Starting phenix.real_space_refine on Tue Nov 19 05:30:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afa_11758/11_2024/7afa_11758_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afa_11758/11_2024/7afa_11758.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afa_11758/11_2024/7afa_11758.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afa_11758/11_2024/7afa_11758.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afa_11758/11_2024/7afa_11758_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afa_11758/11_2024/7afa_11758_neut.cif" } resolution = 2.95 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= 0.004 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 456 5.49 5 Mg 25 5.21 5 S 28 5.16 5 C 9812 2.51 5 N 3440 2.21 5 O 4720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 18482 Number of models: 1 Model: "" Number of chains: 11 Chain: "1" Number of atoms: 9758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 9758 Classifications: {'RNA': 456} Modifications used: {'rna2p_pur': 36, 'rna2p_pyr': 34, 'rna3p': 3, 'rna3p_pur': 212, 'rna3p_pyr': 171} Link IDs: {'rna2p': 70, 'rna3p': 385} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1753 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "C" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1653 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 7, 'TRANS': 203} Chain: "G" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1129 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 5, 'TRANS': 138} Chain: "I" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 795 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "M" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "S" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 658 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "1" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Unusual residues: {' MG': 25} Classifications: {'undetermined': 25} Link IDs: {None: 24} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.86, per 1000 atoms: 0.64 Number of scatterers: 18482 At special positions: 0 Unit cell: (136.71, 113.925, 155.155, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 28 16.00 P 456 15.00 Mg 25 11.99 O 4720 8.00 N 3440 7.00 C 9812 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: 5.15 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 18 " 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2038 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 10 sheets defined 50.2% alpha, 19.0% beta 139 base pairs and 235 stacking pairs defined. Time for finding SS restraints: 9.91 Creating SS restraints... Processing helix chain 'B' and resid 5 through 13 removed outlier: 3.707A pdb=" N ALA B 12 " --> pdb=" O ASP B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Proline residue: B 29 - end of helix Processing helix chain 'B' and resid 42 through 63 Proline residue: B 48 - end of helix Processing helix chain 'B' and resid 76 through 86 Processing helix chain 'B' and resid 103 through 124 removed outlier: 3.616A pdb=" N GLN B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 149 Processing helix chain 'B' and resid 169 through 180 Processing helix chain 'B' and resid 192 through 196 removed outlier: 4.226A pdb=" N GLY B 195 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 227 Processing helix chain 'C' and resid 6 through 11 removed outlier: 3.575A pdb=" N ARG C 11 " --> pdb=" O PRO C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 47 removed outlier: 3.510A pdb=" N ASN C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 77 Processing helix chain 'C' and resid 81 through 96 Processing helix chain 'C' and resid 108 through 111 Processing helix chain 'C' and resid 112 through 126 Processing helix chain 'C' and resid 129 through 144 Processing helix chain 'C' and resid 156 through 160 Processing helix chain 'G' and resid 20 through 31 Processing helix chain 'G' and resid 35 through 55 Processing helix chain 'G' and resid 57 through 68 Processing helix chain 'G' and resid 92 through 112 removed outlier: 3.566A pdb=" N ALA G 98 " --> pdb=" O VAL G 94 