Starting phenix.real_space_refine on Tue Apr 9 16:30:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bge_12179/04_2024/7bge_12179.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bge_12179/04_2024/7bge_12179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bge_12179/04_2024/7bge_12179.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bge_12179/04_2024/7bge_12179.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bge_12179/04_2024/7bge_12179.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bge_12179/04_2024/7bge_12179.pdb" } resolution = 3.6 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= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 465 5.49 5 S 21 5.16 5 C 8882 2.51 5 N 3119 2.21 5 O 4501 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b ARG 113": "NH1" <-> "NH2" Residue "b GLU 118": "OE1" <-> "OE2" Residue "b GLU 122": "OE1" <-> "OE2" Residue "b GLU 127": "OE1" <-> "OE2" Residue "b GLU 136": "OE1" <-> "OE2" Residue "c GLU 25": "OE1" <-> "OE2" Residue "c GLU 48": "OE1" <-> "OE2" Residue "c GLU 55": "OE1" <-> "OE2" Residue "c GLU 124": "OE1" <-> "OE2" Residue "c PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 169": "OE1" <-> "OE2" Residue "c GLU 187": "OE1" <-> "OE2" Residue "g ARG 10": "NH1" <-> "NH2" Residue "g GLU 64": "OE1" <-> "OE2" Residue "g GLU 74": "OE1" <-> "OE2" Residue "g ARG 79": "NH1" <-> "NH2" Residue "g GLU 94": "OE1" <-> "OE2" Residue "g ARG 95": "NH1" <-> "NH2" Residue "g GLU 113": "OE1" <-> "OE2" Residue "g GLU 146": "OE1" <-> "OE2" Residue "i ARG 9": "NH1" <-> "NH2" Residue "i GLU 39": "OE1" <-> "OE2" Residue "i GLU 91": "OE1" <-> "OE2" Residue "i GLU 95": "OE1" <-> "OE2" Residue "i ARG 111": "NH1" <-> "NH2" Residue "j GLU 23": "OE1" <-> "OE2" Residue "j ARG 53": "NH1" <-> "NH2" Residue "j GLU 99": "OE1" <-> "OE2" Residue "m ARG 14": "NH1" <-> "NH2" Residue "m ARG 87": "NH1" <-> "NH2" Residue "m ARG 92": "NH1" <-> "NH2" Residue "m ARG 93": "NH1" <-> "NH2" Residue "n ARG 23": "NH1" <-> "NH2" Residue "s GLU 13": "OE1" <-> "OE2" Residue "s GLU 20": "OE1" <-> "OE2" Residue "s GLU 23": "OE1" <-> "OE2" Residue "s PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 55": "NH1" <-> "NH2" Residue "s ARG 78": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 16988 Number of models: 1 Model: "" Number of chains: 9 Chain: "a" Number of atoms: 9920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 9920 Classifications: {'RNA': 465} Modifications used: {'rna2p_pur': 44, 'rna2p_pyr': 35, 'rna3p_pur': 204, 'rna3p_pyr': 182} Link IDs: {'rna2p': 79, 'rna3p': 385} Chain: "b" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 864 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain breaks: 1 Chain: "c" Number of atoms: 1596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1596 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 3, 'TRANS': 198} Chain: "g" Number of atoms: 1177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1177 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain breaks: 1 Chain: "i" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 987 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain: "j" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 773 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 6, 'TRANS': 90} Chain: "m" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 584 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain breaks: 2 Chain: "n" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 497 Classifications: {'peptide': 59} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain: "s" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 590 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Time building chain proxies: 9.17, per 1000 atoms: 0.54 Number of scatterers: 16988 At special positions: 0 Unit cell: (116.62, 119, 135.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 21 16.00 P 465 15.00 O 4501 8.00 N 3119 7.00 C 8882 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=0, symmetry=0 Time building additional restraints: 8.15 Conformation dependent library (CDL) restraints added in 1.5 seconds 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1632 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 9 sheets defined 35.0% alpha, 12.1% beta 133 base pairs and 251 stacking pairs defined. Time for finding SS restraints: 6.97 Creating SS restraints... Processing helix chain 'b' and resid 107 through 120 removed outlier: 3.798A pdb=" N LYS b 119 " --> pdb=" O SER b 115 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 147 removed outlier: 3.939A pdb=" N VAL b 134 " --> pdb=" O PRO b 130 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL b 135 " --> pdb=" O LYS b 131 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N GLU b 136 " --> pdb=" O LYS b 132 " (cutoff:3.500A) Processing helix chain 'b' and resid 169 through 174 Processing helix chain 'c' and resid 28 through 50 removed outlier: 3.889A pdb=" N HIS c 33 " --> pdb=" O ALA c 29 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N GLU c 34 " --> pdb=" O SER c 30 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASN c 44 " --> pdb=" O LYS c 40 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU c 