Starting phenix.real_space_refine on Sun Feb 18 08:34:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcs_20306/02_2024/6pcs_20306_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcs_20306/02_2024/6pcs_20306.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcs_20306/02_2024/6pcs_20306_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/6pcs_20306/02_2024/6pcs_20306_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcs_20306/02_2024/6pcs_20306_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcs_20306/02_2024/6pcs_20306.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcs_20306/02_2024/6pcs_20306.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcs_20306/02_2024/6pcs_20306_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcs_20306/02_2024/6pcs_20306_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= -0.010 sd= 1.420 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3015 5.49 5 S 22 5.16 5 C 33528 2.51 5 N 13324 2.21 5 O 22277 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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 ARG 167": "NH1" <-> "NH2" Residue "K ARG 177": "NH1" <-> "NH2" Residue "K ASP 187": "OD1" <-> "OD2" 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 PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 258": "NH1" <-> "NH2" Residue "K ASP 264": "OD1" <-> "OD2" Residue "K ARG 269": "NH1" <-> "NH2" Residue "K ARG 270": "NH1" <-> "NH2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L GLU 51": "OE1" <-> "OE2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L GLU 115": "OE1" <-> "OE2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M ASP 7": "OD1" <-> "OD2" 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 GLU 17": "OE1" <-> "OE2" Residue "N ARG 33": "NH1" <-> "NH2" Residue "N ARG 59": "NH1" <-> "NH2" Residue "N ARG 77": "NH1" <-> "NH2" Residue "N GLU 81": "OE1" <-> "OE2" Residue "N ARG 83": "NH1" <-> "NH2" Residue "N GLU 86": "OE1" <-> "OE2" Residue "N 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: 72169 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: 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: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'O8S': 1} Classifications: {'undetermined': 1} Time building chain proxies: 27.27, per 1000 atoms: 0.38 Number of scatterers: 72169 At special positions: 0 Unit cell: (227.783, 221.984, 189.681, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 22 16.00 P 3015 15.00 F 3 9.00 O 22277 8.00 N 13324 7.00 C 33528 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: 31.92 Conformation dependent library (CDL) restraints added in 1.5 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: 23 helices and 12 sheets defined 17.9% alpha, 13.1% beta 889 base pairs and 1655 stacking pairs defined. Time for finding SS restraints: 37.42 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 'L' and resid 57 through 60 No H-bonds generated for 'chain 'L' and resid 57 through 60' Processing helix chain 'L' and resid 79 through 85 removed outlier: 4.447A pdb=" N ALA L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 95 No H-bonds generated for 'chain 'L' and resid 92 through 95' Processing helix chain 'L' and resid 129 through 137 Processing helix chain 'M' and resid 16 through 19 No H-bonds generated for 'chain 'M' and resid 16 through 19' Processing helix chain 'M' and resid 25 through 39 removed outlier: 3.563A pdb=" N ALA M 39 " --> pdb=" O TYR M 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 114 Processing helix chain 'M' and resid 131 through 140 Processing helix chain 'M' and resid 155 through 160 removed outlier: 3.879A pdb=" N LEU M 159 " --> pdb=" O GLU M 155 " (cutoff:3.500A) Processing helix chain 'M' and resid 177 through 182 Processing helix chain 'M' and resid 190 through 200 removed outlier: 3.574A pdb=" N LYS M 194 " --> pdb=" O ALA M 190 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN M 195 " --> pdb=" O ASP M 191 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 71 removed outlier: 3.847A 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: 4.430A pdb=" N GLU O 31 " --> pdb=" O ARG O 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 59 through 61 No H-bonds generated for 'chain 'O' and resid 59 through 61' Processing helix chain 'O' and resid 66 through 71 removed outlier: 4.384A pdb=" N ARG O 69 " --> pdb=" O GLY O 66 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP O 71 " --> pdb=" O LYS O 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 107 Proline residue: O 97 - end of helix removed outlier: 4.514A pdb=" N VAL O 100 " --> pdb=" O ARG O 96 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE O 101 " --> pdb=" O PRO O 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 115 through 121 removed outlier: 4.258A pdb=" N ARG O 120 " --> pdb=" O ARG O 116 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS O 121 " --> pdb=" O ALA O 117 " (cutoff:3.500A) Processing helix chain 'O' and resid 133 through 135 No H-bonds generated for 'chain 'O' and resid 133 through 135' Processing sheet with id= A, first strand: chain 'K' and resid 3 through 5 Processing sheet with id= B, first strand: chain 'K' and resid 34 through 36 Processing sheet with id= C, first strand: chain 'K' and resid 101 through 105 removed outlier: 3.653A pdb=" N ARG K 80 " --> pdb=" O LEU K 93 