Starting phenix.real_space_refine on Sat Nov 16 19:50:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9j_34569/11_2024/8h9j_34569.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9j_34569/11_2024/8h9j_34569.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9j_34569/11_2024/8h9j_34569.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9j_34569/11_2024/8h9j_34569.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9j_34569/11_2024/8h9j_34569.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9j_34569/11_2024/8h9j_34569.cif" } resolution = 3.26 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= 0.014 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: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 7930 2.51 5 N 1932 2.21 5 O 2157 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 94 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 12082 Number of models: 1 Model: "" Number of chains: 19 Chain: "6" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "7" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "8" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "1" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "2" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "3" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "4" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "5" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "G" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1485 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 5, 'TRANS': 185} Chain: "H" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 975 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "I" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 354 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "K" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 6, 'TRANS': 88} Chain: "M" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 311 Classifications: {'peptide': 36} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 30} Chain: "N" Number of atoms: 1718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1718 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 208} Chain: "P" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 344 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "R" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 621 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 604 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 4, 'TRANS': 72} Chain: "T" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 346 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 39} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 307 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 5, 'TRANS': 32} Time building chain proxies: 9.78, per 1000 atoms: 0.81 Number of scatterers: 12082 At special positions: 0 Unit cell: (125.56, 87.6, 137.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 2157 8.00 N 1932 7.00 C 7930 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 - 3.00 Amino acid : True - 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: 3.27 Conformation dependent library (CDL) restraints added in 1.7 seconds 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2896 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 4 sheets defined 77.8% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain '6' and resid 1 through 17 removed outlier: 4.121A pdb=" N GLY 6 17 " --> pdb=" O ALA 6 13 " (cutoff:3.500A) Processing helix chain '6' and resid 18 through 39 Processing helix chain '6' and resid 42 through 73 Processing helix chain '7' and resid 2 through 17 removed outlier: 4.122A pdb=" N GLY 7 17 " --> pdb=" O ALA 7 13 " (cutoff:3.500A) Processing helix chain '7' and resid 18 through 39 Processing helix chain '7' and resid 42 through 73 Processing helix chain '8' and resid 2 through 17 removed outlier: 4.121A pdb=" N GLY 8 17 " --> pdb=" O ALA 8 13 " (cutoff:3.500A) Processing helix chain '8' and resid 18 through 39 Processing helix chain '8' and resid 42 through 73 Processing helix chain '1' and resid 2 through 17 removed outlier: 4.122A pdb=" N GLY 1 17 " --> pdb=" O ALA 1 13 " (cutoff:3.500A) Processing helix chain '1' and resid 18 through 39 Processing helix chain '1' and resid 42 through 73 Processing helix chain '2' and resid 2 through 17 removed outlier: 4.122A pdb=" N GLY 2 17 " --> pdb=" O ALA 2 13 " (cutoff:3.500A) Processing helix chain '2' and resid 18 through 39 Processing helix chain '2' and resid 42 through 73 Processing helix chain '3' and resid 2 through 17 removed outlier: 4.121A pdb=" N GLY 3 17 " --> pdb=" O ALA 3 13 " (cutoff:3.500A) Processing helix chain '3' and resid 18 through 39 Processing helix chain '3' and resid 42 through 73 Processing helix chain '4' and resid 2 through 17 removed outlier: 4.122A pdb=" N GLY 4 17 " --> pdb=" O ALA 4 13 " (cutoff:3.500A) Processing helix chain '4' and resid 18 through 39 Processing helix chain '4' and resid 42 through 73 Processing helix chain '5' and resid 2 through 17 removed outlier: 4.122A pdb=" N GLY 5 17 " --> pdb=" O ALA 5 13 " (cutoff:3.500A) Processing helix chain '5' and resid 18 through 39 Processing helix chain '5' and resid 42 through 73 Processing helix chain 'G' and resid 33 through 48 removed outlier: 