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY G 112 " --> pdb=" O ALA G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 129 removed outlier: 3.576A pdb=" N GLU G 129 " --> pdb=" O SER G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 144 Processing helix chain 'I' and resid 34 through 39 Processing helix chain 'I' and resid 41 through 48 Processing helix chain 'I' and resid 49 through 55 Processing helix chain 'I' and resid 71 through 91 Processing helix chain 'I' and resid 94 through 101 Processing helix chain 'J' and resid 14 through 33 Processing helix chain 'J' and resid 83 through 90 Processing helix chain 'M' and resid 14 through 20 removed outlier: 3.836A pdb=" N THR M 20 " --> pdb=" O VAL M 16 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 38 Processing helix chain 'M' and resid 49 through 63 removed outlier: 4.162A pdb=" N THR M 55 " --> pdb=" O GLY M 51 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE M 63 " --> pdb=" O GLU M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 84 removed outlier: 3.697A pdb=" N GLY M 84 " --> pdb=" O LEU M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 94 Processing helix chain 'M' and resid 106 through 111 Processing helix chain 'N' and resid 3 through 33 removed outlier: 3.505A pdb=" N LYS N 7 " --> pdb=" O LYS N 3 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS N 19 " --> pdb=" O ALA N 15 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ALA N 22 " --> pdb=" O ASP N 18 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LYS N 23 " --> pdb=" O LYS N 19 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 49 removed outlier: 4.022A pdb=" N GLN N 49 " --> pdb=" O VAL N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 51 No H-bonds generated for 'chain 'N' and resid 50 through 51' Processing helix chain 'N' and resid 52 through 60 Proline residue: N 57 - end of helix Processing helix chain 'N' and resid 82 through 90 Processing helix chain 'S' and resid 12 through 26 Processing helix chain 'S' and resid 41 through 45 Processing helix chain 'S' and resid 63 through 67 Processing helix chain 'S' and resid 70 through 75 Processing sheet with id=AA1, first strand: chain 'B' and resid 16 through 19 removed outlier: 5.604A pdb=" N PHE B 16 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ILE B 41 " --> pdb=" O PHE B 16 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N HIS B 18 " --> pdb=" O HIS B 39 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY B 33 " --> pdb=" O ILE B 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 90 through 92 removed outlier: 5.800A pdb=" N ILE B 67 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VAL B 92 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE B 69 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA B 185 " --> pdb=" O PHE B 198 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 58 removed outlier: 6.751A pdb=" N HIS C 69 " --> pdb=" O SER C 53 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ILE C 55 " --> pdb=" O THR C 67 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N THR C 67 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE C 57 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ARG C 65 " --> pdb=" O ILE C 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 52 through 58 removed outlier: 6.751A pdb=" N HIS C 69 " --> pdb=" O SER C 53 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ILE C 55 " --> pdb=" O THR C 67 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N THR C 67 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE C 57 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ARG C 65 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ALA C 104 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ILE C 68 " --> pdb=" O ALA C 104 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 164 through 171 removed outlier: 6.390A pdb=" N ASP C 181 " --> pdb=" O LYS C 204 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 73 through 78 Processing sheet with id=AA7, first strand: chain 'I' and resid 6 through 12 removed outlier: 6.250A pdb=" N VAL I 29 " --> pdb=" O ILE I 