Starting phenix.real_space_refine on Sun Feb 18 08:58:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcr_20305/02_2024/6pcr_20305_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcr_20305/02_2024/6pcr_20305.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcr_20305/02_2024/6pcr_20305_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcr_20305/02_2024/6pcr_20305_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcr_20305/02_2024/6pcr_20305_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcr_20305/02_2024/6pcr_20305.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcr_20305/02_2024/6pcr_20305.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcr_20305/02_2024/6pcr_20305_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcr_20305/02_2024/6pcr_20305_neut_updated.pdb" } resolution = 2.5 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= -0.018 sd= 1.061 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Br 1 7.06 5 P 3015 5.49 5 S 22 5.16 5 C 33526 2.51 5 N 13325 2.21 5 O 22277 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K ARG 52": "NH1" <-> "NH2" Residue "K ARG 63": "NH1" <-> "NH2" Residue "K ARG 80": "NH1" <-> "NH2" Residue "K ARG 133": "NH1" <-> "NH2" Residue "K ARG 167": "NH1" <-> "NH2" Residue "K ARG 177": "NH1" <-> "NH2" Residue "K GLU 185": "OE1" <-> "OE2" Residue "K ARG 189": "NH1" <-> "NH2" Residue "K ARG 203": "NH1" <-> "NH2" Residue "K ARG 212": "NH1" <-> "NH2" Residue "K ARG 221": "NH1" <-> "NH2" Residue "K ARG 258": "NH1" <-> "NH2" Residue "K ARG 269": "NH1" <-> "NH2" Residue "K ARG 270": "NH1" <-> "NH2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L GLU 51": "OE1" <-> "OE2" 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 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 127": "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 GLU 74": "OE1" <-> "OE2" Residue "N ARG 77": "NH1" <-> "NH2" Residue "N GLU 81": "OE1" <-> "OE2" Residue "N ARG 83": "NH1" <-> "NH2" Residue "N GLU 168": "OE1" <-> "OE2" Residue "N ARG 169": "NH1" <-> "NH2" Residue "N ARG 184": "NH1" <-> "NH2" Residue "O GLU 9": "OE1" <-> "OE2" Residue "O ARG 13": "NH1" <-> "NH2" Residue "O ARG 37": "NH1" <-> "NH2" Residue "O GLU 43": "OE1" <-> "OE2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "O GLU 102": "OE1" <-> "OE2" Residue "O ARG 120": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 72166 Number of models: 1 Model: "" Number of chains: 8 Chain: "I" Number of atoms: 62206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2897, 62206 Classifications: {'RNA': 2897} Modifications used: {'rna2p': 7, 'rna2p_pur': 280, 'rna2p_pyr': 151, 'rna3p': 14, 'rna3p_pur': 1384, 'rna3p_pyr': 1061} Link IDs: {'rna2p': 438, 'rna3p': 2458} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 13 Chain: "J" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2529 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 48} Link IDs: {'rna2p': 13, 'rna3p': 104} Chain: "K" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2083 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "L" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "M" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "N" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} 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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'O8P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 28.80, per 1000 atoms: 0.40 Number of scatterers: 72166 At special positions: 0 Unit cell: (228.611, 221.984, 190.509, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Br 1 34.99 S 22 16.00 P 3015 15.00 O 22277 8.00 N 13325 7.00 C 33526 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: 34.55 Conformation dependent library (CDL) restraints added in 1.8 seconds 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1712 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 13 sheets defined 18.5% alpha, 14.3% beta 925 base pairs and 1664 stacking pairs defined. Time for finding SS restraints: 40.41 Creating SS restraints... Processing helix chain 'K' and resid 31 through 33 No H-bonds generated for 'chain 'K' and resid 31 through 33' Processing helix chain 'K' and resid 198 through 200 No H-bonds generated for 'chain 'K' and resid 198 through 200' Processing helix chain 'K' and resid 209 through 213 Processing helix chain 'K' and resid 227 through 229 No H-bonds generated for 'chain 'K' and resid 227 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 79 through 81 No H-bonds generated for 'chain 'L' and resid 79 through 81' Processing helix chain 'L' and resid 83 through 85 No H-bonds generated for 'chain 'L' and resid 83 through 85' Processing helix chain 'L' and resid 92 through 97 removed outlier: 3.616A pdb=" N LYS L 96 " --> pdb=" O LEU L 92 " (cutoff:3.500A) removed outlier: 3.755A 