45 " --> pdb=" O PHE c 41 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS c 47 " --> pdb=" O ASP c 43 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLU c 48 " --> pdb=" O ASN c 44 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER c 50 " --> pdb=" O LEU c 46 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 75 removed outlier: 3.684A pdb=" N MET c 74 " --> pdb=" O LYS c 71 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL c 75 " --> pdb=" O PRO c 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 71 through 75' Processing helix chain 'c' and resid 80 through 95 removed outlier: 3.652A pdb=" N GLU c 84 " --> pdb=" O GLY c 80 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 124 Processing helix chain 'c' and resid 128 through 142 removed outlier: 3.521A pdb=" N VAL c 132 " --> pdb=" O SER c 128 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 31 removed outlier: 4.078A pdb=" N THR g 24 " --> pdb=" O SER g 20 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS g 25 " --> pdb=" O LYS g 21 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 54 removed outlier: 3.801A pdb=" N ALA g 39 " --> pdb=" O LYS g 35 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR g 44 " --> pdb=" O GLN g 40 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER g 45 " --> pdb=" O ARG g 41 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA g 46 " --> pdb=" O ILE g 42 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 67 removed outlier: 3.612A pdb=" N ASN g 67 " --> pdb=" O GLU g 63 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 109 Processing helix chain 'g' and resid 115 through 128 removed outlier: 4.635A pdb=" N ALA g 121 " --> pdb=" O GLU g 117 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASN g 122 " --> pdb=" O ASP g 118 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU g 123 " --> pdb=" O ARG g 119 " (cutoff:3.500A) Processing helix chain 'g' and resid 133 through 148 Processing helix chain 'i' and resid 52 through 57 removed outlier: 3.506A pdb=" N THR i 57 " --> pdb=" O PRO i 53 " (cutoff:3.500A) Processing helix chain 'i' and resid 74 through 93 Processing helix chain 'i' and resid 96 through 102 Processing helix chain 'j' and resid 15 through 32 removed outlier: 3.518A pdb=" N ASP j 19 " --> pdb=" O HIS j 15 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLN j 20 " --> pdb=" O ARG j 16 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER j 21 " --> pdb=" O VAL j 17 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL j 26 " --> pdb=" O ALA j 22 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU j 27 " --> pdb=" O GLU j 23 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 88 removed outlier: 3.945A pdb=" N VAL j 84 " --> pdb=" O THR j 80 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP j 85 " --> pdb=" O PRO j 81 " (cutoff:3.500A) Processing helix chain 'm' and resid 67 through 81 Processing helix chain 'm' and resid 106 through 110 Processing helix chain 'n' and resid 4 through 11 removed outlier: 3.603A pdb=" N GLN n 11 " --> pdb=" O VAL n 7 " (cutoff:3.500A) Processing helix chain 'n' and resid 40 through 50 removed outlier: 3.636A pdb=" N ARG n 45 " --> pdb=" O ARG n 41 " (cutoff:3.500A) Processing helix chain 's' and resid 16 through 22 removed outlier: 3.724A pdb=" N ALA s 21 " --> pdb=" O LYS s 17 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLN s 22 " --> pdb=" O LYS s 18 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'b' and resid 161 through 163 removed outlier: 6.020A pdb=" N LEU b 161 " --> pdb=" O VAL b 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'c' and resid 51 through 58 removed outlier: 6.853A pdb=" N HIS c 68 " --> pdb=" O SER c 52 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL c 54 " --> pdb=" O ALA c 66 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA c 66 " --> pdb=" O VAL c 54 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ILE c 56 " --> pdb=" O ASN c 64 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASN c 64 " --> pdb=" O ILE c 56 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ILE c 103 " --> pdb=" O ILE c 65 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE c 67 " --> pdb=" O ILE c 103 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'c' and resid 163 through 166 removed outlier: 3.515A pdb=" N GLU c 165 " --> pdb=" O VAL c 152 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'c' and resid 163 through 166 removed outlier: 3.515A pdb=" N GLU c 165 " --> pdb=" O VAL c 152 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY c 147 " --> pdb=" O TYR c 202 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY c 196 " --> pdb=" O SER c 153 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY c 193 " --> pdb=" O THR c 190 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA c 186 " --> pdb=" O VAL c 197 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'g' and resid 73 through 74 removed outlier: 3.549A pdb=" N GLU g 74 " --> pdb=" O VAL g 89 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'i' and resid 11 through 13 removed outlier: 6.144A pdb=" N THR i 31 " --> pdb=" O VAL i 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'j' and resid 6 through 11 removed outlier: 4.677A pdb=" N ASP j 75 " --> pdb=" O GLY j 38 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N GLY j 38 " --> pdb=" O ASP j 75 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'j' and resid 47 through 52 Processing sheet with id=AA9, first strand: chain 's' and resid 31 through 33 removed outlier: 6.711A pdb=" N ILE s 31 " --> pdb=" O ALA s 50 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N TYR s 52 " --> pdb=" O ILE s 31 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N THR s 33 " --> pdb=" O TYR s 52 " (cutoff:3.500A) 225 hydrogen bonds defined for protein. 