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU K 95 " --> pdb=" O VAL K 78 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N VAL K 78 " --> pdb=" O LEU K 95 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'K' and resid 129 through 131 removed outlier: 3.602A pdb=" N LEU K 130 " --> pdb=" O ALA K 190 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'K' and resid 181 through 185 removed outlier: 3.902A pdb=" N ALA K 166 " --> pdb=" O THR K 173 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ARG K 175 " --> pdb=" O ILE K 164 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE K 164 " --> pdb=" O ARG K 175 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'L' and resid 89 through 91 removed outlier: 6.497A pdb=" N THR L 121 " --> pdb=" O VAL L 90 " (cutoff:3.500A) removed outlier: 6.712A 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: 6.320A pdb=" N VAL M 186 " --> pdb=" O ILE M 119 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL M 121 " --> pdb=" O VAL M 186 " (cutoff:3.500A) removed outlier: 6.557A 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: 3.528A pdb=" N LYS N 204 " --> pdb=" O ASP N 108 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N THR N 112 " --> pdb=" O ASP N 200 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ASP N 200 " --> pdb=" O THR N 112 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL N 26 " --> pdb=" O VAL N 9 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N MET N 11 " --> pdb=" O VAL N 24 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL N 24 " --> pdb=" O MET N 11 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ARG N 13 " --> pdb=" O ILE N 22 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE N 22 " --> pdb=" O ARG N 13 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL N 189 " --> pdb=" O THR N 25 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 80 through 83 removed outlier: 6.457A pdb=" N THR N 51 " --> pdb=" O VAL N 34 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N VAL N 34 " --> pdb=" O THR N 51 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'O' and resid 15 through 19 removed outlier: 6.460A pdb=" N TYR O 53 " --> pdb=" O TYR O 16 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL O 18 " --> pdb=" O TYR O 53 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE O 55 " --> pdb=" O VAL O 18 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'O' and resid 73 through 76 removed outlier: 3.637A pdb=" N ALA O 87 " --> pdb=" O TYR O 74 " (cutoff:3.500A) 129 hydrogen bonds defined for protein. 360 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2203 hydrogen bonds 3594 hydrogen bond angles 0 basepair planarities 889 basepair parallelities 1655 stacking parallelities Total time for adding SS restraints: 134.10 Time building geometry restraints manager: 34.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7200 1.33 - 1.45: 38321 1.45 - 1.57: 28434 1.57 - 1.69: 6047 1.69 - 1.81: 42 Bond restraints: 80044 Sorted by residual: bond pdb=" C4 5MU I 747 " pdb=" C5 5MU I 747 " ideal model delta sigma weight residual 1.802 1.411 0.391 2.00e-02 2.50e+03 3.82e+02 bond pdb=" C4 5MU I1939 " pdb=" C5 5MU I1939 " ideal model delta sigma weight residual 1.802 1.411 0.391 2.00e-02 2.50e+03 3.82e+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 1.83e+02 bond pdb=" N1 5MU I 747 " pdb=" C6 5MU I 747 " ideal model delta sigma weight residual 1.635 1.368 0.267 2.00e-02 2.50e+03 1.79e+02 bond pdb=" C5 5MU I1939 " pdb=" C6 5MU I1939 " ideal model delta sigma weight residual 1.155 1.347 -0.192 2.00e-02 2.50e+03 9.26e+01 ... (remaining 80039 not shown) Histogram of bond angle deviations from ideal: 99.69 - 106.72: 17915 106.72 - 113.74: 49220 113.74 - 120.77: 32870 120.77 - 127.80: 18143 127.80 - 134.82: 5087 Bond angle restraints: 123235 Sorted by residual: angle pdb=" C1' 6MZ I1618 " pdb=" N9 6MZ I1618 " pdb=" C8 6MZ I1618 " ideal model delta sigma weight residual 91.39 126.15 -34.76 3.00e+00 1.11e-01 1.34e+02 angle pdb=" C1' 6MZ I1618 " pdb=" N9 6MZ I1618 " pdb=" C4 6MZ I1618 " ideal model delta sigma weight residual 154.15 126.58 27.57 3.00e+00 1.11e-01 8.45e+01 angle pdb=" C1' 1MG I 745 " pdb=" N9 1MG I 745 " pdb=" C8 1MG I 745 " ideal model delta sigma weight residual 100.16 126.34 -26.18 3.00e+00 1.11e-01 7.62e+01 angle pdb=" C1' 1MG I 745 " pdb=" N9 1MG I 745 " pdb=" C4 1MG I 745 " ideal model delta sigma weight residual 146.15 126.15 20.00 3.00e+00 1.11e-01 4.44e+01 angle pdb=" N GLN N 150 " pdb=" CA GLN N 150 " pdb=" C GLN N 150 " ideal model delta sigma weight residual 111.71 119.16 -7.45 1.15e+00 7.56e-01 4.19e+01 ... (remaining 123230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 44161 35.80 - 71.60: 6629 71.60 - 107.40: 789 107.40 - 143.20: 5 143.20 - 179.00: 7 Dihedral angle restraints: 51591 sinusoidal: 48901 harmonic: 2690 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 49.98 -177.98 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 42.59 -170.59 1 1.70e+01 3.46e-03 6.60e+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 88.58 111.42 1 1.50e+01 4.44e-03 5.82e+01 ... (remaining 51588 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 15855 0.055 - 0.111: 256 0.111 - 0.166: 19 0.166 - 0.222: 2 0.222 - 0.277: 1 Chirality restraints: 16133 Sorted by residual: chirality pdb=" CA GLN N 150 " pdb=" N GLN N 150 " pdb=" C GLN N 150 " pdb=" CB GLN N 150 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.92e+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 2.31 0.20 2.00e-01 2.50e+01 9.92e-01 chirality pdb=" CA VAL M 83 " pdb=" N VAL M 83 " pdb=" C VAL M 83 " pdb=" CB VAL M 83 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.87e-01 ... (remaining 16130 not shown) Planarity restraints: 4351 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 1MG I 745 " -0.045 2.00e-02 2.50e+03 6.05e-01 8.24e+03 pdb=" C4' 1MG I 745 " -0.455 2.00e-02 2.50e+03 pdb=" O4' 1MG I 745 " -0.718 2.00e-02 2.50e+03 pdb=" C3' 1MG I 745 " 0.593 2.00e-02 2.50e+03 pdb=" O3' 1MG I 745 " 0.609 2.00e-02 2.50e+03 pdb=" C2' 1MG I 745 " 0.204 2.00e-02 2.50e+03 pdb=" O2' 1MG I 745 " -0.930 2.00e-02 2.50e+03 pdb=" C1' 1MG I 745 " -0.205 2.00e-02 2.50e+03 pdb=" N9 1MG I 745 " 0.948 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I2445 " -0.031 2.00e-02 2.50e+03 5.97e-01 8.02e+03 pdb=" C4' 2MG I2445 " -0.457 2.00e-02 2.50e+03 pdb=" O4' 2MG I2445 " -0.738 2.00e-02 2.50e+03 pdb=" C3' 2MG I2445 " 0.588 2.00e-02 2.50e+03 pdb=" O3' 2MG I2445 " 0.582 2.00e-02 2.50e+03 pdb=" C2' 2MG I2445 " 0.222 2.00e-02 2.50e+03 pdb=" O2' 2MG I2445 " -0.898 2.00e-02 2.50e+03 pdb=" C1' 2MG I2445 " -0.203 2.00e-02 2.50e+03 pdb=" N9 2MG I2445 " 0.933 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG I2251 " 0.047 2.00e-02 2.50e+03 5.94e-01 7.95e+03 pdb=" C4' OMG I2251 " 0.444 2.00e-02 2.50e+03 pdb=" O4' OMG I2251 " 0.672 2.00e-02 2.50e+03 pdb=" C3' OMG I2251 " -0.598 2.00e-02 2.50e+03 pdb=" O3' OMG I2251 " -0.608 2.00e-02 2.50e+03 pdb=" C2' OMG I2251 " -0.199 2.00e-02 2.50e+03 pdb=" O2' OMG I2251 " 0.938 2.00e-02 2.50e+03 pdb=" C1' OMG I2251 " 0.217 2.00e-02 2.50e+03 pdb=" N9 OMG I2251 " -0.913 2.00e-02 2.50e+03 ... (remaining 4348 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.31: 126 2.31 - 2.96: 28597 2.96 - 3.60: 121426 3.60 - 4.25: 227066 4.25 - 4.90: 294050 Nonbonded interactions: 671265 Sorted by model distance: nonbonded pdb=" N3 G I2032 " pdb=" NE2 GLN N 150 " model vdw 1.658 2.600 nonbonded pdb=" O2' A I1084 " pdb=" O2' U I1105 " model vdw 1.911 2.440 nonbonded pdb=" C4 G I2032 " pdb=" NE2 GLN N 150 " model vdw 1.930 3.340 nonbonded pdb=" O2' G I1715 " pdb=" O6 G I1743 " model vdw 1.989 2.440 nonbonded pdb=" O2' G I1826 " pdb=" OP2 U I1971 " model vdw 2.009 2.440 ... (remaining 671260 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: 10.410 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: 0.060 Extract box with map and model: 45.060 Check model and map are aligned: 0.980 Set scattering table: 0.610 Process input model: 270.690 Find NCS groups from input model: 0.910 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:10.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 339.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.391 80044 Z= 0.318 Angle : 0.401 34.759 123235 Z= 0.202 Chirality : 0.024 0.277 16133 Planarity : 0.031 0.605 4351 Dihedral : 23.650 179.000 49879 Min Nonbonded Distance : 1.658 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.75 % Favored : 94.15 % Rotamer: Outliers : 1.31 % Allowed : 13.87 % Favored : 84.82 % 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: -3.87 (0.23), residues: 957 helix: -3.40 (0.28), residues: 161 sheet: -2.58 (0.33), residues: 172 loop : -2.44 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 78 HIS 0.003 0.001 HIS K 230 PHE 0.005 0.001 PHE N 156 TYR 0.006 0.001 TYR L 58 ARG 0.002 0.000 ARG M 79 *********************** 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 239 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 229 time to evaluate : 2.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 255 LYS cc_start: 0.8492 (tttm) cc_final: 0.8263 (ttmm) REVERT: L 4 ASN cc_start: 0.8828 (p0) cc_final: 0.8505 (p0) REVERT: L 91 ASP cc_start: 0.8322 (t0) cc_final: 0.8091 (t0) REVERT: L 117 THR cc_start: 0.8263 (p) cc_final: 0.7971 (t) REVERT: M 155 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6676 (tt0) REVERT: N 108 ASP cc_start: 0.7619 (m-30) cc_final: 0.7224 (p0) REVERT: N 150 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7906 (tt0) REVERT: O 58 ASN cc_start: 0.8403 (m-40) cc_final: 0.8167 (m-40) outliers start: 10 outliers final: 1 residues processed: 237 average time/residue: 1.8312 time to fit residues: 554.3442 Evaluate side-chains 147 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 144 time to evaluate : 2.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain M residue 155 GLU Chi-restraints excluded: chain N residue 150 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 333 optimal weight: 0.4980 chunk 299 optimal weight: 10.0000 chunk 166 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 201 optimal weight: 8.9990 chunk 159 optimal weight: 10.0000 chunk 309 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 188 optimal weight: 10.0000 chunk 230 optimal weight: 10.0000 chunk 358 optimal weight: 2.9990 overall best weight: 6.