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 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: 3.503A pdb=" N ALA M 34 " --> pdb=" O GLN M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 114 removed outlier: 3.518A pdb=" N ARG M 114 " --> pdb=" O SER M 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 140 Processing helix chain 'M' and resid 157 through 160 No H-bonds generated for 'chain 'M' and resid 157 through 160' Processing helix chain 'M' and resid 172 through 174 No H-bonds generated for 'chain 'M' and resid 172 through 174' Processing helix chain 'M' and resid 177 through 182 Processing helix chain 'M' and resid 190 through 200 removed outlier: 3.524A pdb=" N LYS M 194 " --> pdb=" O ALA M 190 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 71 removed outlier: 4.007A pdb=" N ALA N 71 " --> pdb=" O HIS N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 101 Processing helix chain 'N' and resid 121 through 124 No H-bonds generated for 'chain 'N' and resid 121 through 124' Processing helix chain 'O' and resid 25 through 37 removed outlier: 4.494A pdb=" N GLU O 31 " --> pdb=" O ARG O 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 59 through 61 No H-bonds generated for 'chain 'O' and resid 59 through 61' Processing helix chain 'O' and resid 68 through 71 No H-bonds generated for 'chain 'O' and resid 68 through 71' Processing helix chain 'O' and resid 89 through 108 Proline residue: O 97 - end of helix removed outlier: 4.356A pdb=" N VAL O 100 " --> pdb=" O ARG O 96 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ILE O 101 " --> pdb=" O PRO O 97 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET O 108 " --> pdb=" O ALA O 104 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 121 removed outlier: 4.080A pdb=" N ARG O 120 " --> pdb=" O ARG O 116 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS O 121 " --> pdb=" O ALA O 117 " (cutoff:3.500A) Processing helix chain 'O' and resid 133 through 135 No H-bonds generated for 'chain 'O' and resid 133 through 135' Processing sheet with id= A, first strand: chain 'K' and resid 3 through 5 Processing sheet with id= B, first strand: chain 'K' and resid 101 through 105 removed outlier: 3.565A pdb=" N ARG K 80 " --> pdb=" O LEU K 93 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LEU K 95 " --> pdb=" O VAL K 78 " (cutoff:3.500A) removed outlier: 5.632A 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 Processing sheet with id= D, first strand: chain 'K' and resid 181 through 185 removed outlier: 3.517A pdb=" N ALA K 166 " --> pdb=" O THR K 173 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG K 175 " --> pdb=" O ILE K 164 " (cutoff:3.500A) removed outlier: 6.110A 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: 6.587A 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: 6.376A pdb=" N THR L 121 " --> pdb=" O VAL L 90 " (cutoff:3.500A) removed outlier: 6.460A 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: 6.159A pdb=" N VAL M 186 " --> pdb=" O ILE M 119 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N VAL M 121 " --> pdb=" O VAL M 186 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N MET M 188 " --> pdb=" O VAL M 121 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 169 through 172 removed outlier: 4.642A pdb=" N THR N 112 " --> pdb=" O ASP N 200 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ASP N 200 " --> pdb=" O THR N 112 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL N 26 " --> pdb=" O VAL N 9 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N MET N 11 " --> pdb=" O VAL N 24 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL N 24 " --> pdb=" O MET N 11 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ARG N 13 " --> pdb=" O ILE N 22 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE N 22 " --> pdb=" O ARG N 13 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N LYS N 190 " --> pdb=" O VAL N 177 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL N 177 " --> pdb=" O LYS N 190 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 80 through 83 removed outlier: 6.378A pdb=" N THR N 51 " --> pdb=" O VAL N 34 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N VAL N 34 " --> pdb=" O THR N 51 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'N' and resid 115 through 119 removed outlier: 5.997A pdb=" N MET N 165 " --> pdb=" O LYS N 116 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N PHE N 118 " --> pdb=" O GLY N 163 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLY N 163 " --> pdb=" O PHE N 118 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'O' and resid 15 through 19 removed outlier: 6.501A pdb=" N TYR O 53 " --> pdb=" O TYR O 16 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N VAL O 18 " --> pdb=" O TYR O 53 " (cutoff:3.500A) removed outlier: 6.149A 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 76 133 hydrogen bonds defined for protein. 