4.097A pdb=" N LYS G 39 " --> pdb=" O GLU G 35 " (cutoff:3.500A) Proline residue: G 40 - end of helix Processing helix chain 'G' and resid 49 through 55 Processing helix chain 'G' and resid 80 through 99 Processing helix chain 'G' and resid 109 through 118 removed outlier: 4.339A pdb=" N ARG G 118 " --> pdb=" O GLY G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 150 removed outlier: 3.538A pdb=" N ALA G 141 " --> pdb=" O THR G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 187 Processing helix chain 'G' and resid 188 through 193 Processing helix chain 'G' and resid 197 through 221 Processing helix chain 'H' and resid 101 through 103 No H-bonds generated for 'chain 'H' and resid 101 through 103' Processing helix chain 'H' and resid 104 through 122 removed outlier: 3.966A pdb=" N ALA H 108 " --> pdb=" O ASP H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 146 Processing helix chain 'I' and resid 3 through 8 Processing helix chain 'I' and resid 11 through 26 Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.956A pdb=" N ALA I 33 " --> pdb=" O THR I 29 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ASN I 34 " --> pdb=" O GLU I 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 30 Proline residue: K 27 - end of helix Processing helix chain 'K' and resid 31 through 48 removed outlier: 4.635A pdb=" N TYR K 35 " --> pdb=" O VAL K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 96 removed outlier: 3.631A pdb=" N PHE K 58 " --> pdb=" O SER K 54 " (cutoff:3.500A) Proline residue: K 76 - end of helix Processing helix chain 'M' and resid 131 through 139 Processing helix chain 'M' and resid 140 through 143 removed outlier: 3.540A pdb=" N LYS M 143 " --> pdb=" O PRO M 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 140 through 143' Processing helix chain 'N' and resid 5 through 10 removed outlier: 4.350A pdb=" N SER N 8 " --> pdb=" O LEU N 5 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE N 10 " --> pdb=" O ALA N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 26 Processing helix chain 'N' and resid 27 through 31 Processing helix chain 'N' and resid 40 through 59 removed outlier: 3.677A pdb=" N THR N 59 " --> pdb=" O LYS N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 67 Processing helix chain 'N' and resid 68 through 86 Processing helix chain 'N' and resid 93 through 96 Processing helix chain 'N' and resid 97 through 119 Proline residue: N 107 - end of helix removed outlier: 3.853A pdb=" N SER N 119 " --> pdb=" O MET N 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 120 through 128 removed outlier: 4.015A pdb=" N PHE N 128 " --> pdb=" O ALA N 124 " (cutoff:3.500A) Processing helix chain 'N' and resid 134 through 136 No H-bonds generated for 'chain 'N' and resid 134 through 136' Processing helix chain 'N' and resid 137 through 181 Proline residue: N 153 - end of helix removed outlier: 3.815A pdb=" N ASN N 163 " --> pdb=" O ARG N 159 " (cutoff:3.500A) Processing helix chain 'N' and resid 185 through 225 Processing helix chain 'P' and resid 4 through 9 removed outlier: 3.578A pdb=" N ASN P 8 " --> pdb=" O SER P 4 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 20 removed outlier: 3.686A pdb=" N LYS P 19 " --> pdb=" O PRO P 15 " (cutoff:3.500A) Processing helix chain 'P' and resid 21 through 41 Processing helix chain 'R' and resid 26 through 32 removed outlier: 3.531A pdb=" N LEU R 30 " --> pdb=" O PRO R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 35 through 55 Processing helix chain 'R' and resid 62 through 80 removed outlier: 4.372A pdb=" N VAL R 68 " --> pdb=" O GLY R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 85 Processing helix chain 'R' and resid 86 through 88 No H-bonds generated for 'chain 'R' and resid 86 through 88' Processing helix chain 'S' and resid 27 through 37 Processing helix chain 'S' and resid 44 through 62 Processing helix chain 'S' and resid 63 through 67 Processing helix chain 'S' and resid 68 through 95 removed outlier: 3.502A pdb=" N ARG S 95 " --> pdb=" O ILE S 91 " (cutoff:3.500A) Processing helix chain 'T' and resid 8 through 43 Proline residue: T 35 - end of helix Processing helix chain 'T' and resid 44 through 45 No H-bonds generated for 'chain 'T' and resid 44 through 45' Processing helix chain 'Q' and resid 1 through 5 Processing helix chain 'Q' and resid 9 through 22 Proline residue: Q 15 - end of helix Processing helix chain 'Q' and resid 22 through 30 removed outlier: 3.579A pdb=" N ASN Q 30 " --> pdb=" O LEU Q 26 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 171 through 179 removed outlier: 5.218A pdb=" N ASN G 163 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N HIS G 66 " --> pdb=" O MET G 104 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N VAL G 106 " --> pdb=" O HIS G 66 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU G 68 " --> pdb=" O VAL G 106 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ILE G 108 " --> pdb=" O LEU G 68 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLY G 70 " --> pdb=" O ILE G 108 " (cutoff:3.500A) removed outlier: 9.714A pdb=" N VAL G 126 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU G 105 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N PHE G 128 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLY G 107 " --> pdb=" O PHE G 128 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 43 through 47 removed outlier: 3.615A pdb=" N ALA H 31 " --> pdb=" O PHE H 18 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N SER H 17 " --> pdb=" O VAL H 90 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LEU H 92 " --> pdb=" O SER H 17 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 43 through 47 removed outlier: 7.113A pdb=" N LEU H 62 " --> pdb=" O PRO H 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 12 through 13 966 hydrogen bonds defined for protein. 