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 58 HIS K 134 ASN ** K 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 GLN N 49 GLN N 58 ASN ** N 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 86 GLN O 135 GLN O 138 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 80044 Z= 0.448 Angle : 0.787 17.827 123235 Z= 0.413 Chirality : 0.040 0.318 16133 Planarity : 0.009 0.147 4351 Dihedral : 23.629 175.940 48080 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.17 % Favored : 93.63 % Rotamer: Outliers : 5.76 % Allowed : 21.99 % 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: -2.65 (0.25), residues: 957 helix: -2.03 (0.33), residues: 176 sheet: -1.59 (0.35), residues: 196 loop : -1.76 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP M 78 HIS 0.008 0.002 HIS K 200 PHE 0.010 0.002 PHE M 158 TYR 0.017 0.002 TYR K 103 ARG 0.006 0.001 ARG O 13 *********************** 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 197 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 153 time to evaluate : 2.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 23 GLU cc_start: 0.7830 (mp0) cc_final: 0.7254 (tp30) REVERT: K 66 ASP cc_start: 0.8005 (t0) cc_final: 0.7783 (t0) REVERT: K 246 THR cc_start: 0.8640 (OUTLIER) cc_final: 0.8392 (p) REVERT: L 1 MET cc_start: 0.7526 (ttp) cc_final: 0.7296 (ttp) REVERT: L 18 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.7449 (mtm-85) REVERT: N 108 ASP cc_start: 0.7625 (m-30) cc_final: 0.7238 (p0) REVERT: O 31 GLU cc_start: 0.7400 (tp30) cc_final: 0.6910 (mm-30) REVERT: O 32 LEU cc_start: 0.9363 (mt) cc_final: 0.9149 (mt) outliers start: 44 outliers final: 23 residues processed: 180 average time/residue: 1.6220 time to fit residues: 383.7770 Evaluate side-chains 168 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 143 time to evaluate : 2.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 45 ASN Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 246 THR Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 22 ASP Chi-restraints excluded: chain M residue 165 HIS Chi-restraints excluded: chain M residue 194 LYS Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 131 ASP Chi-restraints excluded: chain N residue 145 SER Chi-restraints excluded: chain N residue 157 LYS Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 67 ASN 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: 6.9990 chunk 111 optimal weight: 10.0000 chunk 298 optimal weight: 8.9990 chunk 244 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 359 optimal weight: 0.9990 chunk 388 optimal weight: 4.9990 chunk 320 optimal weight: 0.9990 chunk 356 optimal weight: 7.9990 chunk 122 optimal weight: 8.9990 chunk 288 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 45 ASN K 117 GLN ** K 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 138 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 80044 Z= 0.276 Angle : 0.644 16.656 123235 Z= 0.352 Chirality : 0.033 0.273 16133 Planarity : 0.008 0.132 4351 Dihedral : 23.605 176.092 48074 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.64 % Favored : 94.25 % Rotamer: Outliers : 5.37 % Allowed : 24.08 % Favored : 70.55 % 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: -1.81 (0.26), residues: 957 helix: -1.17 (0.37), residues: 176 sheet: -1.04 (0.38), residues: 186 loop : -1.27 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 78 HIS 0.005 0.001 HIS K 200 PHE 0.009 0.001 PHE N 90 TYR 0.007 0.001 TYR O 53 ARG 0.006 0.001 ARG O 13 *********************** 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 202 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 161 time to evaluate : 2.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 23 GLU cc_start: 0.7767 (mp0) cc_final: 0.7248 (tp30) REVERT: K 66 ASP cc_start: 0.8002 (t0) cc_final: 0.7790 (t0) REVERT: K 271 ARG cc_start: 0.6973 (OUTLIER) cc_final: 0.5995 (ptt-90) REVERT: L 1 MET cc_start: 0.7550 (ttp) cc_final: 0.7265 (ttp) REVERT: N 108 ASP cc_start: 0.7678 (m-30) cc_final: 0.7342 (p0) REVERT: N 165 MET cc_start: 0.8601 (ttt) cc_final: 0.8354 (ttt) REVERT: O 1 MET cc_start: 0.6861 (OUTLIER) cc_final: 0.6490 (ttt) REVERT: O 13 ARG cc_start: 0.8613 (mtt90) cc_final: 0.8188 (mtt90) REVERT: O 31 GLU cc_start: 0.7435 (tp30) cc_final: 0.6947 (mm-30) REVERT: O 32 LEU cc_start: 0.9354 (mt) cc_final: 0.9136 (mt) outliers start: 41 outliers final: 17 residues processed: 187 average time/residue: 1.5994 time to fit residues: 393.3387 Evaluate side-chains 169 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 150 time to evaluate : 2.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 114 ASP Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 271 ARG Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 22 ASP Chi-restraints excluded: chain M residue 191 ASP Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 92 VAL Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 81 ILE 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: 0.5980 chunk 270 optimal weight: 10.0000 chunk 186 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 171 optimal weight: 10.0000 chunk 241 optimal weight: 8.9990 chunk 360 optimal weight: 1.9990 chunk 381 optimal weight: 0.0370 chunk 188 optimal weight: 10.0000 chunk 341 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 overall best weight: 4.1264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN ** K 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 138 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 80044 Z= 0.306 Angle : 0.670 16.756 123235 Z= 0.365 Chirality : 0.034 0.288 16133 Planarity : 0.008 0.134 4351 Dihedral : 23.653 177.154 48074 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.37 % Favored : 93.31 % Rotamer: Outliers : 5.24 % Allowed : 25.00 % Favored : 69.76 % 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: -1.59 (0.27), residues: 957 helix: -1.05 (0.37), residues: 179 sheet: -0.90 (0.39), residues: 179 loop : -1.10 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 78 HIS 0.007 0.001 HIS K 200 PHE 0.009 0.001 PHE M 158 TYR 0.006 0.001 TYR O 53 ARG 0.005 0.001 ARG O 13 *********************** 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 197 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 157 time to evaluate : 2.