378 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2338 hydrogen bonds 3774 hydrogen bond angles 0 basepair planarities 925 basepair parallelities 1664 stacking parallelities Total time for adding SS restraints: 158.13 Time building geometry restraints manager: 36.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 14778 1.34 - 1.48: 40530 1.48 - 1.62: 24690 1.62 - 1.76: 0 1.76 - 1.90: 43 Bond restraints: 80041 Sorted by residual: bond pdb=" C4 5MU I 747 " pdb=" C5 5MU I 747 " ideal model delta sigma weight residual 1.802 1.409 0.393 2.00e-02 2.50e+03 3.86e+02 bond pdb=" C4 5MU I1939 " pdb=" C5 5MU I1939 " ideal model delta sigma weight residual 1.802 1.410 0.392 2.00e-02 2.50e+03 3.84e+02 bond pdb=" N1 5MU I1939 " pdb=" C6 5MU I1939 " ideal model delta sigma weight residual 1.635 1.364 0.271 2.00e-02 2.50e+03 1.84e+02 bond pdb=" N1 5MU I 747 " pdb=" C6 5MU I 747 " ideal model delta sigma weight residual 1.635 1.366 0.269 2.00e-02 2.50e+03 1.81e+02 bond pdb=" C21 O8P I3001 " pdb=" C22 O8P I3001 " ideal model delta sigma weight residual 1.592 1.350 0.242 2.00e-02 2.50e+03 1.46e+02 ... (remaining 80036 not shown) Histogram of bond angle deviations from ideal: 99.58 - 106.65: 17918 106.65 - 113.71: 48904 113.71 - 120.78: 33264 120.78 - 127.84: 18049 127.84 - 134.91: 5094 Bond angle restraints: 123229 Sorted by residual: angle pdb=" C1' 6MZ I1618 " pdb=" N9 6MZ I1618 " pdb=" C8 6MZ I1618 " ideal model delta sigma weight residual 91.39 126.49 -35.10 3.00e+00 1.11e-01 1.37e+02 angle pdb=" C02 O8P I3001 " pdb=" C21 O8P I3001 " pdb=" C22 O8P I3001 " ideal model delta sigma weight residual 154.27 122.19 32.08 3.00e+00 1.11e-01 1.14e+02 angle pdb=" C04 O8P I3001 " pdb=" C05 O8P I3001 " pdb=" C06 O8P I3001 " ideal model delta sigma weight residual 154.30 124.44 29.86 3.00e+00 1.11e-01 9.91e+01 angle pdb=" C05 O8P I3001 " pdb=" C06 O8P I3001 " pdb=" C07 O8P I3001 " ideal model delta sigma weight residual 154.29 125.64 28.65 3.00e+00 1.11e-01 9.12e+01 angle pdb=" C1' 6MZ I1618 " pdb=" N9 6MZ I1618 " pdb=" C4 6MZ I1618 " ideal model delta sigma weight residual 154.15 126.25 27.90 3.00e+00 1.11e-01 8.65e+01 ... (remaining 123224 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 44089 35.63 - 71.27: 6674 71.27 - 106.90: 797 106.90 - 142.53: 18 142.53 - 178.17: 14 Dihedral angle restraints: 51592 sinusoidal: 48902 harmonic: 2690 Sorted by residual: dihedral pdb=" C4* PSU I1911 " pdb=" C3* PSU I1911 " pdb=" C2* PSU I1911 " pdb=" C1* PSU I1911 " ideal model delta sinusoidal sigma weight residual -35.00 34.76 -69.76 1 8.00e+00 1.56e-02 9.81e+01 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 80.83 66.17 1 8.00e+00 1.56e-02 8.94e+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 50.17 -178.17 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 51589 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 15788 0.057 - 0.115: 319 0.115 - 0.172: 14 0.172 - 0.230: 3 0.230 - 0.287: 4 Chirality restraints: 16128 Sorted by residual: chirality pdb=" CA ASN K 226 " pdb=" N ASN K 226 " pdb=" C ASN K 226 " pdb=" CB ASN K 226 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.06e+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 2.23 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA THR N 151 " pdb=" N THR N 151 " pdb=" C THR N 151 " pdb=" CB THR N 151 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 16125 not shown) Planarity restraints: 4351 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMG I2251 " 0.049 2.00e-02 2.50e+03 6.02e-01 8.14e+03 pdb=" C4' OMG I2251 " 0.449 2.00e-02 2.50e+03 pdb=" O4' OMG I2251 " 0.697 2.00e-02 2.50e+03 pdb=" C3' OMG I2251 " -0.598 2.00e-02 2.50e+03 pdb=" O3' OMG I2251 " -0.613 2.00e-02 2.50e+03 pdb=" C2' OMG I2251 " -0.201 2.00e-02 2.50e+03 pdb=" O2' OMG I2251 " 0.939 2.00e-02 2.50e+03 pdb=" C1' OMG I2251 " 0.210 2.00e-02 2.50e+03 pdb=" N9 OMG I2251 " -0.932 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 1MG I 745 " -0.041 2.00e-02 2.50e+03 5.96e-01 7.98e+03 pdb=" C4' 1MG I 745 " -0.449 2.00e-02 2.50e+03 pdb=" O4' 1MG I 745 " -0.693 2.00e-02 2.50e+03 pdb=" C3' 1MG I 745 " 0.592 2.00e-02 2.50e+03 pdb=" O3' 1MG I 745 " 0.598 2.00e-02 2.50e+03 pdb=" C2' 1MG I 745 " 0.205 2.00e-02 2.50e+03 pdb=" O2' 1MG I 745 " -0.925 2.00e-02 2.50e+03 pdb=" C1' 1MG I 745 " -0.213 2.00e-02 2.50e+03 pdb=" N9 1MG I 745 " 0.926 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I2445 " -0.027 2.00e-02 2.50e+03 5.88e-01 7.78e+03 pdb=" C4' 2MG I2445 " -0.454 2.00e-02 2.50e+03 pdb=" O4' 2MG I2445 " -0.715 2.00e-02 2.50e+03 pdb=" C3' 2MG I2445 " 0.587 2.00e-02 2.50e+03 pdb=" O3' 2MG I2445 " 0.570 2.00e-02 2.50e+03 pdb=" C2' 2MG I2445 " 0.223 2.00e-02 2.50e+03 pdb=" O2' 2MG I2445 " -0.890 2.00e-02 2.50e+03 pdb=" C1' 