2847 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.92 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3673 1.34 - 1.46: 2307 1.46 - 1.57: 6228 1.57 - 1.69: 0 1.69 - 1.81: 115 Bond restraints: 12323 Sorted by residual: bond pdb=" N ARG 5 38 " pdb=" CA ARG 5 38 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.27e-02 6.20e+03 7.24e+00 bond pdb=" N ILE 3 2 " pdb=" CA ILE 3 2 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.30e-02 5.92e+03 6.99e+00 bond pdb=" N ILE 1 2 " pdb=" CA ILE 1 2 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.30e-02 5.92e+03 6.90e+00 bond pdb=" N ILE 8 2 " pdb=" CA ILE 8 2 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.30e-02 5.92e+03 6.82e+00 bond pdb=" N ILE 2 2 " pdb=" CA ILE 2 2 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.30e-02 5.92e+03 6.79e+00 ... (remaining 12318 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 15788 1.71 - 3.42: 786 3.42 - 5.13: 90 5.13 - 6.84: 19 6.84 - 8.55: 4 Bond angle restraints: 16687 Sorted by residual: angle pdb=" N THR Q 7 " pdb=" CA THR Q 7 " pdb=" C THR Q 7 " ideal model delta sigma weight residual 114.56 106.01 8.55 1.27e+00 6.20e-01 4.53e+01 angle pdb=" C VAL T 5 " pdb=" N GLN T 6 " pdb=" CA GLN T 6 " ideal model delta sigma weight residual 121.31 127.06 -5.75 1.49e+00 4.50e-01 1.49e+01 angle pdb=" N GLN T 6 " pdb=" CA GLN T 6 " pdb=" C GLN T 6 " ideal model delta sigma weight residual 110.35 115.71 -5.36 1.40e+00 5.10e-01 1.47e+01 angle pdb=" C ILE P 9 " pdb=" N TRP P 10 " pdb=" CA TRP P 10 " ideal model delta sigma weight residual 122.79 116.51 6.28 1.78e+00 3.16e-01 1.24e+01 angle pdb=" N PHE N 26 " pdb=" CA PHE N 26 " pdb=" C PHE N 26 " ideal model delta sigma weight residual 109.81 116.94 -7.13 2.21e+00 2.05e-01 1.04e+01 ... (remaining 16682 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.89: 6380 14.89 - 29.79: 642 29.79 - 44.68: 187 44.68 - 59.58: 31 59.58 - 74.47: 8 Dihedral angle restraints: 7248 sinusoidal: 2710 harmonic: 4538 Sorted by residual: dihedral pdb=" CA LYS N 120 " pdb=" C LYS N 120 " pdb=" N ILE N 121 " pdb=" CA ILE N 121 " ideal model delta harmonic sigma weight residual -180.00 -158.98 -21.02 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA ARG N 118 " pdb=" C ARG N 118 " pdb=" N SER N 119 " pdb=" CA SER N 119 " ideal model delta harmonic sigma weight residual 180.00 161.41 18.59 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA MET N 57 " pdb=" C MET N 57 " pdb=" N MET N 58 " pdb=" CA MET N 58 " ideal model delta harmonic sigma weight residual 180.00 -163.47 -16.53 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 7245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1030 0.035 - 0.070: 632 0.070 - 0.106: 215 0.106 - 0.141: 57 0.141 - 0.176: 37 Chirality restraints: 1971 Sorted by residual: chirality pdb=" CA LEU 8 70 " pdb=" N LEU 8 70 " pdb=" C LEU 8 70 " pdb=" CB LEU 8 70 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.76e-01 chirality pdb=" CA THR N 135 " pdb=" N THR N 135 " pdb=" C THR N 135 " pdb=" CB THR N 135 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.68e-01 chirality pdb=" CA LEU 2 70 " pdb=" N LEU 2 70 " pdb=" C LEU 2 70 " pdb=" CB LEU 2 70 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.29e-01 ... (remaining 1968 not shown) Planarity restraints: 2065 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 133 " 0.273 9.50e-02 1.11e+02 1.23e-01 9.23e+00 pdb=" NE ARG G 133 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG G 133 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG G 133 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG G 133 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS T 12 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.20e+00 pdb=" C LYS T 12 " -0.035 2.00e-02 2.50e+03 pdb=" O LYS T 12 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU T 13 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG 8 38 " 0.183 9.50e-02 1.11e+02 8.22e-02 4.14e+00 pdb=" NE ARG 8 38 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG 8 38 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG 8 38 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG 8 38 " 0.007 2.00e-02 2.50e+03 ... (remaining 2062 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2849 2.77 - 3.30: 13032 3.30 - 3.83: 20715 3.83 - 4.37: 24464 4.37 - 4.90: 41016 Nonbonded interactions: 102076 Sorted by model distance: nonbonded pdb=" OD1 ASN M 136 " pdb=" OG1 THR M 142 " model vdw 2.233 3.040 nonbonded pdb=" O MET N 181 " pdb=" OG1 THR N 189 " model vdw 2.235 3.040 nonbonded pdb=" OH TYR R 50 " pdb=" O GLY R 64 " model vdw 2.256 3.040 nonbonded pdb=" O SER