65 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N VAL I 67 " --> pdb=" O VAL I 29 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 35 through 52 removed outlier: 7.225A pdb=" N GLN J 35 " --> pdb=" O VAL J 77 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ASP J 75 " --> pdb=" O ARG J 37 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU J 73 " --> pdb=" O PRO J 39 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N LEU J 71 " --> pdb=" O PRO J 41 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N THR J 69 " --> pdb=" O PRO J 43 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ARG J 45 " --> pdb=" O ILE J 67 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE J 67 " --> pdb=" O ARG J 45 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLU J 47 " --> pdb=" O TYR J 65 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TYR J 65 " --> pdb=" O GLU J 47 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N PHE J 49 " --> pdb=" O ASP J 63 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ASP J 63 " --> pdb=" O PHE J 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 35 through 52 removed outlier: 7.225A pdb=" N GLN J 35 " --> pdb=" O VAL J 77 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ASP J 75 " --> pdb=" O ARG J 37 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU J 73 " --> pdb=" O PRO J 39 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N LEU J 71 " --> pdb=" O PRO J 41 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N THR J 69 " --> pdb=" O PRO J 43 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ARG J 45 " --> pdb=" O ILE J 67 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE J 67 " --> pdb=" O ARG J 45 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLU J 47 " --> pdb=" O TYR J 65 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TYR J 65 " --> pdb=" O GLU J 47 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N PHE J 49 " --> pdb=" O ASP J 63 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ASP J 63 " --> pdb=" O PHE J 49 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 31 through 33 removed outlier: 5.887A pdb=" N LEU S 31 " --> pdb=" O ALA S 50 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N HIS S 52 " --> pdb=" O LEU S 31 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N THR S 33 " --> pdb=" O HIS S 52 " (cutoff:3.500A) 446 hydrogen bonds defined for protein. 1263 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 346 hydrogen bonds 538 hydrogen bond angles 0 basepair planarities 139 basepair parallelities 235 stacking parallelities Total time for adding SS restraints: 9.84 Time building geometry restraints manager: 5.84 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: 3196 1.33 - 1.45: 7085 1.45 - 1.57: 8503 1.57 - 1.69: 911 1.69 - 1.81: 53 Bond restraints: 19748 Sorted by residual: bond pdb=" C5 2MG 1 966 " pdb=" C4 2MG 1 966 " ideal model delta sigma weight residual 1.382 1.459 -0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" C5 2MG 11207 " pdb=" C4 2MG 11207 " ideal model delta sigma weight residual 1.382 1.457 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" N LYS I 22 " pdb=" CA LYS I 22 " ideal model delta sigma weight residual 1.453 1.488 -0.034 9.20e-03 1.18e+04 1.39e+01 bond pdb=" N ILE J 40 " pdb=" CA ILE J 40 " ideal model delta sigma weight residual 1.460 1.492 -0.032 9.30e-03 1.16e+04 1.18e+01 bond pdb=" N VAL G 73 " pdb=" CA VAL G 73 " ideal model delta sigma weight residual 1.458 1.496 -0.039 1.14e-02 7.69e+03 1.15e+01 ... (remaining 19743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 28428 2.71 - 5.42: 414 5.42 - 8.14: 27 8.14 - 10.85: 8 10.85 - 13.56: 1 Bond angle restraints: 28878 Sorted by residual: angle pdb=" N VAL J 57 " pdb=" CA VAL J 57 " pdb=" C VAL J 57 " ideal model delta sigma weight residual 109.34 122.90 -13.56 2.08e+00 2.31e-01 4.25e+01 angle pdb=" N LYS G 114 " pdb=" CA LYS G 114 " pdb=" C LYS G 114 " ideal model delta sigma weight residual 113.51 123.15 -9.64 1.52e+00 4.33e-01 4.02e+01 angle pdb=" N SER G 57 " pdb=" CA SER G 57 " pdb=" C SER G 57 " ideal model delta sigma