2MG I2445 " -0.210 2.00e-02 2.50e+03 pdb=" N9 2MG I2445 " 0.916 2.00e-02 2.50e+03 ... (remaining 4348 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 238 2.43 - 3.04: 39396 3.04 - 3.66: 137648 3.66 - 4.28: 217579 4.28 - 4.90: 281170 Nonbonded interactions: 676031 Sorted by model distance: nonbonded pdb=" NH1 ARG K 258 " pdb=" OD1 ASP K 264 " model vdw 1.808 2.520 nonbonded pdb=" O2' A I1508 " pdb=" O4' A I1509 " model vdw 1.940 2.440 nonbonded pdb=" O2' G I1715 " pdb=" O6 G I1743 " model vdw 1.941 2.440 nonbonded pdb=" O2' G I1826 " pdb=" OP2 U I1971 " model vdw 1.955 2.440 nonbonded pdb=" O2* PSU I1911 " pdb=" OP1 A I1912 " model vdw 1.967 3.040 ... (remaining 676026 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 20.120 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: 0.040 Extract box with map and model: 46.650 Check model and map are aligned: 0.830 Set scattering table: 0.520 Process input model: 307.350 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.150 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:11.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 388.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.393 80041 Z= 0.353 Angle : 0.475 35.097 123229 Z= 0.228 Chirality : 0.026 0.287 16128 Planarity : 0.030 0.602 4351 Dihedral : 23.872 178.168 49880 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.22 % Favored : 94.57 % Rotamer: Outliers : 2.36 % Allowed : 11.52 % Favored : 86.13 % 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: -3.36 (0.23), residues: 957 helix: -2.90 (0.28), residues: 157 sheet: -1.72 (0.35), residues: 190 loop : -2.31 (0.22), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 78 HIS 0.003 0.001 HIS K 200 PHE 0.005 0.001 PHE M 85 TYR 0.007 0.001 TYR L 58 ARG 0.002 0.000 ARG O 120 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 216 time to evaluate : 2.314 Fit side-chains revert: symmetry clash REVERT: L 7 SER cc_start: 0.8664 (t) cc_final: 0.8323 (p) REVERT: N 13 ARG cc_start: 0.6316 (ptp-170) cc_final: 0.5892 (ptm160) outliers start: 18 outliers final: 6 residues processed: 229 average time/residue: 1.8067 time to fit residues: 527.3667 Evaluate side-chains 152 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 146 time to evaluate : 2.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 84 THR Chi-restraints excluded: chain N residue 121 THR Chi-restraints excluded: chain O residue 81 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 333 optimal weight: 2.9990 chunk 299 optimal weight: 10.0000 chunk 166 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 201 optimal weight: 6.9990 chunk 159 optimal weight: 6.9990 chunk 309 optimal weight: 8.9990 chunk 119 optimal weight: 6.9990 chunk 188 optimal weight: 10.0000 chunk 230 optimal weight: 10.0000 chunk 358 optimal weight: 0.0000 overall best weight: 4.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 58 HIS K 117 GLN K 200 HIS L 4 ASN M 30 GLN M 94 GLN N 32 ASN N 36 GLN N 164 GLN O 128 ASN O 135 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 80041 Z= 0.440 Angle : 0.735 17.475 123229 Z= 0.393 Chirality : 0.039 0.298 16128 Planarity : 0.009 0.138 4351 Dihedral : 23.759 179.182 48081 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.22 % Favored : 94.67 % Rotamer: Outliers : 4.84 % Allowed : 19.37 % Favored : 75.79 % 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: -1.67 (0.25), residues: 957 helix: -1.05 (0.36), residues: 167 sheet: -0.74 (0.42), residues: 151 loop : -1.25 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP M 78 HIS 0.006 0.001 HIS K 200 PHE 0.009 0.002 PHE M 183 TYR 0.014 0.002 TYR K 103 ARG 0.007 0.001 ARG K 133 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 156 time to evaluate : 2.280 Fit side-chains revert: symmetry clash REVERT: K 82 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7805 (mt-10) REVERT: K 182 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.6860 (ttm-80) REVERT: N 13 ARG cc_start: 0.6934 (OUTLIER) cc_final: 0.5962 (ptm160) REVERT: O 106 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8534 (ttpt) outliers start: 37 outliers final: 20 residues processed: 178 average time/residue: 1.4893 time to fit residues: 356.8759 Evaluate side-chains 172 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 149 time to evaluate : 2.