648 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 327 hydrogen bonds 524 hydrogen bond angles 0 basepair planarities 133 basepair parallelities 251 stacking parallelities Total time for adding SS restraints: 7.75 Time building geometry restraints manager: 8.71 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: 2413 1.33 - 1.45: 7170 1.45 - 1.57: 7722 1.57 - 1.69: 932 1.69 - 1.81: 37 Bond restraints: 18274 Sorted by residual: bond pdb=" C ARG g 92 " pdb=" N PRO g 93 " ideal model delta sigma weight residual 1.335 1.394 -0.060 1.19e-02 7.06e+03 2.50e+01 bond pdb=" C GLN i 52 " pdb=" N PRO i 53 " ideal model delta sigma weight residual 1.337 1.366 -0.029 1.06e-02 8.90e+03 7.62e+00 bond pdb=" CA ARG i 124 " pdb=" CB ARG i 124 " ideal model delta sigma weight residual 1.532 1.566 -0.034 1.48e-02 4.57e+03 5.38e+00 bond pdb=" N PRO s 42 " pdb=" CA PRO s 42 " ideal model delta sigma weight residual 1.468 1.485 -0.018 7.90e-03 1.60e+04 5.06e+00 bond pdb=" N1 C a 946 " pdb=" C2 C a 946 " ideal model delta sigma weight residual 1.397 1.442 -0.045 2.00e-02 2.50e+03 5.01e+00 ... (remaining 18269 not shown) Histogram of bond angle deviations from ideal: 97.71 - 105.61: 2534 105.61 - 113.51: 10472 113.51 - 121.41: 9170 121.41 - 129.31: 4350 129.31 - 137.21: 398 Bond angle restraints: 26924 Sorted by residual: angle pdb=" C ALA i 123 " pdb=" N ARG i 124 " pdb=" CA ARG i 124 " ideal model delta sigma weight residual 122.63 133.59 -10.96 1.44e+00 4.82e-01 5.79e+01 angle pdb=" CA ARG i 124 " pdb=" CB ARG i 124 " pdb=" CG ARG i 124 " ideal model delta sigma weight residual 114.10 126.96 -12.86 2.00e+00 2.50e-01 4.13e+01 angle pdb=" C GLY b 99 " pdb=" N LEU b 100 " pdb=" CA LEU b 100 " ideal model delta sigma weight residual 121.54 133.46 -11.92 1.91e+00 2.74e-01 3.89e+01 angle pdb=" C3' U a1054 " pdb=" O3' U a1054 " pdb=" P G a1055 " ideal model delta sigma weight residual 120.20 129.45 -9.25 1.50e+00 4.44e-01 3.80e+01 angle pdb=" C ASN i 33 " pdb=" N ASN i 34 " pdb=" CA ASN i 34 " ideal model delta sigma weight residual 122.08 131.11 -9.03 1.47e+00 4.63e-01 3.77e+01 ... (remaining 26919 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.70: 10367 35.70 - 71.40: 1130 71.40 - 107.10: 137 107.10 - 142.80: 1 142.80 - 178.50: 5 Dihedral angle restraints: 11640 sinusoidal: 9113 harmonic: 2527 Sorted by residual: dihedral pdb=" O4' U a1034 " pdb=" C1' U a1034 " pdb=" N1 U a1034 " pdb=" C2 U a1034 " ideal model delta sinusoidal sigma weight residual 200.00 40.55 159.45 1 1.50e+01 4.44e-03 8.26e+01 dihedral pdb=" O4' C a1169 " pdb=" C1' C a1169 " pdb=" N1 C a1169 " pdb=" C2 C a1169 " ideal model delta sinusoidal sigma weight residual 200.00 67.17 132.83 1 1.50e+01 4.44e-03 7.17e+01 dihedral pdb=" O4' U a 970 " pdb=" C1' U a 970 " pdb=" N1 U a 970 " pdb=" C2 U a 970 " ideal model delta sinusoidal sigma weight residual -128.00 50.50 -178.50 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 11637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2998 0.092 - 0.183: 342 0.183 - 0.275: 38 0.275 - 0.367: 8 0.367 - 0.458: 1 Chirality restraints: 3387 Sorted by residual: chirality pdb=" C3' U a1054 " pdb=" C4' U a1054 " pdb=" O3' U a1054 " pdb=" C2' U a1054 " both_signs ideal model delta sigma weight residual False -2.48 -2.02 -0.46 2.00e-01 2.50e+01 5.25e+00 chirality pdb=" CB VAL c 172 " pdb=" CA VAL c 172 " pdb=" CG1 VAL c 172 " pdb=" CG2 VAL c 172 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" CB ILE c 65 " pdb=" CA ILE c 65 " pdb=" CG1 ILE c 65 " pdb=" CG2 ILE c 65 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 3384 not shown) Planarity restraints: 1703 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU j 42 " -0.076 5.00e-02 4.00e+02 1.15e-01 2.11e+01 pdb=" N PRO j 43 " 0.199 5.00e-02 4.00e+02 pdb=" CA PRO j 43 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO j 43 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG c 39 " -0.022 2.00e-02 2.50e+03 4.38e-02 1.92e+01 pdb=" C ARG c 39 " 0.076 2.00e-02 2.50e+03 pdb=" O ARG c 39 " -0.028 2.00e-02 2.50e+03 pdb=" N LYS c 40 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE c 28 " 0.021 2.00e-02 2.50e+03 4.18e-02 1.75e+01 pdb=" C PHE c 28 " -0.072 2.00e-02 2.50e+03 pdb=" O PHE c 28 " 0.027 2.00e-02 2.50e+03 pdb=" N ALA c 29 " 0.025 2.00e-02 2.50e+03 ... (remaining 1700 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4500 2.82 - 3.34: 12418 3.34 - 3.86: 35251 3.86 - 4.38: 39940 4.38 - 4.90: 55929 Nonbonded interactions: 148038 Sorted by model distance: nonbonded pdb=" O2' U a1332 " pdb=" NE ARG s 78 " model