H 88 " pdb=" OG SER H 88 " model vdw 2.265 3.040 nonbonded pdb=" ND2 ASN N 101 " pdb=" OG1 THR N 161 " model vdw 2.278 3.120 ... (remaining 102071 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' } 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: 10.050 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 32.580 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 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 : 0.010 0.076 12323 Z= 0.671 Angle : 0.846 8.549 16687 Z= 0.497 Chirality : 0.052 0.176 1971 Planarity : 0.006 0.123 2065 Dihedral : 13.196 74.472 4352 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: -3.26 (0.18), residues: 1558 helix: -1.78 (0.13), residues: 1113 sheet: -1.57 (0.53), residues: 87 loop : -2.90 (0.29), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP P 10 HIS 0.007 0.002 HIS N 127 PHE 0.024 0.002 PHE H 45 TYR 0.024 0.002 TYR T 30 ARG 0.004 0.001 ARG 7 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 395 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 60 MET cc_start: 0.7499 (mmm) cc_final: 0.7072 (mpp) REVERT: G 77 LEU cc_start: 0.7792 (mp) cc_final: 0.7385 (tt) REVERT: I 13 ILE cc_start: 0.8979 (mm) cc_final: 0.8739 (mm) REVERT: T 36 ARG cc_start: 0.6748 (mpp80) cc_final: 0.6447 (mpp80) REVERT: Q 1 MET cc_start: 0.7790 (mmm) cc_final: 0.7018 (mmm) outliers start: 0 outliers final: 0 residues processed: 395 average time/residue: 0.2728 time to fit residues: 149.1984 Evaluate side-chains 321 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 137 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 44 GLN G 120 HIS G 163 ASN H 66 HIS H 85 ASN H 111 ASN H 116 GLN I 42 ASN K 23 GLN M 159 ASN N 4 ASN N 46 GLN N 47 GLN N 61 HIS N 123 ASN N 225 ASN P 8 ASN S 50 GLN S 66 GLN Q 32 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12323 Z= 0.224 Angle : 0.617 9.591 16687 Z= 0.327 Chirality : 0.043 0.173 1971 Planarity : 0.004 0.051 2065 Dihedral : 4.652 60.434 1685 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.55 % Allowed : 15.72 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.20), residues: 1558 helix: 0.15 (0.14), residues: 1148 sheet: -1.42 (0.58), residues: 72 loop : -1.72 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP S 30 HIS 0.008 0.001 HIS N 127 PHE 0.027 0.002 PHE R 79 TYR 0.018 0.001 TYR K 74 ARG 0.008 0.001 ARG G 118 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 335 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 7 75 MET cc_start: 0.6479 (tpp) cc_final: 0.5902 (mtt) REVERT: 5 75 MET cc_start: 0.6528 (ppp) cc_final: 0.6249 (ptt) REVERT: G 211 ASN cc_start: 0.8234 (m-40) cc_final: 0.7996 (m-40) REVERT: H 102 MET cc_start: 0.5803 (ttm) cc_final: 0.5553 (ttm) REVERT: N 159 ARG cc_start: 0.9049 (ttm110) cc_final: 0.8724 (ttm110) REVERT: R 29 ILE cc_start: 0.8351 (mp) cc_final: 0.7845 (tp) outliers start: 32 outliers final: 17 residues processed: 350 average time/residue: 0.2630 time to fit residues: 129.1365 Evaluate side-chains 310 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 293 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 16 VAL Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 8 residue 54 PHE Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 31 SER Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 4 residue 3 ASP Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 71 ILE Chi-restraints excluded: chain 5 residue 72 LEU Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain H residue 114 LYS Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 4 ASN Chi-restraints excluded: chain T residue 5 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 76 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 114 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 137 optimal weight: 7.9990 chunk 148 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 136 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 45 GLN 3 45 GLN 4 45 GLN 5 45 GLN H 85 ASN M 159 ASN P 8 ASN S 57 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 12323 Z= 0.314 Angle : 0.629 8.184 16687 Z= 0.331 Chirality : 0.045 0.178 1971 Planarity : 0.004 0.051 2065 Dihedral : 4.619 63.223 1685 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.91 % Allowed : 17.72 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.21), residues: 1558 helix: 0.89 (0.15), residues: 1148 sheet: -1.27 (0.58), residues: 72 loop : -1.39 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 28 HIS 0.007 0.001 HIS N 127 PHE 0.034 0.002 PHE 2 69 TYR 0.020 0.001 TYR T 30 ARG 0.003 0.000 ARG H 128 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 315 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 7 LYS cc_start: 0.8023 (mmtp) cc_final: 0.7722 (mmtp) REVERT: 5 75 MET cc_start: 0.6700 (ppp) cc_final: 0.6463 (ptt) REVERT: N 36 TYR cc_start: 0.7998 (m-10) cc_final: 0.7520 (m-10) REVERT: N 159 ARG cc_start: 0.9112 (ttm110) cc_final: 0.8770 (ttm110) REVERT: R 29 ILE cc_start: 0.8343 (mp) cc_final: 0.7911 (tp) outliers start: 49 outliers final: 34 residues processed: 338 average time/residue: 0.2764 time to fit residues: 132.1198 Evaluate side-chains 330 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 296 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 