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 121 ASP Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 182 ARG Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 84 THR Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 112 THR Chi-restraints excluded: chain N residue 121 THR Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 150 GLN Chi-restraints excluded: chain N residue 207 VAL Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 106 LYS Chi-restraints excluded: chain O residue 142 ILE 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: 3.9990 chunk 98 optimal weight: 5.9990 chunk 359 optimal weight: 0.9990 chunk 388 optimal weight: 5.9990 chunk 320 optimal weight: 2.9990 chunk 356 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 288 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 163 GLN M 94 GLN O 86 GLN O 128 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 80041 Z= 0.362 Angle : 0.677 17.925 123229 Z= 0.370 Chirality : 0.036 0.280 16128 Planarity : 0.008 0.136 4351 Dihedral : 23.752 178.624 48079 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.54 % Favored : 94.36 % Rotamer: Outliers : 5.10 % Allowed : 20.81 % Favored : 74.08 % 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: -1.11 (0.26), residues: 957 helix: -0.53 (0.38), residues: 174 sheet: -0.09 (0.46), residues: 133 loop : -0.95 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 78 HIS 0.005 0.001 HIS K 200 PHE 0.008 0.001 PHE M 183 TYR 0.015 0.001 TYR K 103 ARG 0.008 0.001 ARG O 99 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 152 time to evaluate : 2.240 Fit side-chains REVERT: K 82 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7815 (mt-10) REVERT: K 182 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.6704 (ttm-80) REVERT: L 7 SER cc_start: 0.9010 (t) cc_final: 0.8751 (p) REVERT: N 13 ARG cc_start: 0.7114 (OUTLIER) cc_final: 0.5990 (ptm160) REVERT: N 128 ARG cc_start: 0.8291 (mtp180) cc_final: 0.7604 (mtp180) REVERT: O 128 ASN cc_start: 0.8765 (OUTLIER) cc_final: 0.8434 (t0) outliers start: 39 outliers final: 20 residues processed: 171 average time/residue: 1.6617 time to fit residues: 373.9033 Evaluate side-chains 170 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 147 time to evaluate : 2.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 163 GLN Chi-restraints excluded: chain K residue 182 ARG Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 112 THR Chi-restraints excluded: chain N residue 121 THR Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 150 GLN 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 128 ASN Chi-restraints excluded: chain O residue 142 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 355 optimal weight: 2.9990 chunk 270 optimal weight: 6.9990 chunk 186 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 171 optimal weight: 10.0000 chunk 241 optimal weight: 6.9990 chunk 360 optimal weight: 7.9990 chunk 381 optimal weight: 0.6980 chunk 188 optimal weight: 10.0000 chunk 341 optimal weight: 0.8980 chunk 102 optimal weight: 7.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 94 GLN M 136 GLN M 165 HIS N 58 ASN O 86 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 80041 Z= 0.353 Angle : 0.676 17.911 123229 Z= 0.370 Chirality : 0.036 0.280 16128 Planarity : 0.008 0.137 4351 Dihedral : 23.781 178.512 48078 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.43 % Favored : 94.46 % Rotamer: Outliers : 4.45 % Allowed : 22.91 % Favored : 72.64 % 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: -0.88 (0.26), residues: 957 helix: -0.17 (0.39), residues: 177 sheet: -0.08 (0.45), residues: 142 loop : -0.83 (0.24), residues: 638 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 0.009 0.001 PHE M 183 TYR 0.016 0.002 TYR K 103 ARG 0.010 0.001 ARG K 175 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 145 time to evaluate : 2.326 Fit side-chains revert: symmetry clash REVERT: K 182 ARG cc_start: 0.9173 (OUTLIER) cc_final: 0.6729 (ttm-80) REVERT: L 7 SER cc_start: 0.8977 (t) cc_final: 0.8706 (p) REVERT: M 1 MET cc_start: 0.8148 (tpp) cc_final: 0.7271 (ttp) REVERT: N 13 ARG cc_start: 0.7103 (OUTLIER) cc_final: 0.5973 (ptm160) outliers start: 34 outliers final: 22 residues processed: 164 average time/residue: 1.6203 time to fit residues: 352.8901 Evaluate side-chains 166 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 142 time to evaluate : 2.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 182 ARG Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain K residue 194 GLU Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 84 THR Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 112 THR Chi-restraints excluded: chain N residue 121 THR Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 150 GLN Chi-restraints excluded: chain N residue 207 VAL Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 93 ILE Chi-restraints excluded: chain O residue 142 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 317 optimal weight: 5.9990 chunk 216 optimal weight: 40.0000 chunk 5 optimal weight: 5.9990 chunk 284 optimal weight: 6.9990 chunk 157 optimal weight: 10.0000 chunk 325 optimal weight: 2.9990 chunk 263 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 194 optimal weight: 6.9990 chunk 342 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 