vdw 2.296 2.520 nonbonded pdb=" O2' U a1246 " pdb=" OP1 G a1316 " model vdw 2.339 2.440 nonbonded pdb=" O2' C a1260 " pdb=" O GLY i 72 " model vdw 2.356 2.440 nonbonded pdb=" O2' G a1281 " pdb=" O2' U a1324 " model vdw 2.370 2.440 nonbonded pdb=" O2 C a1126 " pdb=" OG SER n 60 " model vdw 2.371 2.440 ... (remaining 148033 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.930 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: 0.000 Extract box with map and model: 7.860 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 52.400 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 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 0.061 18274 Z= 0.400 Angle : 1.329 14.342 26924 Z= 0.653 Chirality : 0.059 0.458 3387 Planarity : 0.009 0.115 1703 Dihedral : 22.858 178.504 10008 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.29 % Favored : 89.59 % Rotamer: Outliers : 2.13 % Allowed : 12.77 % Favored : 85.11 % Cbeta Deviations : 0.37 % 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: -5.86 (0.20), residues: 855 helix: -4.56 (0.12), residues: 303 sheet: -2.20 (0.41), residues: 139 loop : -3.99 (0.22), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.004 TRP c 200 HIS 0.007 0.001 HIS s 69 PHE 0.036 0.004 PHE s 44 TYR 0.029 0.003 TYR g 107 ARG 0.013 0.001 ARG j 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 262 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 8 PRO cc_start: 0.8167 (Cg_endo) cc_final: 0.7935 (Cg_exo) REVERT: g 10 ARG cc_start: 0.5093 (pmt170) cc_final: 0.3955 (tmm-80) REVERT: g 91 VAL cc_start: 0.6203 (m) cc_final: 0.5214 (m) REVERT: g 116 MET cc_start: 0.7983 (tpt) cc_final: 0.7739 (tpt) REVERT: s 27 LYS cc_start: 0.5846 (OUTLIER) cc_final: 0.5483 (mtmt) outliers start: 16 outliers final: 3 residues processed: 273 average time/residue: 0.3764 time to fit residues: 142.5811 Evaluate side-chains 179 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 175 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 152 VAL Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain s residue 27 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.5980 chunk 98 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 0.0970 chunk 75 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 103 ASN c 3 GLN ** c 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 99 HIS c 125 ASN g 28 ASN i 29 ASN i 70 HIS ** i 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 56 HIS j 67 GLN s 22 GLN s 47 HIS s 57 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18274 Z= 0.168 Angle : 0.611 7.750 26924 Z= 0.318 Chirality : 0.036 0.224 3387 Planarity : 0.005 0.073 1703 Dihedral : 23.098 178.355 8181 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 3.46 % Allowed : 19.95 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.23 (0.23), residues: 855 helix: -2.31 (0.23), residues: 314 sheet: -1.92 (0.42), residues: 142 loop : -3.59 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP c 200 HIS 0.006 0.001 HIS i 70 PHE 0.014 0.001 PHE s 44 TYR 0.009 0.001 TYR n 21 ARG 0.008 0.001 ARG g 56 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 190 time to evaluate : 1.093 Fit side-chains revert: symmetry clash REVERT: g 10 ARG cc_start: 0.5700 (pmt170) cc_final: 0.4751 (pmt-80) REVERT: s 34 TRP cc_start: 0.8304 (m100) cc_final: 0.7837 (m100) outliers start: 26 outliers final: 9 residues processed: 204 average time/residue: 0.2978 time to fit residues: 90.6069 Evaluate side-chains 171 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 162 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 10 LEU Chi-restraints excluded: chain c residue 81 SER Chi-restraints excluded: chain g residue 31 MET Chi-restraints excluded: chain g residue 54 SER Chi-restraints excluded: chain i residue 62 ASN Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain n residue 61 TRP Chi-restraints excluded: chain s residue 77 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 127 optimal weight: 0.0470 chunk 105 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 94 optimal weight: 0.0870 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 151 GLN g 40 GLN g 67 ASN g 142 HIS i 29 ASN j 15 HIS ** n 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 47 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18274 Z= 0.156 Angle : 0.563 8.783 26924 Z= 0.290 Chirality : 0.034 0.233 3387 Planarity : 0.005 0.067 1703 Dihedral : 22.979 179.367 8174 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 4.39 % Allowed : 19.95 % Favored : 75.66 % 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: -3.05 (0.26), residues: 855 helix: -0.84 (0.29), residues: 304 sheet: -1.54 (0.45), residues: 132 loop : -3.18 (0.26), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP c 200 HIS 0.006 0.001 HIS c 99 PHE 0.016 0.001 PHE s 44 TYR 0.008 0.001 TYR n 21 ARG 0.007 0.000 ARG i 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 177 time to evaluate : 1.174 Fit side-chains REVERT: c 200 TRP cc_start: 0.7914 (OUTLIER) cc_final: 0.7208 (m100) REVERT: g 10 ARG cc_start: 0.6075 (pmt170) cc_final: 0.5642 (pmt-80) REVERT: g 51 GLU cc_start: 0.6594 (mm-30) cc_final: 0.5885 (tp30) REVERT: j 27 GLU cc_start: 0.5739 (tm-30) cc_final: 0.5348 (tm-30) REVERT: s 34 TRP cc_start: 0.8357 (m100) cc_final: 0.8035 (m100) outliers start: 33 outliers final: 16 residues processed: 196 average time/residue: 0.3186 time to fit residues: 91.8242 Evaluate side-chains 180 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 163 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 126 PHE Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain c residue 10 LEU Chi-restraints excluded: chain c residue 65 ILE Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 93 LEU Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain g residue 54 SER Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain i residue 62 ASN Chi-restraints excluded: chain i residue 95 GLU Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain m residue 27 THR Chi-restraints excluded: chain s residue 77 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 7.9990 chunk 88 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 118 optimal weight: 0.4980 chunk 125 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 142 HIS i 29 ASN ** n 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18274 Z= 0.252 Angle : 0.621 10.012 26924 Z= 0.319 Chirality : 0.037 0.227 3387 Planarity : 0.005 0.069 1703 Dihedral : 22.914 179.256 8174 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.06 % Favored : 89.94 % Rotamer: Outliers : 5.05 % Allowed : 21.68 % Favored : 73.27 % 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: -2.68 (0.28), residues: 855 helix: -0.36 (0.31), residues: 301 sheet: -1.47 (0.46), residues: 134 loop : -3.06 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP c 200 HIS 0.004 0.001 HIS s 47 PHE 0.017 0.002 PHE s 44 TYR 0.011 0.001 TYR n 21 ARG 0.009 0.001 ARG i 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 175 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 189 THR cc_start: 0.3587 (OUTLIER) cc_final: 0.3381 (p) REVERT: c 45 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6629 (pt0) REVERT: c 99 HIS cc_start: 0.6666 (m170) cc_final: 0.6224 (m170) REVERT: c 200 TRP cc_start: 0.7999 (OUTLIER) cc_final: 0.7356 (m100) REVERT: i 49 ASP cc_start: 0.6149 (OUTLIER) cc_final: 0.5389 (m-30) REVERT: j 82 LYS cc_start: 0.7257 (mppt) cc_final: 0.6818 (mtmm) REVERT: s 34 TRP cc_start: 0.8384 (m100) cc_final: 0.8040 (m100) outliers start: 38 outliers final: 21 residues processed: 196 average time/residue: 0.3107 time to fit residues: 90.3963 Evaluate side-chains 190 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 165 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 101 LEU Chi-restraints excluded: chain b residue 126 PHE Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain b residue 189 THR Chi-restraints excluded: chain c residue 10 LEU Chi-restraints excluded: chain c residue 45 GLU Chi-restraints excluded: chain c residue 65 ILE Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 93 LEU Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain g residue 31 MET Chi-restraints excluded: chain g residue 54 SER Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain i residue 49 ASP Chi-restraints excluded: chain i residue 62 ASN Chi-restraints excluded: chain i residue 95 GLU Chi-restraints excluded: chain i residue 100 LEU Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain m residue 19 LEU Chi-restraints excluded: chain m residue 27 THR Chi-restraints excluded: chain n residue 61 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 107 optimal weight: 0.3980 chunk 86 optimal weight: 0.4980 chunk 0 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 112 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 64 ASN ** c 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 142 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18274 Z= 0.270 Angle : 0.629 10.330 26924 Z= 0.323 Chirality : 0.037 0.232 3387 Planarity : 0.005 0.070 1703 Dihedral : 22.947 179.610 8174 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 5.85 % Allowed : 24.47 % Favored : 69.68 % 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: -2.50 (0.28), residues: 855 helix: -0.13 (0.31), residues: 301 sheet: -1.58 (0.45), residues: 138 loop : -2.95 (0.27), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP c 200 HIS 0.004 0.001 HIS i 83 PHE 0.019 0.002 PHE s 44 TYR 0.012 0.001 TYR n 21 ARG 0.011 0.001 ARG i 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 174 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 189 THR cc_start: 0.3914 (OUTLIER) cc_final: 0.3632 (p) REVERT: c 45 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.6848 (pt0) REVERT: c 200 TRP cc_start: 0.8008 (OUTLIER) cc_final: 0.7299 (m100) REVERT: g 15 ASP cc_start: 0.7685 (p0) cc_final: 0.7473 (p0) REVERT: g 51 GLU cc_start: 0.6929 (mm-30) cc_final: 0.6398 (tp30) REVERT: j 27 GLU cc_start: 0.5862 (tm-30) cc_final: 0.5602 (tm-30) REVERT: m 25 ILE cc_start: 0.7352 (mp) cc_final: 0.7094 (mp) outliers start: 44 outliers final: 30 residues processed: 197 average time/residue: 0.3010 time to fit residues: 88.6643 Evaluate side-chains 198 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 165 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 126 