16 VAL Chi-restraints excluded: chain 7 residue 45 GLN Chi-restraints excluded: chain 7 residue 54 PHE Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain 8 residue 27 THR Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 8 residue 54 PHE Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 31 SER Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 3 residue 16 VAL Chi-restraints excluded: chain 3 residue 25 ILE Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 4 residue 3 ASP Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 4 residue 71 ILE Chi-restraints excluded: chain 5 residue 4 THR Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 65 LEU Chi-restraints excluded: chain 5 residue 71 ILE Chi-restraints excluded: chain 5 residue 72 LEU Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain H residue 114 LYS Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 130 MET Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 19 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 135 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 137 optimal weight: 0.6980 chunk 145 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 45 GLN 3 45 GLN 5 45 GLN ** G 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 4 ASN P 8 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12323 Z= 0.205 Angle : 0.574 7.525 16687 Z= 0.303 Chirality : 0.042 0.181 1971 Planarity : 0.004 0.042 2065 Dihedral : 4.517 60.131 1685 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 4.15 % Allowed : 18.68 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 1.06 (0.21), residues: 1558 helix: 1.41 (0.15), residues: 1147 sheet: -1.07 (0.58), residues: 72 loop : -1.22 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 28 HIS 0.007 0.001 HIS N 127 PHE 0.027 0.001 PHE R 79 TYR 0.024 0.001 TYR T 30 ARG 0.002 0.000 ARG G 118 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 314 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 71 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.8138 (mm) REVERT: 3 32 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7859 (tp) REVERT: 5 7 LYS cc_start: 0.8003 (mmtp) cc_final: 0.7763 (mmtp) REVERT: G 147 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7647 (tp30) REVERT: H 128 ARG cc_start: 0.8199 (mtp85) cc_final: 0.7997 (mtp85) REVERT: K 87 GLU cc_start: 0.7093 (mp0) cc_final: 0.6824 (mp0) REVERT: N 36 TYR cc_start: 0.7973 (m-10) cc_final: 0.7577 (m-10) REVERT: N 159 ARG cc_start: 0.9093 (ttm110) cc_final: 0.8777 (ttm110) REVERT: P 7 LYS cc_start: 0.7358 (mtmm) cc_final: 0.7014 (mtmm) REVERT: R 29 ILE cc_start: 0.8368 (mp) cc_final: 0.7931 (tp) REVERT: R 69 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7457 (mp) REVERT: T 13 LEU cc_start: 0.6994 (mm) cc_final: 0.6708 (mm) outliers start: 52 outliers final: 29 residues processed: 340 average time/residue: 0.2604 time to fit residues: 124.4087 Evaluate side-chains 323 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 291 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 8 residue 45 GLN Chi-restraints excluded: chain 8 residue 54 PHE Chi-restraints excluded: chain 1 residue 2 ILE Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 2 residue 31 SER Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 4 residue 3 ASP Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 45 GLN Chi-restraints excluded: chain 5 residue 71 ILE Chi-restraints excluded: chain 5 residue 72 LEU Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain H residue 114 LYS Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 130 MET Chi-restraints excluded: chain N residue 4 ASN Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 19 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 121 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 131 optimal weight: 0.0570 chunk 36 optimal weight: 4.9990 overall best weight: 1.0902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 45 GLN 5 45 GLN ** G 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12323 Z= 0.232 Angle : 0.582 7.661 16687 Z= 0.305 Chirality : 0.042 0.185 1971 Planarity : 0.004 0.045 2065 Dihedral : 4.499 61.280 1685 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 4.63 % Allowed : 20.19 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 1.29 (0.21), residues: 1558 helix: 1.58 (0.15), residues: 1142 sheet: -0.86 (0.56), residues: 80 loop : -1.14 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 28 HIS 0.007 0.001 HIS N 127 PHE 0.027 0.002 PHE R 79 TYR 0.027 0.001 TYR T 30 ARG 0.009 0.000 ARG G 118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 299 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 71 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8133 (mm) REVERT: 4 63 PHE cc_start: 0.8478 (m-10) cc_final: 0.8167 (m-80) REVERT: 5 7 LYS cc_start: 0.8070 (mmtp) cc_final: 0.7813 (mmtp) REVERT: G 147 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7635 (tp30) REVERT: H 128 ARG cc_start: 0.8172 (mtp85) cc_final: 0.7957 (mtp85) REVERT: N 36 TYR cc_start: 0.7972 (m-10) cc_final: 0.7588 (m-10) REVERT: N 159 ARG cc_start: 0.9159 (ttm110) cc_final: 0.8838 (ttm110) REVERT: R 29 ILE cc_start: 0.8319 (mp) cc_final: 0.7929 (tp) REVERT: R 69 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7434 (mp) REVERT: R 82 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8207 (mmtt) outliers start: 58 outliers final: 39 residues processed: 329 average time/residue: 0.2819 time to fit residues: 130.5152 Evaluate side-chains 334 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 292 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 65 LEU Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 16 VAL Chi-restraints excluded: chain 7 residue 54 PHE Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 8 residue 54 PHE Chi-restraints excluded: chain 1 residue 2 ILE Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 31 SER Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 3 residue 25 ILE Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 4 residue 3 ASP Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 71 ILE Chi-restraints excluded: chain 5 residue 72 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 114 LYS Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 130 MET Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 2 LEU Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 82 LYS Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain Q residue 11 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 49 optimal weight: 5.9990 chunk 131 optimal weight: 0.2980 chunk 28 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 36 optimal weight: 0.5980 chunk 146 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 45 GLN 5 39 ASN ** G 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 ASN ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12323 Z= 0.195 Angle : 0.566 9.701 16687 Z= 0.295 Chirality : 0.042 0.191 1971 Planarity : 0.004 0.043 2065 Dihedral : 4.430 58.584 1685 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.59 % Allowed : 21.55 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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 (0.21), residues: 1558 helix: 1.81 (0.15), residues: 1137 sheet: -0.80 (0.56), residues: 80 loop : -0.87 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP R 28 HIS 0.007 0.001 HIS N 127 PHE 0.025 0.001 PHE R 79 TYR 0.031 0.001 TYR T 30 ARG 0.002 0.000 ARG G 118 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 299 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 71 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.8097 (mm) REVERT: 4 63 PHE cc_start: 0.8418 (m-10) cc_final: 0.8127 (m-80) REVERT: 5 7 LYS cc_start: 0.8012 (mmtp) cc_final: 0.7794 (mmtp) REVERT: G 147 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7623 (tp30) REVERT: G 189 SER cc_start: 0.7340 (t) cc_final: 0.7106 (p) REVERT: K 87 GLU cc_start: 0.7110 (mp0) cc_final: 0.6904 (mp0) REVERT: N 36 TYR cc_start: 0.7934 (m-10) cc_final: 0.7598 (m-10) REVERT: N 159 ARG cc_start: 0.9176 (ttm110) cc_final: 0.8874 (ttm110) REVERT: R 82 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8201 (mmtt) outliers start: 45 outliers final: 34 residues processed: 323 average time/residue: 0.2606 time to fit residues: 117.4808 Evaluate side-chains 327 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 291 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 28 VAL Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 8 residue 54 PHE Chi-restraints excluded: chain 8 residue 58 GLU Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 31 SER Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 4 residue 3 ASP Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 71 ILE Chi-restraints excluded: chain 5 residue 72 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 114 LYS Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 130 MET Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 14 LYS Chi-restraints excluded: chain R residue 82 LYS Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain Q residue 11 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 140 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 106 optimal weight: 0.2980 chunk 82 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 145 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 39 ASN ** 1 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 45 GLN ** G 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 4 ASN P 8 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12323 Z= 0.257 Angle : 0.605 9.183 16687 Z= 0.314 Chirality : 0.043 0.207 1971 Planarity : 0.004 0.042 2065 Dihedral : 4.488 61.191 1685 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 4.31 % Allowed : 21.95 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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 (0.21), residues: 1558 helix: 1.80 (0.15), residues: 1136 sheet: -0.77 (0.56), residues: 80 loop : -0.77 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP R 28 HIS 0.007 0.001 HIS N 127 PHE 0.026 0.002 PHE R 79 TYR 0.031 0.001 TYR T 30 ARG 0.011 0.000 ARG G 118 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 299 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 71 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.8113 (mm) REVERT: 4 63 PHE cc_start: 0.8496 (m-10) cc_final: 0.8232 (m-80) REVERT: 5 7 LYS cc_start: 0.7996 (mmtp) cc_final: 0.7780 (mmtp) REVERT: G 46 LEU cc_start: 0.8407 (mm) cc_final: 0.8206 (mt) REVERT: G 147 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7638 (tp30) REVERT: H 128 ARG cc_start: 0.8192 (mtp85) cc_final: 0.7971 (mtp85) REVERT: N 36 TYR cc_start: 0.7982 (m-10) cc_final: 0.7628 (m-10) REVERT: N 147 ILE cc_start: 0.8896 (tp) cc_final: 0.8612 (tp) REVERT: N 159 ARG cc_start: 0.9190 (ttm110) cc_final: 0.8858 (ttm110) REVERT: R 69 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7451 (mp) REVERT: R 82 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8203 (mmtt) REVERT: T 33 LEU cc_start: 0.3393 (OUTLIER) cc_final: 0.2399 (tt) outliers start: 54 outliers final: 38 residues processed: 329 average time/residue: 0.2675 time to fit residues: 124.2019 Evaluate side-chains 324 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 282 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 28 VAL Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 8 residue 54 PHE Chi-restraints excluded: chain 8 residue 58 GLU Chi-restraints excluded: chain 1 residue 2 ILE Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 31 SER Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 3 residue 25 ILE Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 4 residue 3 ASP Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 71 ILE Chi-restraints excluded: chain 5 residue 72 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 182 ASN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 114 LYS Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 130 MET Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 2 LEU Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 82 LYS Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain Q residue 11 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 90 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 132 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 45 GLN ** G 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 23 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 12323 Z= 0.222 Angle : 0.611 9.087 16687 Z= 0.313 Chirality : 0.042 0.224 1971 Planarity : 0.004 0.043 2065 Dihedral : 4.447 59.978 1685 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.75 % Allowed : 23.78 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 1.78 (0.21), residues: 1558 helix: 1.90 (0.15), residues: 1129 sheet: -0.76 (0.56), residues: 78 loop : -0.68 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP R 28 HIS 0.007 0.001 HIS N 127 PHE 0.025 0.001 PHE R 79 TYR 0.027 0.001 TYR T 30 ARG 0.008 0.000 ARG T 36 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 292 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 71 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8133 (mm) REVERT: 4 63 PHE cc_start: 0.8471 (m-10) cc_final: 0.8234 (m-80) REVERT: G 46 LEU cc_start: 0.8367 (mm) cc_final: 0.8153 (mt) REVERT: G 147 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7612 (tp30) REVERT: N 36 TYR cc_start: 0.7954 (m-10) cc_final: 0.7615 (m-10) REVERT: N 147 ILE cc_start: 0.8852 (tp) cc_final: 0.8571 (tp) REVERT: N 159 ARG cc_start: 0.9191 (ttm110) cc_final: 0.8876 (ttm110) REVERT: R 29 ILE cc_start: 0.8274 (mp) cc_final: 0.7848 (tp) REVERT: R 82 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8205 (mmtt) outliers start: 47 outliers final: 35 residues processed: 318 average time/residue: 0.2623 time to fit residues: 116.9391 Evaluate side-chains 317 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 280 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 28 VAL Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 8 residue 54 PHE Chi-restraints excluded: chain 8 residue 58 GLU Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 31 SER Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 3 residue 25 ILE Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 4 residue 3 ASP Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 71 ILE Chi-restraints excluded: chain 5 residue 72 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 182 ASN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 130 MET Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain R residue 82 LYS Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain Q residue 11 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 139 optimal weight: 4.9990 chunk 127 optimal weight: 0.0870 chunk 135 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 59 optimal weight: 0.0020 chunk 106 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 89 optimal weight: 0.3980 chunk 143 optimal weight: 0.7980 overall best weight: 0.3966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12323 Z= 0.178 Angle : 0.598 9.453 16687 Z= 0.303 Chirality : 0.042 0.229 1971 Planarity : 0.004 0.047 2065 Dihedral : 4.377 55.337 1685 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.87 % Allowed : 24.74 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 1.92 (0.21), residues: 1558 helix: 2.00 (0.15), residues: 1130 sheet: -0.71 (0.56), residues: 78 loop : -0.63 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP R 28 HIS 0.007 0.001 HIS N 127 PHE 0.025 0.001 PHE R 79 TYR 0.029 0.001 TYR T 30 ARG 0.010 0.000 ARG G 118 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 291 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 71 