94 GLN N 58 ASN O 128 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 80041 Z= 0.426 Angle : 0.725 18.416 123229 Z= 0.391 Chirality : 0.039 0.298 16128 Planarity : 0.009 0.136 4351 Dihedral : 23.880 177.581 48078 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.17 % Favored : 93.73 % Rotamer: Outliers : 5.10 % Allowed : 22.64 % Favored : 72.25 % 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: -0.76 (0.26), residues: 957 helix: -0.21 (0.39), residues: 174 sheet: 0.05 (0.44), residues: 141 loop : -0.71 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 78 HIS 0.006 0.001 HIS K 200 PHE 0.010 0.002 PHE L 64 TYR 0.017 0.002 TYR K 103 ARG 0.011 0.001 ARG K 175 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 148 time to evaluate : 2.268 Fit side-chains revert: symmetry clash REVERT: K 82 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7887 (mt-10) REVERT: K 182 ARG cc_start: 0.9193 (OUTLIER) cc_final: 0.6883 (ttm-80) REVERT: L 7 SER cc_start: 0.8977 (t) cc_final: 0.8705 (p) REVERT: N 13 ARG cc_start: 0.7115 (OUTLIER) cc_final: 0.6003 (ptm160) REVERT: O 128 ASN cc_start: 0.8780 (OUTLIER) cc_final: 0.8480 (t0) outliers start: 39 outliers final: 22 residues processed: 170 average time/residue: 1.6886 time to fit residues: 376.1290 Evaluate side-chains 168 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 143 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 182 ARG Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain K residue 194 GLU Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 84 THR Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 112 THR Chi-restraints excluded: chain N residue 121 THR Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 150 GLN Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 207 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 93 ILE Chi-restraints excluded: chain O residue 128 ASN Chi-restraints excluded: chain O residue 142 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 128 optimal weight: 5.9990 chunk 343 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 224 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 382 optimal weight: 5.9990 chunk 317 optimal weight: 0.9980 chunk 176 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 126 optimal weight: 5.9990 chunk 200 optimal weight: 3.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 94 GLN N 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 80041 Z= 0.343 Angle : 0.685 18.268 123229 Z= 0.375 Chirality : 0.037 0.281 16128 Planarity : 0.008 0.137 4351 Dihedral : 23.877 178.230 48078 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.75 % Favored : 94.15 % Rotamer: Outliers : 4.71 % Allowed : 24.21 % Favored : 71.07 % 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: -0.69 (0.26), residues: 957 helix: -0.20 (0.39), residues: 177 sheet: 0.15 (0.44), residues: 140 loop : -0.66 (0.24), residues: 640 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 0.009 0.001 PHE M 183 TYR 0.018 0.002 TYR K 103 ARG 0.010 0.001 ARG K 175 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 144 time to evaluate : 2.478 Fit side-chains REVERT: K 82 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7813 (mt-10) REVERT: K 182 ARG cc_start: 0.9177 (OUTLIER) cc_final: 0.6853 (ttm-80) REVERT: L 7 SER cc_start: 0.8972 (t) cc_final: 0.8691 (p) REVERT: N 13 ARG cc_start: 0.7085 (OUTLIER) cc_final: 0.6011 (ptm160) outliers start: 36 outliers final: 23 residues processed: 165 average time/residue: 1.7051 time to fit residues: 366.2241 Evaluate side-chains 165 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 140 time to evaluate : 2.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 182 ARG Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain K residue 194 GLU Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 84 THR Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 112 THR Chi-restraints excluded: chain N residue 121 THR Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 131 ASP Chi-restraints excluded: chain N residue 150 GLN Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 207 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 93 ILE Chi-restraints excluded: chain O residue 142 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 368 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 217 optimal weight: 40.0000 chunk 279 optimal weight: 10.0000 chunk 216 optimal weight: 30.0000 chunk 321 optimal weight: 1.9990 chunk 213 optimal weight: 40.0000 chunk 380 optimal weight: 0.0970 chunk 238 optimal weight: 6.9990 chunk 232 optimal weight: 6.9990 chunk 175 optimal weight: 6.9990 overall best weight: 4.