weight residual 111.28 118.14 -6.86 1.35e+00 5.49e-01 2.58e+01 angle pdb=" C THR G 133 " pdb=" CA THR G 133 " pdb=" CB THR G 133 " ideal model delta sigma weight residual 110.06 117.36 -7.30 1.44e+00 4.82e-01 2.57e+01 angle pdb=" CA GLY I 69 " pdb=" C GLY I 69 " pdb=" O GLY I 69 " ideal model delta sigma weight residual 122.57 117.91 4.66 9.20e-01 1.18e+00 2.56e+01 ... (remaining 28873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.30: 11378 35.30 - 70.60: 1100 70.60 - 105.90: 137 105.90 - 141.20: 1 141.20 - 176.50: 3 Dihedral angle restraints: 12619 sinusoidal: 9470 harmonic: 3149 Sorted by residual: dihedral pdb=" O4' U 11008 " pdb=" C1' U 11008 " pdb=" N1 U 11008 " pdb=" C2 U 11008 " ideal model delta sinusoidal sigma weight residual 200.00 23.50 176.50 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C 11158 " pdb=" C1' C 11158 " pdb=" N1 C 11158 " pdb=" C2 C 11158 " ideal model delta sinusoidal sigma weight residual 200.00 72.86 127.14 1 1.50e+01 4.44e-03 6.84e+01 dihedral pdb=" O4' U 1 960 " pdb=" C1' U 1 960 " pdb=" N1 U 1 960 " pdb=" C2 U 1 960 " ideal model delta sinusoidal sigma weight residual 232.00 59.36 172.64 1 1.70e+01 3.46e-03 6.62e+01 ... (remaining 12616 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 3394 0.107 - 0.214: 184 0.214 - 0.321: 20 0.321 - 0.428: 2 0.428 - 0.535: 2 Chirality restraints: 3602 Sorted by residual: chirality pdb=" CA VAL J 57 " pdb=" N VAL J 57 " pdb=" C VAL J 57 " pdb=" CB VAL J 57 " both_signs ideal model delta sigma weight residual False 2.44 1.91 0.53 2.00e-01 2.50e+01 7.15e+00 chirality pdb=" CA LYS G 114 " pdb=" N LYS G 114 " pdb=" C LYS G 114 " pdb=" CB LYS G 114 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.49e+00 chirality pdb=" CA ASN G 130 " pdb=" N ASN G 130 " pdb=" C ASN G 130 " pdb=" CB ASN G 130 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.67e+00 ... (remaining 3599 not shown) Planarity restraints: 1985 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' 2MG 11207 " -0.013 2.00e-02 2.50e+03 2.67e-02 2.32e+01 pdb=" N9 2MG 11207 " -0.006 2.00e-02 2.50e+03 pdb=" C8 2MG 11207 " 0.015 2.00e-02 2.50e+03 pdb=" N7 2MG 11207 " 0.019 2.00e-02 2.50e+03 pdb=" C5 2MG 11207 " 0.005 2.00e-02 2.50e+03 pdb=" C6 2MG 11207 " 0.004 2.00e-02 2.50e+03 pdb=" O6 2MG 11207 " 0.013 2.00e-02 2.50e+03 pdb=" N1 2MG 11207 " -0.012 2.00e-02 2.50e+03 pdb=" C2 2MG 11207 " -0.027 2.00e-02 2.50e+03 pdb=" N2 2MG 11207 " -0.038 2.00e-02 2.50e+03 pdb=" N3 2MG 11207 " -0.022 2.00e-02 2.50e+03 pdb=" C4 2MG 11207 " -0.011 2.00e-02 2.50e+03 pdb=" CM2 2MG 11207 " 0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA I 121 " -0.016 2.00e-02 2.50e+03 3.38e-02 1.14e+01 pdb=" C ALA I 121 " 0.058 2.00e-02 2.50e+03 pdb=" O ALA I 121 " -0.022 2.00e-02 2.50e+03 pdb=" N ARG I 122 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG C 59 " -0.053 5.00e-02 4.00e+02 8.13e-02 1.06e+01 pdb=" N PRO C 60 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO C 60 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 60 " -0.045 5.00e-02 4.00e+02 ... (remaining 1982 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.14: 26 2.14 - 2.83: 5712 2.83 - 3.52: 28444 3.52 - 4.21: 57706 4.21 - 4.90: 79797 Nonbonded interactions: 171685 Sorted by model distance: nonbonded pdb=" OP1 G 11094 " pdb="MG MG 11607 " model vdw 1.456 2.170 nonbonded pdb=" OP1 G 11068 " pdb="MG MG 11607 " model vdw 1.822 2.170 nonbonded pdb=" OP2 C 11054 " pdb="MG MG 11617 " model vdw 1.898 2.170 nonbonded pdb=" OP1 C 11303 " pdb="MG MG 11620 " model vdw 1.907 2.170 nonbonded pdb=" OP1 U 11224 " pdb="MG MG 11611 " model vdw 1.930 2.170 ... (remaining 171680 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.970 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: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.150 Set scattering table: 0.170 Process input model: 55.340 Find NCS groups from input model: 0.180 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: 0.010 Load rotamer database and sin/cos tables:12.