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8163 (mm) REVERT: 7 28 VAL cc_start: 0.7944 (OUTLIER) cc_final: 0.7701 (t) REVERT: 4 63 PHE cc_start: 0.8364 (m-10) cc_final: 0.8152 (m-80) REVERT: G 46 LEU cc_start: 0.8278 (mm) cc_final: 0.8063 (mt) REVERT: G 52 TYR cc_start: 0.6682 (m-80) cc_final: 0.6388 (m-80) REVERT: H 79 SER cc_start: 0.8569 (t) cc_final: 0.8314 (p) REVERT: N 36 TYR cc_start: 0.7931 (m-10) cc_final: 0.7580 (m-10) REVERT: N 147 ILE cc_start: 0.8834 (tp) cc_final: 0.8561 (tp) REVERT: N 159 ARG cc_start: 0.9150 (ttm110) cc_final: 0.8838 (ttm110) REVERT: R 29 ILE cc_start: 0.8232 (mp) cc_final: 0.7878 (tp) REVERT: R 82 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8209 (mmtt) outliers start: 36 outliers final: 27 residues processed: 307 average time/residue: 0.2715 time to fit residues: 115.6951 Evaluate side-chains 307 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 277 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 28 VAL Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 8 residue 54 PHE Chi-restraints excluded: chain 8 residue 58 GLU Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 31 SER Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 4 residue 3 ASP Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 71 ILE Chi-restraints excluded: chain 5 residue 72 LEU Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain H residue 114 LYS Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 140 MET Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain R residue 82 LYS Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain Q residue 11 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 87 optimal weight: 0.7980 chunk 68 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 150 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 127 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 45 GLN ** G 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 12323 Z= 0.213 Angle : 0.619 9.864 16687 Z= 0.312 Chirality : 0.042 0.242 1971 Planarity : 0.004 0.045 2065 Dihedral : 4.350 54.480 1685 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.71 % Allowed : 24.90 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 1.91 (0.21), residues: 1558 helix: 2.00 (0.15), residues: 1130 sheet: -1.05 (0.53), residues: 85 loop : -0.58 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP R 28 HIS 0.007 0.001 HIS N 127 PHE 0.025 0.001 PHE R 79 TYR 0.025 0.001 TYR T 30 ARG 0.008 0.001 ARG I 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 279 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 71 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.8175 (mm) REVERT: 5 60 MET cc_start: 0.7601 (mmm) cc_final: 0.7378 (mmt) REVERT: G 46 LEU cc_start: 0.8327 (mm) cc_final: 0.8109 (mt) REVERT: G 52 TYR cc_start: 0.6708 (m-80) cc_final: 0.6464 (m-80) REVERT: N 36 TYR cc_start: 0.7933 (m-10) cc_final: 0.7672 (m-10) REVERT: N 147 ILE cc_start: 0.8854 (tp) cc_final: 0.8589 (tp) REVERT: N 159 ARG cc_start: 0.9166 (ttm110) cc_final: 0.8848 (ttm110) REVERT: R 82 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8212 (mmtt) outliers start: 34 outliers final: 29 residues processed: 296 average time/residue: 0.2743 time to fit residues: 112.8190 Evaluate side-chains 307 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 276 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 28 VAL Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 8 residue 54 PHE Chi-restraints excluded: chain 8 residue 58 GLU Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 31 SER Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 4 residue 3 ASP Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 71 ILE Chi-restraints excluded: chain 5 residue 72 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain H residue 114 LYS Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain R residue 82 LYS Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain Q residue 11 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 36 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 119 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 15 optimal weight: 0.0970 chunk 22 optimal weight: 0.3980 chunk 105 optimal weight: 0.0270 chunk 6 optimal weight: 7.9990 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 44 GLN 3 45 GLN ** G 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.162493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.127422 restraints weight = 17554.377| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.57 r_work: 0.3466 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 12323 Z= 0.180 Angle : 0.611 10.600 16687 Z= 0.306 Chirality : 0.041 0.242 1971 Planarity : 0.004 0.043 2065 Dihedral : 4.290 48.542 1685 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.47 % Allowed : 25.30 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 2.01 (0.21), residues: 1558 helix: 2.08 (0.15), residues: 1130 sheet: -0.96 (0.53), residues: 85 loop : -0.56 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 5 HIS 0.007 0.001 HIS N 127 PHE 0.024 0.001 PHE R 79 TYR 0.027 0.001 TYR T 30 ARG 0.008 0.000 ARG I 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3483.93 seconds wall clock time: 64 minutes 13.01 seconds (3853.01 seconds total)