 0.000 ARG M 88 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11298.63 seconds wall clock time: 203 minutes 30.79 seconds (12210.79 seconds total)