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 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 : 0.007 0.077 19748 Z= 0.469 Angle : 0.807 13.558 28878 Z= 0.527 Chirality : 0.053 0.535 3602 Planarity : 0.004 0.081 1985 Dihedral : 21.501 176.502 10581 Min Nonbonded Distance : 1.456 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Cbeta Deviations : 0.59 % 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: -1.10 (0.24), residues: 1085 helix: -0.23 (0.22), residues: 492 sheet: -0.52 (0.37), residues: 183 loop : -1.27 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP N 42 HIS 0.005 0.001 HIS S 14 PHE 0.028 0.002 PHE B 90 TYR 0.009 0.001 TYR I 64 ARG 0.003 0.001 ARG G 111 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 1.328 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 129 LEU cc_start: 0.8698 (mt) cc_final: 0.8279 (mp) REVERT: C 112 ASP cc_start: 0.8233 (m-30) cc_final: 0.7910 (m-30) REVERT: C 123 GLN cc_start: 0.9196 (mt0) cc_final: 0.8994 (mt0) REVERT: C 168 TYR cc_start: 0.8444 (t80) cc_final: 0.8209 (t80) REVERT: G 17 LYS cc_start: 0.9374 (tttt) cc_final: 0.9120 (tttt) REVERT: I 60 LYS cc_start: 0.8918 (mppt) cc_final: 0.8622 (mmtm) REVERT: J 20 GLN cc_start: 0.8429 (tp-100) cc_final: 0.7725 (tm-30) REVERT: J 24 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8175 (mm-30) REVERT: J 46 LYS cc_start: 0.9266 (mttm) cc_final: 0.8955 (mtpp) REVERT: J 71 LEU cc_start: 0.9382 (tp) cc_final: 0.9172 (tm) REVERT: J 96 VAL cc_start: 0.9615 (t) cc_final: 0.9350 (m) REVERT: N 26 GLU cc_start: 0.8339 (tm-30) cc_final: 0.8102 (tm-30) REVERT: N 30 ILE cc_start: 0.9432 (mm) cc_final: 0.9226 (mp) REVERT: N 82 ILE cc_start: 0.9713 (mm) cc_final: 0.9446 (mp) REVERT: S 17 LYS cc_start: 0.9384 (mttm) cc_final: 0.9108 (mmmm) REVERT: S 21 LYS cc_start: 0.9214 (mtmm) cc_final: 0.8661 (mmtm) REVERT: S 65 GLU cc_start: 0.8658 (tp30) cc_final: 0.8036 (tp30) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 1.5635 time to fit residues: 536.8635 Evaluate side-chains 184 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 61 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 138 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 ASN B 122 GLN B 170 HIS B 227 GLN C 102 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 ASN ** G 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 4 ASN J 64 GLN J 70 HIS ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 12 HIS ** M 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 GLN S 56 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19748 Z= 0.247 Angle : 0.634 8.753 28878 Z= 0.333 Chirality : 0.039 0.218 3602 Planarity : 0.005 0.047 1985 Dihedral : 22.369 175.892 8367 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.27 % Allowed : 21.92 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.24), residues: 1085 helix: 0.53 (0.22), residues: 500 sheet: -0.09 (0.39), residues: 170 loop : -0.72 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP N 42 HIS 0.017 0.002 HIS B 94 PHE 0.017 0.002 PHE S 74 TYR 0.028 0.003 TYR B 213 ARG 0.009 0.001 ARG C 164 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 224 time to evaluate : 1.306 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: B 90 PHE cc_start: 0.3740 (m-80) cc_final: 0.3430 (m-80) REVERT: B 105 LYS cc_start: 0.8074 (pttm) cc_final: 0.7794 (pttp) REVERT: B 120 GLN cc_start: 0.6755 (OUTLIER) cc_final: 0.6130 (tm-30) REVERT: B 154 MET cc_start: 0.7030 (tpt) cc_final: 0.6716 (mmm) REVERT: C 123 GLN cc_start: 0.9146 (mt0) cc_final: 0.8929 (mt0) REVERT: C 168 TYR cc_start: 0.8422 (t80) cc_final: 0.8172 (t80) REVERT: C 181 ASP cc_start: 0.8840 (t70) cc_final: 0.8151 (p0) REVERT: I 25 ASN cc_start: 0.8533 (p0) cc_final: 0.8295 (p0) REVERT: J 20 GLN cc_start: 0.8373 (tp-100) cc_final: 0.7554 (tm-30) REVERT: J 24 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8041 (mm-30) REVERT: J 46 LYS cc_start: 0.9283 (mttm) cc_final: 0.8986 (mtpp) REVERT: J 63 ASP cc_start: 0.8247 (p0) cc_final: 0.8019 (p0) REVERT: N 26 GLU cc_start: 0.8236 (tm-30) cc_final: 0.8006 (tm-30) REVERT: N 30 ILE cc_start: 0.9381 (mm) cc_final: 0.9181 (mp) REVERT: N 38 ASP cc_start: 0.8774 (p0) cc_final: 0.8090 (p0) REVERT: N 82 ILE cc_start: 0.9505 (mm) cc_final: 