PHE Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain b residue 189 THR Chi-restraints excluded: chain c residue 10 LEU Chi-restraints excluded: chain c residue 45 GLU Chi-restraints excluded: chain c residue 65 ILE Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 93 LEU Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain c residue 189 ASP Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain g residue 31 MET Chi-restraints excluded: chain g residue 54 SER Chi-restraints excluded: chain g residue 66 ILE Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 62 ASN Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 95 GLU Chi-restraints excluded: chain i residue 100 LEU Chi-restraints excluded: chain i residue 109 ASP Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 17 VAL Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain m residue 19 LEU Chi-restraints excluded: chain m residue 27 THR Chi-restraints excluded: chain n residue 4 THR Chi-restraints excluded: chain s residue 38 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 73 optimal weight: 0.3980 chunk 31 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 58 optimal weight: 0.3980 chunk 10 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 122 GLN ** c 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 67 ASN g 142 HIS i 29 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 18274 Z= 0.322 Angle : 0.674 10.814 26924 Z= 0.345 Chirality : 0.039 0.231 3387 Planarity : 0.005 0.071 1703 Dihedral : 22.976 178.513 8174 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.70 % Favored : 88.30 % Rotamer: Outliers : 6.65 % Allowed : 25.80 % Favored : 67.55 % 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: -2.52 (0.29), residues: 855 helix: -0.16 (0.31), residues: 304 sheet: -1.54 (0.46), residues: 137 loop : -2.99 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP c 200 HIS 0.009 0.002 HIS s 14 PHE 0.023 0.002 PHE s 74 TYR 0.012 0.001 TYR n 21 ARG 0.010 0.001 ARG i 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 166 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 189 THR cc_start: 0.4352 (OUTLIER) cc_final: 0.4065 (p) REVERT: c 45 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7415 (pt0) REVERT: c 122 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.7158 (mp-120) REVERT: c 200 TRP cc_start: 0.8036 (OUTLIER) cc_final: 0.7357 (m100) REVERT: g 51 GLU cc_start: 0.7162 (mm-30) cc_final: 0.6664 (tp30) REVERT: g 92 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.7148 (mtm180) REVERT: i 49 ASP cc_start: 0.6694 (OUTLIER) cc_final: 0.6045 (m-30) REVERT: s 74 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.7768 (m-80) outliers start: 50 outliers final: 31 residues processed: 194 average time/residue: 0.3219 time to fit residues: 91.6536 Evaluate side-chains 197 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 159 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 101 LEU Chi-restraints excluded: chain b residue 126 PHE Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain b residue 189 THR Chi-restraints excluded: chain c residue 10 LEU Chi-restraints excluded: chain c residue 45 GLU Chi-restraints excluded: chain c residue 65 ILE Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 93 LEU Chi-restraints excluded: chain c residue 122 GLN Chi-restraints excluded: chain c residue 189 ASP Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain g residue 31 MET Chi-restraints excluded: chain g residue 54 SER Chi-restraints excluded: chain g residue 66 ILE Chi-restraints excluded: chain g residue 92 ARG Chi-restraints excluded: chain g residue 115 THR Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 21 VAL Chi-restraints excluded: chain i residue 49 ASP Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 62 ASN Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 77 GLN Chi-restraints excluded: chain i residue 95 GLU Chi-restraints excluded: chain i residue 100 LEU Chi-restraints excluded: chain i residue 109 ASP Chi-restraints excluded: chain j residue 14 ASP Chi-restraints excluded: chain j residue 17 VAL Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain m residue 19 LEU Chi-restraints excluded: chain m residue 27 THR Chi-restraints excluded: chain n residue 61 TRP Chi-restraints excluded: chain s residue 74 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 91 optimal weight: 0.0670 chunk 105 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 76 optimal weight: 0.0370 chunk 57 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 67 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18274 Z= 0.153 Angle : 0.563 9.505 26924 Z= 0.291 Chirality : 0.034 0.228 3387 Planarity : 0.004 0.068 1703 Dihedral : 22.931 178.861 8174 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 4.26 % Allowed : 28.46 % Favored : 67.29 % 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: -2.26 (0.29), residues: 855 helix: 0.13 (0.31), residues: 304 sheet: -1.39 (0.46), residues: 138 loop : -2.90 (0.28), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP c 200 HIS 0.004 0.001 HIS c 175 PHE 0.014 0.001 PHE s 44 TYR 0.007 0.001 TYR b 104 ARG 0.010 0.000 ARG i 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 