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 94 GLN M 136 GLN N 58 ASN O 58 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 80041 Z= 0.430 Angle : 0.717 18.358 123229 Z= 0.388 Chirality : 0.039 0.299 16128 Planarity : 0.009 0.141 4351 Dihedral : 23.894 177.878 48078 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.17 % Favored : 93.73 % Rotamer: Outliers : 4.45 % Allowed : 24.74 % Favored : 70.81 % 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: -0.68 (0.26), residues: 957 helix: -0.16 (0.39), residues: 175 sheet: -0.18 (0.42), residues: 153 loop : -0.58 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 78 HIS 0.007 0.001 HIS K 200 PHE 0.009 0.001 PHE L 64 TYR 0.020 0.002 TYR K 103 ARG 0.009 0.001 ARG K 175 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 141 time to evaluate : 2.379 Fit side-chains REVERT: K 82 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7883 (mt-10) REVERT: K 182 ARG cc_start: 0.9204 (OUTLIER) cc_final: 0.6968 (ttm-80) REVERT: L 7 SER cc_start: 0.8970 (t) cc_final: 0.8681 (p) REVERT: N 13 ARG cc_start: 0.7133 (OUTLIER) cc_final: 0.6021 (ptm160) REVERT: N 165 MET cc_start: 0.9013 (ttt) cc_final: 0.8752 (ttt) REVERT: O 128 ASN cc_start: 0.8811 (t160) cc_final: 0.8601 (t0) outliers start: 34 outliers final: 24 residues processed: 162 average time/residue: 1.6792 time to fit residues: 357.4095 Evaluate side-chains 165 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 139 time to evaluate : 2.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 163 GLN Chi-restraints excluded: chain K residue 182 ARG Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain K residue 194 GLU Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 84 THR Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 112 THR Chi-restraints excluded: chain N residue 121 THR Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 131 ASP Chi-restraints excluded: chain N residue 150 GLN Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 207 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 93 ILE Chi-restraints excluded: chain O residue 142 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 235 optimal weight: 5.9990 chunk 152 optimal weight: 10.0000 chunk 227 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 242 optimal weight: 5.9990 chunk 259 optimal weight: 5.9990 chunk 188 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 299 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 94 GLN N 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.093 80041 Z= 0.532 Angle : 0.776 18.883 123229 Z= 0.413 Chirality : 0.044 0.323 16128 Planarity : 0.009 0.143 4351 Dihedral : 23.968 178.357 48078 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.06 % Favored : 93.83 % Rotamer: Outliers : 4.45 % Allowed : 24.48 % Favored : 71.07 % 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: -0.70 (0.26), residues: 957 helix: -0.23 (0.39), residues: 174 sheet: 0.06 (0.44), residues: 141 loop : -0.64 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M 78 HIS 0.007 0.001 HIS K 200 PHE 0.011 0.002 PHE L 64 TYR 0.021 0.002 TYR K 103 ARG 0.012 0.001 ARG O 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 141 time to evaluate : 2.656 Fit side-chains revert: symmetry clash REVERT: K 82 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7954 (mt-10) REVERT: K 181 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.8097 (mmt) REVERT: K 182 ARG cc_start: 0.9203 (OUTLIER) cc_final: 0.7014 (ttm-80) REVERT: L 7 SER cc_start: 0.8972 (t) cc_final: 0.8690 (p) REVERT: M 16 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7405 (mm-30) REVERT: N 13 ARG cc_start: 0.7140 (OUTLIER) cc_final: 0.6016 (ptm160) REVERT: O 128 ASN cc_start: 0.8959 (t160) cc_final: 0.8740 (t0) outliers start: 34 outliers final: 22 residues processed: 160 average time/residue: 1.7341 time to fit residues: 360.9512 Evaluate side-chains 164 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 138 time to evaluate : 2.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 181 MET Chi-restraints excluded: chain K residue 182 ARG Chi-restraints excluded: chain K residue 194 GLU Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 16 GLU Chi-restraints excluded: chain M residue 84 THR Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 112 THR Chi-restraints excluded: chain N residue 121 THR Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 150 GLN Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 207 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 93 ILE Chi-restraints excluded: chain O residue 142 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 346 optimal weight: 0.7980 chunk 364 optimal weight: 2.9990 chunk 332 optimal weight: 0.9990 chunk 354 optimal weight: 0.9990 chunk 213 optimal weight: 40.0000 chunk 154 optimal weight: 6.9990 chunk 278 optimal weight: 10.0000 chunk 108 optimal weight: 30.0000 chunk 320 optimal weight: 0.9990 chunk 335 optimal weight: 0.9990 chunk 353 optimal weight: 6.