0.9126 (mp) REVERT: S 17 LYS cc_start: 0.9334 (mttm) cc_final: 0.8807 (mtpp) REVERT: S 21 LYS cc_start: 0.8994 (mtmm) cc_final: 0.8580 (mtmt) REVERT: S 65 GLU cc_start: 0.8537 (tp30) cc_final: 0.7865 (tp30) outliers start: 30 outliers final: 8 residues processed: 241 average time/residue: 1.3202 time to fit residues: 358.3906 Evaluate side-chains 200 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 191 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain N residue 35 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 138 optimal weight: 0.6980 chunk 149 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 ASN C 102 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 ASN ** G 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 19748 Z= 0.293 Angle : 0.624 9.718 28878 Z= 0.328 Chirality : 0.039 0.238 3602 Planarity : 0.005 0.049 1985 Dihedral : 22.271 174.540 8367 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.58 % Allowed : 23.66 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.25), residues: 1085 helix: 0.70 (0.22), residues: 503 sheet: 0.14 (0.40), residues: 160 loop : -0.45 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 42 HIS 0.004 0.001 HIS S 14 PHE 0.018 0.002 PHE I 127 TYR 0.026 0.002 TYR B 213 ARG 0.007 0.001 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 213 time to evaluate : 1.465 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: B 90 PHE cc_start: 0.5295 (m-80) cc_final: 0.4946 (m-80) REVERT: B 120 GLN cc_start: 0.6278 (OUTLIER) cc_final: 0.5934 (tm-30) REVERT: B 136 MET cc_start: 0.8377 (mmp) cc_final: 0.8060 (mmp) REVERT: B 154 MET cc_start: 0.7213 (tpt) cc_final: 0.7007 (mmm) REVERT: C 123 GLN cc_start: 0.9143 (mt0) cc_final: 0.8905 (mt0) REVERT: C 168 TYR cc_start: 0.8447 (t80) cc_final: 0.8214 (t80) REVERT: C 181 ASP cc_start: 0.8887 (t70) cc_final: 0.8178 (p0) REVERT: G 144 MET cc_start: 0.7797 (mpm) cc_final: 0.7542 (mpm) REVERT: I 42 GLU cc_start: 0.8338 (tp30) cc_final: 0.7824 (tp30) REVERT: I 46 MET cc_start: 0.7528 (mmm) cc_final: 0.6957 (mmm) REVERT: I 94 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8963 (mp) REVERT: J 20 GLN cc_start: 0.8435 (tp-100) cc_final: 0.7482 (tm-30) REVERT: J 24 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8062 (mm-30) REVERT: J 46 LYS cc_start: 0.9301 (mttm) cc_final: 0.8970 (mtpp) REVERT: N 82 ILE cc_start: 0.9381 (mm) cc_final: 0.9140 (mp) REVERT: S 21 LYS cc_start: 0.9033 (mtmm) cc_final: 0.8580 (mttt) REVERT: S 64 ASP cc_start: 0.8531 (p0) cc_final: 0.7895 (p0) outliers start: 42 outliers final: 13 residues processed: 232 average time/residue: 1.3916 time to fit residues: 361.1848 Evaluate side-chains 207 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 192 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain S residue 13 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 138 optimal weight: 0.7980 chunk 146 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 102 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 ASN ** G 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19748 Z= 0.310 Angle : 0.639 10.416 28878 Z= 0.335 Chirality : 0.039 0.187 3602 Planarity : 0.005 0.086 1985 Dihedral : 22.237 174.510 8367 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 5.78 % Allowed : 23.77 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.25), residues: 1085 helix: 0.61 (0.23), residues: 502 sheet: 0.27 (0.40), residues: 160 loop : -0.46 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP N 42 HIS 0.005 0.001 HIS M 12 PHE 0.033 0.002 PHE B 32 TYR 0.018 0.002 TYR B 213 ARG 0.008 0.001 ARG J 31 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 201 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 PHE cc_start: 0.4776 (OUTLIER) cc_final: 0.4492 (t80) REVERT: B 50 PHE cc_start: 0.4843 (t80) cc_final: 0.4598 (t80) REVERT: B 94 HIS cc_start: 0.7015 (OUTLIER) cc_final: 0.6405 (p-80) REVERT: B 136 MET cc_start: 0.8410 (mmp) cc_final: 0.7646 (mmp) REVERT: B 137 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8016 (mtp180) REVERT: C 123 GLN cc_start: 0.9146 (mt0) cc_final: 0.8911 (mt0) REVERT: C 181 ASP cc_start: 