181 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 131 LYS cc_start: 0.7024 (tppt) cc_final: 0.6535 (tppt) REVERT: c 45 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7098 (pt0) REVERT: c 200 TRP cc_start: 0.7954 (OUTLIER) cc_final: 0.7152 (m100) REVERT: g 69 ILE cc_start: 0.8425 (mt) cc_final: 0.8197 (mt) REVERT: i 57 THR cc_start: 0.8101 (p) cc_final: 0.7888 (p) REVERT: s 34 TRP cc_start: 0.8250 (m100) cc_final: 0.7836 (m100) REVERT: s 74 PHE cc_start: 0.7560 (OUTLIER) cc_final: 0.7276 (m-80) outliers start: 32 outliers final: 18 residues processed: 199 average time/residue: 0.3160 time to fit residues: 92.8625 Evaluate side-chains 193 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 172 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 126 PHE Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain c residue 10 LEU Chi-restraints excluded: chain c residue 45 GLU Chi-restraints excluded: chain c residue 65 ILE Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 189 ASP Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain g residue 31 MET Chi-restraints excluded: chain i residue 62 ASN Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 95 GLU Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain m residue 19 LEU Chi-restraints excluded: chain m residue 27 THR Chi-restraints excluded: chain n residue 61 TRP Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 74 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 79 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 98 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 chunk 120 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 67 ASN i 128 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18274 Z= 0.179 Angle : 0.574 16.116 26924 Z= 0.292 Chirality : 0.035 0.232 3387 Planarity : 0.004 0.068 1703 Dihedral : 22.826 178.893 8174 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 3.86 % Allowed : 29.26 % Favored : 66.89 % 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: -2.08 (0.29), residues: 855 helix: 0.27 (0.32), residues: 302 sheet: -1.30 (0.46), residues: 138 loop : -2.77 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP c 200 HIS 0.004 0.001 HIS c 33 PHE 0.015 0.001 PHE s 44 TYR 0.011 0.001 TYR c 23 ARG 0.007 0.000 ARG i 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 174 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: c 45 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7165 (pt0) REVERT: c 200 TRP cc_start: 0.7865 (OUTLIER) cc_final: 0.7159 (m100) REVERT: g 69 ILE cc_start: 0.8496 (mt) cc_final: 0.8255 (mt) REVERT: j 27 GLU cc_start: 0.5944 (tm-30) cc_final: 0.5622 (tm-30) REVERT: j 53 ARG cc_start: 0.8539 (mtp85) cc_final: 0.8272 (ttm-80) REVERT: s 34 TRP cc_start: 0.8284 (m100) cc_final: 0.7843 (m100) REVERT: s 74 PHE cc_start: 0.7524 (OUTLIER) cc_final: 0.7253 (m-80) outliers start: 29 outliers final: 22 residues processed: 187 average time/residue: 0.3060 time to fit residues: 85.6667 Evaluate side-chains 193 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 168 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 101 LEU Chi-restraints excluded: chain b residue 126 PHE Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain c residue 10 LEU Chi-restraints excluded: chain c residue 45 GLU Chi-restraints excluded: chain c residue 65 ILE Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 108 VAL Chi-restraints excluded: chain c residue 189 ASP Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain g residue 31 MET Chi-restraints excluded: chain g residue 66 ILE Chi-restraints excluded: chain g residue 142 HIS Chi-restraints excluded: chain i residue 62 ASN Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 95 GLU Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain m residue 19 LEU Chi-restraints excluded: chain m residue 27 THR Chi-restraints excluded: chain n residue 61 TRP Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 74 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 120 optimal weight: 0.5980 chunk 70 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 110 optimal weight: 0.0010 chunk 76 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18274 Z= 0.157 Angle : 0.562 14.013 26924 Z= 0.285 Chirality : 0.034 0.232 3387 Planarity : 0.004 0.066 1703 Dihedral : 22.763 179.195 8174 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 3.86 % Allowed : 28.19 % Favored : 67.95 % 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: -1.95 (0.29), residues: 855 helix: 0.28 (0.32), residues: 309 sheet: -1.14 (0.46), residues: 138 loop : -2.69 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP c 200 HIS 0.003 0.001 HIS c 33 PHE 0.014 0.001 PHE s 44 TYR 0.008 0.001 TYR b 104 ARG 0.013 0.000 ARG i 102 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 179 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 131 LYS cc_start: 0.6938 (tppt) cc_final: 0.6532 (tptm) REVERT: c 45 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.7061 (pt0) REVERT: c 200 TRP cc_start: 0.7799 (OUTLIER) cc_final: 0.7092 (m100) REVERT: g 69 ILE cc_start: 0.8466 (mt) cc_final: 0.8222 (mt) REVERT: j 27 GLU cc_start: 0.5853 (tm-30) cc_final: 0.5547 (tm-30) REVERT: j 53 ARG cc_start: 0.8463 (mtp85) cc_final: 0.8248 (ttm-80) REVERT: m 109 ARG cc_start: 0.8221 (mtp85) cc_final: 0.7976 (mmm-85) REVERT: s 34 TRP cc_start: 0.8298 (m100) cc_final: 0.7892 (m100) REVERT: s 74 PHE cc_start: 0.7579 (OUTLIER) cc_final: 0.7370 (m-80) outliers start: 29 outliers final: 22 residues processed: 194 average time/residue: 0.3282 time to fit residues: 93.8797 Evaluate side-chains 197 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 172 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 101 LEU Chi-restraints excluded: chain b residue 126 PHE Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain c residue 10 LEU Chi-restraints excluded: chain c residue 45 GLU Chi-restraints excluded: chain c residue 65 ILE Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 189 ASP Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain g residue 31 MET Chi-restraints excluded: chain g residue 142 HIS Chi-restraints excluded: chain i residue 62 ASN Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 95 GLU Chi-restraints excluded: chain i residue 109 ASP Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain m residue 19 LEU Chi-restraints excluded: chain m residue 27 THR Chi-restraints excluded: chain n residue 61 TRP Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 74 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 103 optimal weight: 0.2980 chunk 10 optimal weight: 9.9990 chunk 79 optimal weight: 0.0670 chunk 63 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18274 Z= 0.148 Angle : 0.550 14.046 26924 Z= 0.278 Chirality : 0.033 0.234 3387 Planarity : 0.004 0.067 1703 Dihedral : 22.700 179.227 8174 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 4.12 % Allowed : 28.06 % Favored : 67.82 % 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: -1.72 (0.30), residues: 855 helix: 0.52 (0.32), residues: 308 sheet: -0.93 (0.47), residues: 138 loop : -2.61 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP c 200 HIS 0.004 0.001 HIS m 91 PHE 0.014 0.001 PHE s 44 TYR 0.008 0.001 TYR b 104 ARG 0.006 0.000 ARG i 102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 174 time to evaluate : 1.221 Fit side-chains revert: symmetry clash REVERT: b 131 LYS cc_start: 0.7047 (tppt) cc_final: 0.6635 (tptm) REVERT: c 45 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6449 (pt0) REVERT: c 200 TRP cc_start: 0.7752 (OUTLIER) cc_final: 0.7014 (m100) REVERT: g 69 ILE cc_start: 0.8450 (mt) cc_final: 0.8221 (mt) REVERT: i 39 GLU cc_start: 0.5537 (tt0) cc_final: 0.5231 (tt0) REVERT: j 53 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.8215 (ttm-80) REVERT: m 109 ARG cc_start: 0.8245 (mtp85) cc_final: 0.7987 (mmm-85) REVERT: s 34 TRP cc_start: 0.8319 (m100) cc_final: 0.7892 (m100) REVERT: s 74 PHE cc_start: 0.7605 (OUTLIER) cc_final: 0.7392 (m-80) outliers start: 31 outliers final: 22 residues processed: 188 average time/residue: 0.3249 time to fit residues: 89.1124 Evaluate side-chains 197 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 171 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain c residue 10 LEU Chi-restraints excluded: chain c residue 45 GLU Chi-restraints excluded: chain c residue 65 ILE Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 108 VAL Chi-restraints excluded: chain c residue 189 ASP Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain g residue 31 MET Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain g residue 142 HIS Chi-restraints excluded: chain i residue 62 ASN Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 95 GLU Chi-restraints excluded: chain i residue 109 ASP Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 53 ARG Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain m residue 19 LEU Chi-restraints excluded: chain m residue 27 THR Chi-restraints excluded: chain n residue 61 TRP Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 74 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 103 optimal weight: 0.0570 chunk 43 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 90 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 142 HIS j 64 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.120688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.098903 restraints weight = 31407.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.100059 restraints weight = 23594.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.101250 restraints weight = 17854.510| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 18274 Z= 0.329 Angle : 0.693 14.912 26924 Z= 0.350 Chirality : 0.039 0.265 3387 Planarity : 0.005 0.067 1703 Dihedral : 22.791 179.465 8174 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 4.12 % Allowed : 28.59 % Favored : 67.29 % 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: -2.03 (0.29), residues: 855 helix: 0.26 (0.31), residues: 304 sheet: -0.96 (0.45), residues: 145 loop : -2.87 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP c 200 HIS 0.005 0.001 HIS c 33 PHE 0.024 0.002 PHE s 44 TYR 0.015 0.002 TYR i 96 ARG 0.012 0.001 ARG i 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2796.31 seconds wall clock time: 53 minutes 25.81 seconds (3205.81 seconds total)