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 23 GLU cc_start: 0.7762 (mp0) cc_final: 0.7245 (tp30) REVERT: K 66 ASP cc_start: 0.8104 (t0) cc_final: 0.7847 (t0) REVERT: K 271 ARG cc_start: 0.7109 (OUTLIER) cc_final: 0.6075 (ptt-90) REVERT: L 1 MET cc_start: 0.7557 (ttp) cc_final: 0.7289 (ttp) REVERT: M 155 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6971 (tt0) REVERT: N 108 ASP cc_start: 0.7572 (m-30) cc_final: 0.7307 (p0) REVERT: N 165 MET cc_start: 0.8634 (ttt) cc_final: 0.8397 (ttt) REVERT: O 1 MET cc_start: 0.6874 (OUTLIER) cc_final: 0.6528 (ttt) REVERT: O 31 GLU cc_start: 0.7528 (tp30) cc_final: 0.7010 (mm-30) REVERT: O 32 LEU cc_start: 0.9356 (mt) cc_final: 0.9127 (mt) outliers start: 40 outliers final: 24 residues processed: 184 average time/residue: 1.6319 time to fit residues: 396.2670 Evaluate side-chains 178 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 151 time to evaluate : 2.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 114 ASP Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 271 ARG Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 22 ASP Chi-restraints excluded: chain M residue 155 GLU Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 92 VAL Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 131 ASP Chi-restraints excluded: chain N residue 145 SER Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 67 ASN 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: 4.9990 chunk 216 optimal weight: 40.0000 chunk 5 optimal weight: 10.0000 chunk 284 optimal weight: 10.0000 chunk 157 optimal weight: 10.0000 chunk 325 optimal weight: 3.9990 chunk 263 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 194 optimal weight: 10.0000 chunk 342 optimal weight: 6.9990 chunk 96 optimal weight: 8.9990 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 86 ASN K 117 GLN ** K 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 138 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 80044 Z= 0.501 Angle : 0.806 17.311 123235 Z= 0.423 Chirality : 0.043 0.333 16133 Planarity : 0.009 0.141 4351 Dihedral : 23.850 178.005 48074 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.31 % Favored : 92.37 % Rotamer: Outliers : 5.76 % Allowed : 25.39 % Favored : 68.85 % 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: -1.72 (0.26), residues: 957 helix: -1.24 (0.36), residues: 179 sheet: -0.71 (0.40), residues: 167 loop : -1.26 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP M 78 HIS 0.007 0.001 HIS K 200 PHE 0.016 0.002 PHE M 23 TYR 0.015 0.002 TYR K 103 ARG 0.008 0.001 ARG O 13 *********************** 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 189 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 145 time to evaluate : 2.056 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 23 GLU cc_start: 0.7935 (mp0) cc_final: 0.7354 (tp30) REVERT: K 66 ASP cc_start: 0.8197 (t0) cc_final: 0.7894 (t0) REVERT: K 246 THR cc_start: 0.8773 (t) cc_final: 0.8563 (p) REVERT: K 271 ARG cc_start: 0.7266 (OUTLIER) cc_final: 0.6110 (ptt-90) REVERT: L 1 MET cc_start: 0.7545 (ttp) cc_final: 0.7298 (ttp) REVERT: N 108 ASP cc_start: 0.7583 (m-30) cc_final: 0.7297 (p0) REVERT: O 1 MET cc_start: 0.6960 (OUTLIER) cc_final: 0.6622 (ttt) REVERT: O 31 GLU cc_start: 0.7497 (tp30) cc_final: 0.6982 (mm-30) outliers start: 44 outliers final: 28 residues processed: 173 average time/residue: 1.5900 time to fit residues: 365.1598 Evaluate side-chains 179 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 149 time to evaluate : 2.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 114 ASP Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 271 ARG Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 22 ASP Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M 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 2 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 92 VAL Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 131 ASP Chi-restraints excluded: chain N residue 145 SER Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 67 ASN 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: 6.9990 chunk 343 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 224 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 382 optimal weight: 3.9990 chunk 317 optimal weight: 0.3980 chunk 176 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 chunk 200 optimal weight: 4.