0.8894 (t70) cc_final: 0.8177 (p0) REVERT: G 144 MET cc_start: 0.7939 (mpm) cc_final: 0.7724 (mpm) REVERT: J 20 GLN cc_start: 0.8447 (tp-100) cc_final: 0.7640 (tm-30) REVERT: J 24 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8240 (mm-30) REVERT: J 46 LYS cc_start: 0.9321 (mttm) cc_final: 0.9005 (mtpp) REVERT: M 52 GLN cc_start: 0.9409 (OUTLIER) cc_final: 0.8881 (pm20) REVERT: N 82 ILE cc_start: 0.9481 (mm) cc_final: 0.9278 (mp) REVERT: S 21 LYS cc_start: 0.9016 (mtmm) cc_final: 0.8559 (mttt) outliers start: 53 outliers final: 18 residues processed: 235 average time/residue: 1.4212 time to fit residues: 378.4105 Evaluate side-chains 201 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 95 ARG Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 31 LYS Chi-restraints excluded: chain M residue 52 GLN Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain S residue 51 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 0.6980 chunk 83 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 125 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 75 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 168 HIS C 102 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 GLN G 97 ASN ** G 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 12 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19748 Z= 0.231 Angle : 0.627 11.810 28878 Z= 0.328 Chirality : 0.037 0.180 3602 Planarity : 0.004 0.057 1985 Dihedral : 22.215 174.717 8367 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 5.34 % Allowed : 25.19 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.25), residues: 1085 helix: 0.54 (0.23), residues: 503 sheet: 0.44 (0.41), residues: 160 loop : -0.38 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP N 42 HIS 0.004 0.001 HIS B 94 PHE 0.025 0.002 PHE B 32 TYR 0.016 0.002 TYR B 213 ARG 0.007 0.001 ARG B 113 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 202 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 PHE cc_start: 0.4779 (OUTLIER) cc_final: 0.4517 (t80) REVERT: B 94 HIS cc_start: 0.7081 (OUTLIER) cc_final: 0.6561 (p-80) REVERT: B 194 ASP cc_start: 0.5613 (OUTLIER) cc_final: 0.5380 (p0) REVERT: C 123 GLN cc_start: 0.9128 (mt0) cc_final: 0.8823 (mt0) REVERT: C 181 ASP cc_start: 0.8867 (t70) cc_final: 0.8157 (p0) REVERT: G 103 TRP cc_start: 0.8898 (m-10) cc_final: 0.8647 (m-10) REVERT: G 126 ASP cc_start: 0.8395 (p0) cc_final: 0.8132 (p0) REVERT: G 144 MET cc_start: 0.7930 (mpm) cc_final: 0.7692 (mpm) REVERT: I 42 GLU cc_start: 0.8366 (tp30) cc_final: 0.8023 (tp30) REVERT: I 46 MET cc_start: 0.7602 (mmm) cc_final: 0.6910 (mmm) REVERT: I 110 GLN cc_start: 0.8131 (pt0) cc_final: 0.7448 (pt0) REVERT: J 20 GLN cc_start: 0.8391 (tp-100) cc_final: 0.7578 (tm-30) REVERT: J 24 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8231 (mm-30) REVERT: J 46 LYS cc_start: 0.9332 (mttm) cc_final: 0.9030 (mtpp) REVERT: J 96 VAL cc_start: 0.9684 (OUTLIER) cc_final: 0.9461 (m) REVERT: M 52 GLN cc_start: 0.9360 (OUTLIER) cc_final: 0.8857 (pm20) REVERT: M 72 GLU cc_start: 0.8314 (tm-30) cc_final: 0.7254 (tm-30) REVERT: N 82 ILE cc_start: 0.9440 (mm) cc_final: 0.9228 (mp) REVERT: S 21 LYS cc_start: 0.9043 (mtmm) cc_final: 0.8714 (mttt) outliers start: 49 outliers final: 15 residues processed: 235 average time/residue: 1.2721 time to fit residues: 338.7196 Evaluate side-chains 201 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 181 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 52 GLN Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 104 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 3.9990 chunk 132 optimal weight: 0.0870 chunk 29 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 147 optimal weight: 0.0980 chunk 122 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 overall best weight: 3.0364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN B 168 HIS B 177 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 19748 Z= 0.340 Angle : 0.678 10.706 28878 Z= 0.353 Chirality : 0.040 0.213 3602 Planarity : 0.005 0.061 1985 Dihedral : 22.172 173.970 8367 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.47 % Allowed : 28.46 % Favored : 67.