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 94 GLN M 136 GLN N 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 80041 Z= 0.123 Angle : 0.603 17.345 123229 Z= 0.339 Chirality : 0.029 0.240 16128 Planarity : 0.008 0.123 4351 Dihedral : 23.904 178.261 48078 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.83 % Allowed : 27.09 % Favored : 71.07 % 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: -0.34 (0.27), residues: 957 helix: 0.34 (0.41), residues: 167 sheet: 0.06 (0.42), residues: 150 loop : -0.42 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 78 HIS 0.006 0.001 HIS K 200 PHE 0.007 0.001 PHE O 4 TYR 0.011 0.001 TYR M 101 ARG 0.014 0.001 ARG O 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 156 time to evaluate : 2.263 Fit side-chains revert: symmetry clash REVERT: L 7 SER cc_start: 0.8933 (t) cc_final: 0.8731 (p) REVERT: N 13 ARG cc_start: 0.7002 (ptp-170) cc_final: 0.5923 (ptm160) REVERT: O 81 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8155 (mp) REVERT: O 128 ASN cc_start: 0.8900 (t160) cc_final: 0.8672 (t0) outliers start: 14 outliers final: 7 residues processed: 164 average time/residue: 1.6433 time to fit residues: 355.2308 Evaluate side-chains 154 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 146 time to evaluate : 2.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 121 THR Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 142 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 232 optimal weight: 7.9990 chunk 375 optimal weight: 7.9990 chunk 228 optimal weight: 8.9990 chunk 177 optimal weight: 6.9990 chunk 260 optimal weight: 6.9990 chunk 393 optimal weight: 0.0870 chunk 362 optimal weight: 3.9990 chunk 313 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 242 optimal weight: 7.9990 chunk 192 optimal weight: 8.9990 overall best weight: 4.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 94 GLN N 58 ASN N 150 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 80041 Z= 0.444 Angle : 0.716 17.956 123229 Z= 0.385 Chirality : 0.039 0.299 16128 Planarity : 0.009 0.141 4351 Dihedral : 23.867 177.830 48078 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 1.83 % Allowed : 26.83 % Favored : 71.34 % 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: -0.48 (0.27), residues: 957 helix: 0.03 (0.39), residues: 174 sheet: -0.16 (0.42), residues: 152 loop : -0.41 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 78 HIS 0.006 0.001 HIS K 200 PHE 0.009 0.002 PHE L 64 TYR 0.010 0.002 TYR O 75 ARG 0.011 0.001 ARG K 175 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 142 time to evaluate : 2.362 Fit side-chains revert: symmetry clash REVERT: K 182 ARG cc_start: 0.9187 (OUTLIER) cc_final: 0.6687 (ttm-80) REVERT: L 7 SER cc_start: 0.8967 (t) cc_final: 0.8731 (p) REVERT: N 13 ARG cc_start: 0.7120 (ptp-170) cc_final: 0.5971 (ptm160) REVERT: O 128 ASN cc_start: 0.8929 (t160) cc_final: 0.8673 (t0) outliers start: 14 outliers final: 9 residues processed: 150 average time/residue: 1.6954 time to fit residues: 332.3103 Evaluate side-chains 149 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 139 time to evaluate : 2.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 163 GLN Chi-restraints excluded: chain K residue 182 ARG Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain N residue 121 THR Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain O residue 2 LYS Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 142 ILE 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: 0.0670 chunk 95 optimal weight: 5.9990 chunk 288 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 313 optimal weight: 0.9980 chunk 131 optimal weight: 5.9990 chunk 322 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 overall best weight: 2.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 136 GLN N 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.114010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.084518 restraints weight = 119782.380| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 0.47 r_work: 0.2954 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 80041 Z= 0.225 Angle : 0.653 18.018 123229 Z= 0.360 Chirality : 0.032 0.255 16128 Planarity : 0.008 0.135 4351 Dihedral : 23.939 178.185 48078 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 1.31 % Allowed : 27.49 % Favored : 71.20 % 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: -0.45 (0.27), residues: 957 helix: 0.09 (0.39), residues: 174 sheet: -0.20 (0.42), residues: 152 loop : -0.39 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 78 HIS 0.006 0.001 HIS K 200 PHE 0.009 0.001 PHE M 183 TYR 0.011 0.001 TYR K 103 ARG 0.014 0.001 ARG O 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11580.04 seconds wall clock time: 208 minutes 9.57 seconds (12489.57 seconds total)