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN ** K 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 115 GLN N 49 GLN O 138 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 80044 Z= 0.249 Angle : 0.676 17.028 123235 Z= 0.372 Chirality : 0.035 0.298 16133 Planarity : 0.008 0.131 4351 Dihedral : 23.883 177.775 48074 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.27 % Favored : 93.52 % Rotamer: Outliers : 5.76 % Allowed : 25.39 % Favored : 68.85 % 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: -1.44 (0.27), residues: 957 helix: -0.90 (0.38), residues: 178 sheet: -0.88 (0.40), residues: 160 loop : -0.99 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 78 HIS 0.011 0.001 HIS M 165 PHE 0.019 0.001 PHE M 23 TYR 0.011 0.002 TYR O 53 ARG 0.007 0.001 ARG K 203 *********************** 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 210 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 166 time to evaluate : 2.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 23 GLU cc_start: 0.7839 (mp0) cc_final: 0.7376 (tp30) REVERT: K 66 ASP cc_start: 0.8110 (t0) cc_final: 0.7817 (t0) REVERT: K 177 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.7299 (mmm-85) REVERT: K 271 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.6110 (ptt-90) REVERT: L 17 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8151 (mttt) REVERT: M 115 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8357 (mp10) REVERT: M 155 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6859 (tt0) REVERT: N 108 ASP cc_start: 0.7530 (m-30) cc_final: 0.7282 (p0) REVERT: O 31 GLU cc_start: 0.7460 (tp30) cc_final: 0.6949 (mm-30) outliers start: 44 outliers final: 27 residues processed: 194 average time/residue: 1.6237 time to fit residues: 413.2058 Evaluate side-chains 187 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 155 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 114 ASP Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 177 ARG Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 271 ARG Chi-restraints excluded: chain L residue 17 LYS Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 22 ASP Chi-restraints excluded: chain M residue 115 GLN Chi-restraints excluded: chain M residue 116 ASP Chi-restraints excluded: chain M residue 155 GLU Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 11 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 92 VAL Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 131 ASP Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 67 ASN 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: 5.9990 chunk 43 optimal weight: 10.0000 chunk 217 optimal weight: 30.0000 chunk 279 optimal weight: 10.0000 chunk 216 optimal weight: 50.0000 chunk 321 optimal weight: 4.9990 chunk 213 optimal weight: 30.0000 chunk 380 optimal weight: 7.9990 chunk 238 optimal weight: 10.0000 chunk 232 optimal weight: 10.0000 chunk 175 optimal weight: 10.0000 overall best weight: 7.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN ** K 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 138 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.070 80044 Z= 0.562 Angle : 0.848 17.374 123235 Z= 0.438 Chirality : 0.045 0.338 16133 Planarity : 0.009 0.143 4351 Dihedral : 23.850 178.289 48074 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.42 % Favored : 92.27 % Rotamer: Outliers : 6.81 % Allowed : 25.00 % Favored : 68.19 % 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: -1.70 (0.26), residues: 957 helix: -1.14 (0.37), residues: 179 sheet: -0.91 (0.40), residues: 160 loop : -1.19 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP M 78 HIS 0.005 0.002 HIS O 76 PHE 0.023 0.002 PHE M 23 TYR 0.010 0.002 TYR O 125 ARG 0.009 0.001 ARG M 44 *********************** 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 195 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 143 time to evaluate : 2.690 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 23 GLU cc_start: 0.7929 (mp0) cc_final: 0.7349 (tp30) REVERT: K 66 ASP cc_start: 0.8256 (t0) cc_final: 0.7983 (t0) REVERT: K 177 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.7413 (mmm-85) REVERT: K 271 ARG cc_start: 0.7441 (OUTLIER) cc_final: 0.6279 (ptt-90) REVERT: M 155 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.6982 (tt0) REVERT: N 108 ASP cc_start: 0.7600 (m-30) cc_final: 0.7310 (p0) REVERT: N 181 ASP cc_start: 0.8159 (t0) cc_final: 0.7863 (t0) REVERT: O 1 MET cc_start: 0.6965 (OUTLIER) cc_final: 0.6645 (ttt) REVERT: O 31 GLU cc_start: 0.7556 (tp30) cc_final: 0.7088 (mm-30) outliers start: 52 outliers final: 31 residues processed: 178 average time/residue: 1.5763 time to fit residues: 372.8381 Evaluate side-chains 181 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 146 time to evaluate : 2.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 114 ASP Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 177 ARG Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 271 ARG Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 22 ASP Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 155 GLU Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 92 VAL Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 131 ASP Chi-restraints excluded: chain N residue 145 SER Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 50 THR Chi-restraints excluded: chain O residue 67 ASN Chi-restraints excluded: chain O residue 93 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: 5.9990 chunk 152 optimal weight: 10.0000 chunk 227 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 242 optimal weight: 3.9990 chunk 259 optimal weight: 4.9990 chunk 188 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 299 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN ** K 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN O 138 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 80044 Z= 0.355 Angle : 0.732 17.343 123235 Z= 0.395 Chirality : 0.037 0.310 16133 Planarity : 0.008 0.137 4351 Dihedral : 23.889 178.066 48074 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.79 % Favored : 92.89 % Rotamer: Outliers : 5.76 % Allowed : 27.09 % Favored : 67.15 % 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: -1.62 (0.26), residues: 957 helix: -0.95 (0.38), residues: 179 sheet: -1.07 (0.38), residues: 170 loop : -1.10 (0.25), residues: 608 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 0.037 0.002 PHE M 23 TYR 0.019 0.002 TYR K 83 ARG 0.013 0.001 ARG K 203 *********************** 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 194 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 150 time to evaluate : 2.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 23 GLU cc_start: 0.7900 (mp0) cc_final: 0.7314 (tp30) REVERT: K 66 ASP cc_start: 0.8165 (t0) cc_final: 0.7858 (t0) REVERT: K 177 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.7384 (mmm-85) REVERT: K 246 THR cc_start: 0.8705 (OUTLIER) cc_final: 0.8499 (p) REVERT: K 271 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.6234 (ptt-90) REVERT: L 17 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8191 (mttt) REVERT: L 115 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7481 (pp20) REVERT: M 155 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.6986 (tt0) REVERT: N 108 ASP cc_start: 0.7591 (m-30) cc_final: 0.7313 (p0) REVERT: O 31 GLU cc_start: 0.7564 (tp30) cc_final: 0.7101 (mm-30) outliers start: 44 outliers final: 27 residues processed: 178 average time/residue: 1.5730 time to fit residues: 371.6835 Evaluate side-chains 174 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 141 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 114 ASP Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 121 ASP Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 177 ARG Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 246 THR Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 271 ARG Chi-restraints excluded: chain L residue 17 LYS Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 115 GLU Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 22 ASP Chi-restraints excluded: chain M residue 155 GLU Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 92 VAL Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 131 ASP Chi-restraints excluded: chain N residue 145 SER Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 67 ASN 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: 4.9990 chunk 364 optimal weight: 0.9980 chunk 332 optimal weight: 5.9990 chunk 354 optimal weight: 0.9980 chunk 213 optimal weight: 30.0000 chunk 154 optimal weight: 10.0000 chunk 278 optimal weight: 10.0000 chunk 108 optimal weight: 30.0000 chunk 320 optimal weight: 7.9990 chunk 335 optimal weight: 10.0000 chunk 353 optimal weight: 10.0000 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN ** K 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 115 GLN N 49 GLN ** N 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 138 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 80044 Z= 0.318 Angle : 0.719 17.230 123235 Z= 0.387 Chirality : 0.037 0.299 16133 Planarity : 0.008 0.135 4351 Dihedral : 23.865 178.299 48074 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.11 % Favored : 92.69 % Rotamer: Outliers : 5.89 % Allowed : 26.96 % Favored : 67.15 % 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: -1.64 (0.26), residues: 957 helix: -0.97 (0.37), residues: 184 sheet: -1.07 (0.38), residues: 170 loop : -1.13 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP M 78 HIS 0.009 0.001 HIS K 200 PHE 0.046 0.002 PHE M 23 TYR 0.022 0.002 TYR K 83 ARG 0.020 0.001 ARG O 13 *********************** 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 185 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 140 time to evaluate : 2.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 18 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.7979 (mtpp) REVERT: K 23 GLU cc_start: 0.7874 (mp0) cc_final: 0.7375 (tp30) REVERT: K 66 ASP cc_start: 0.8164 (t0) cc_final: 0.7880 (t0) REVERT: K 177 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.7380 (mmm-85) REVERT: K 271 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.6214 (ptt-90) REVERT: L 17 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8184 (mttt) REVERT: L 115 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7446 (pp20) REVERT: M 155 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.6998 (tt0) REVERT: N 108 ASP cc_start: 0.7553 (m-30) cc_final: 0.7289 (p0) REVERT: O 31 GLU cc_start: 0.7569 (tp30) cc_final: 0.7106 (mm-30) outliers start: 45 outliers final: 31 residues processed: 173 average time/residue: 1.5638 time to fit residues: 362.5751 Evaluate side-chains 177 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 140 time to evaluate : 2.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 18 LYS Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 114 ASP Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 121 ASP Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 177 ARG Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 271 ARG Chi-restraints excluded: chain L residue 17 LYS Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 115 GLU Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 22 ASP Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 155 GLU Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 11 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 92 VAL Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 131 ASP Chi-restraints excluded: chain N residue 145 SER Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 67 ASN Chi-restraints excluded: chain O residue 92 MET 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: 7.9990 chunk 228 optimal weight: 10.0000 chunk 177 optimal weight: 7.9990 chunk 260 optimal weight: 7.9990 chunk 393 optimal weight: 4.9990 chunk 362 optimal weight: 9.9990 chunk 313 optimal weight: 0.8980 chunk 32 optimal weight: 10.0000 chunk 242 optimal weight: 10.0000 chunk 192 optimal weight: 9.9990 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN ** K 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 115 GLN ** M 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 138 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 80044 Z= 0.429 Angle : 0.752 17.393 123235 Z= 0.400 Chirality : 0.039 0.315 16133 Planarity : 0.009 0.140 4351 Dihedral : 23.824 178.357 48074 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.00 % Favored : 92.69 % Rotamer: Outliers : 5.76 % Allowed : 27.23 % Favored : 67.02 % 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: -1.65 (0.26), residues: 957 helix: -1.05 (0.37), residues: 185 sheet: -0.91 (0.40), residues: 162 loop : -1.16 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP M 78 HIS 0.005 0.001 HIS M 165 PHE 0.024 0.002 PHE M 23 TYR 0.021 0.002 TYR K 83 ARG 0.009 0.001 ARG O 13 ********************** 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 187 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 143 time to evaluate : 2.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 18 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.7972 (mtpp) REVERT: K 23 GLU cc_start: 0.7903 (mp0) cc_final: 0.7327 (tp30) REVERT: K 66 ASP cc_start: 0.8186 (t0) cc_final: 0.7905 (t0) REVERT: K 177 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.7439 (mmm-85) REVERT: K 271 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.6298 (ptt-90) REVERT: L 17 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8227 (mttt) REVERT: L 115 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7507 (pp20) REVERT: M 155 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.6966 (tt0) REVERT: N 108 ASP cc_start: 0.7593 (m-30) cc_final: 0.7310 (p0) REVERT: O 31 GLU cc_start: 0.7662 (tp30) cc_final: 0.7195 (mm-30) outliers start: 44 outliers final: 30 residues processed: 175 average time/residue: 1.6101 time to fit residues: 374.1480 Evaluate side-chains 177 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 141 time to evaluate : 2.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 18 LYS Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 111 LYS Chi-restraints excluded: chain K residue 114 ASP Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 121 ASP Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 177 ARG Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 271 ARG Chi-restraints excluded: chain L residue 17 LYS Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 115 GLU Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 22 ASP Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 123 LYS Chi-restraints excluded: chain M residue 155 GLU 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 91 THR Chi-restraints excluded: chain N residue 92 VAL Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 131 ASP Chi-restraints excluded: chain N residue 145 SER Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain O residue 67 ASN 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: 8.9990 chunk 333 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 288 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 313 optimal weight: 7.9990 chunk 131 optimal weight: 7.9990 chunk 322 optimal weight: 0.9980 chunk 39 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 117 GLN ** K 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN O 138 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.115928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.092072 restraints weight = 142770.861| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 0.64 r_work: 0.3096 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 80044 Z= 0.365 Angle : 0.726 17.387 123235 Z= 0.390 Chirality : 0.038 0.308 16133 Planarity : 0.008 0.139 4351 Dihedral : 23.833 178.275 48074 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.21 % Favored : 92.48 % Rotamer: Outliers : 5.10 % Allowed : 28.14 % Favored : 66.75 % 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: -1.61 (0.26), residues: 957 helix: -1.00 (0.37), residues: 185 sheet: -0.93 (0.40), residues: 160 loop : -1.13 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP M 78 HIS 0.005 0.001 HIS M 165 PHE 0.033 0.002 PHE M 23 TYR 0.021 0.002 TYR K 83 ARG 0.029 0.001 ARG K 203 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11231.05 seconds wall clock time: 202 minutes 48.32 seconds (12168.32 seconds total)