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.25), residues: 1085 helix: 0.43 (0.23), residues: 498 sheet: 0.40 (0.40), residues: 162 loop : -0.39 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP N 42 HIS 0.003 0.001 HIS B 94 PHE 0.028 0.002 PHE N 21 TYR 0.028 0.002 TYR M 86 ARG 0.006 0.001 ARG G 109 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 188 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 PHE cc_start: 0.5018 (OUTLIER) cc_final: 0.4289 (t80) REVERT: B 136 MET cc_start: 0.8102 (mmp) cc_final: 0.7855 (mmp) REVERT: B 223 GLU cc_start: 0.4450 (OUTLIER) cc_final: 0.3722 (pt0) REVERT: C 123 GLN cc_start: 0.9107 (mt0) cc_final: 0.8897 (mt0) REVERT: C 181 ASP cc_start: 0.8903 (t70) cc_final: 0.8173 (p0) REVERT: G 144 MET cc_start: 0.7933 (mpm) cc_final: 0.7715 (mpm) REVERT: J 20 GLN cc_start: 0.8435 (tp-100) cc_final: 0.7612 (tm-30) REVERT: J 24 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8255 (mm-30) REVERT: J 46 LYS cc_start: 0.9307 (mttm) cc_final: 0.8998 (mtpp) REVERT: J 66 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7657 (tm-30) REVERT: M 52 GLN cc_start: 0.9374 (OUTLIER) cc_final: 0.9144 (mp10) REVERT: M 72 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7903 (tm-30) REVERT: N 82 ILE cc_start: 0.9477 (mm) cc_final: 0.9264 (mp) REVERT: S 21 LYS cc_start: 0.9010 (mtmm) cc_final: 0.8661 (mttt) outliers start: 41 outliers final: 20 residues processed: 214 average time/residue: 1.2135 time to fit residues: 295.8192 Evaluate side-chains 191 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 52 GLN Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain S residue 51 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 107 optimal weight: 0.3980 chunk 123 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 146 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 67 optimal weight: 0.1980 chunk 90 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 168 HIS ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19748 Z= 0.196 Angle : 0.646 13.007 28878 Z= 0.335 Chirality : 0.037 0.203 3602 Planarity : 0.004 0.055 1985 Dihedral : 22.181 175.202 8367 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.60 % Allowed : 30.53 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.25), residues: 1085 helix: 0.37 (0.23), residues: 494 sheet: 0.56 (0.41), residues: 159 loop : -0.38 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP N 42 HIS 0.003 0.001 HIS B 94 PHE 0.027 0.002 PHE I 127 TYR 0.017 0.002 TYR B 213 ARG 0.005 0.000 ARG J 31 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 198 time to evaluate : 1.435 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: symmetry clash revert: symmetry clash REVERT: B 9 MET cc_start: 0.2153 (pmm) cc_final: -0.0218 (ppp) REVERT: B 16 PHE cc_start: 0.4783 (OUTLIER) cc_final: 0.3942 (t80) REVERT: B 122 GLN cc_start: 0.8351 (mm-40) cc_final: 0.7640 (mt0) REVERT: C 41 GLN cc_start: 0.9104 (pp30) cc_final: 0.8824 (pp30) REVERT: C 123 GLN cc_start: 0.9071 (mt0) cc_final: 0.8816 (mt0) REVERT: C 181 ASP cc_start: 0.8859 (t70) cc_final: 0.8143 (p0) REVERT: G 54 SER cc_start: 0.8761 (t) cc_final: 0.8541 (p) REVERT: G 110 LYS cc_start: 0.8603 (pptt) cc_final: 0.8354 (pptt) REVERT: G 144 MET cc_start: 0.8093 (mpm) cc_final: 0.7890 (mpm) REVERT: I 61 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8802 (mm) REVERT: J 20 GLN cc_start: 0.8398 (tp-100) cc_final: 0.7531 (tm-30) REVERT: J 24 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8219 (mm-30) REVERT: S 21 LYS cc_start: 0.9083 (mtmm) cc_final: 0.8720 (mttt) outliers start: 33 outliers final: 16 residues processed: 217 average time/residue: 1.2448 time to fit residues: 307.0372 Evaluate side-chains 197 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain S residue 64 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 44 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 140 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN B 168 HIS ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.3826 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: