Starting phenix.real_space_refine on Wed Aug 7 04:04:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afh_11765/08_2024/7afh_11765_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afh_11765/08_2024/7afh_11765.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afh_11765/08_2024/7afh_11765.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afh_11765/08_2024/7afh_11765.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afh_11765/08_2024/7afh_11765_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afh_11765/08_2024/7afh_11765_neut.cif" } resolution = 3.59 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= 0.003 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 11 5.21 5 S 28 5.16 5 C 9820 2.51 5 N 3442 2.21 5 O 4724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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': 37, 'rna2p_pyr': 34, 'rna3p': 3, 'rna3p_pur': 211, 'rna3p_pyr': 171} Link IDs: {'rna2p': 71, 'rna3p': 384} 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: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1143 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 5, 'TRANS': 140} 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: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' MG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} 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: 11.83, per 1000 atoms: 0.64 Number of scatterers: 18482 At special positions: 0 Unit cell: (116.095, 116.095, 158.41, 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 11 11.99 O 4724 8.00 N 3442 7.00 C 9820 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.93 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 18 " 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2042 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 9 sheets defined 50.0% alpha, 14.9% beta 130 base pairs and 210 stacking pairs defined. Time for finding SS restraints: 10.11 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: 3.586A pdb=" N VAL B 107 " --> pdb=" O ASN B 103 " (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: 3.781A pdb=" N ARG C 11 " --> pdb=" O PRO C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 47 Processing helix chain 'C' and resid 48 through 50 No H-bonds generated for 'chain 'C' and resid 48 through 50' Processing helix chain 'C' and resid 72 through 78 Processing helix chain 'C' and resid 81 through 96 Processing helix chain 'C' and resid 108 through 112 Processing helix chain 'C' and resid 113 through 126 Processing helix chain 'C' and resid 129 through 145 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 54 removed outlier: 4.003A pdb=" N ILE G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR G 49 " --> pdb=" O SER G 45 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN G 52 " --> pdb=" O GLU G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 70 removed outlier: 4.294A pdb=" N GLU G 63 " --> pdb=" O LEU G 59 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASN G 68 " --> pdb=" O VAL G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 110 removed outlier: 3.584A pdb=" N ARG G 96 " --> pdb=" O ARG G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 129 Processing helix chain 'G' and resid 133 through 147 Processing helix chain 'I' and resid 35 through 39 Processing helix chain 'I' and resid 41 through 56 removed outlier: 3.676A pdb=" N ARG I 45 " --> pdb=" O ARG I 41 " (cutoff:3.500A) Proline residue: I 51 - end of helix Processing helix chain 'I' and resid 71 through 92 Processing helix chain 'I' and resid 94 through 102 Processing helix chain 'J' and resid 14 through 32 Processing helix chain 'J' and resid 80 through 89 removed outlier: 3.872A pdb=" N ALA J 86 " --> pdb=" O LYS J 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 22 removed outlier: 3.845A pdb=" N ILE M 22 " --> pdb=" O ALA M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 38 Processing helix chain 'M' and resid 49 through 62 removed outlier: 4.497A pdb=" N THR M 55 " --> pdb=" O GLY M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 83 Processing helix chain 'M' and resid 85 through 93 Processing helix chain 'M' and resid 106 through 111 Processing helix chain 'N' and resid 3 through 20 removed outlier: 3.577A pdb=" N TYR N 20 " --> pdb=" O LEU N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 33 Processing helix chain 'N' and resid 39 through 51 removed outlier: 3.864A pdb=" N LEU N 51 " --> pdb=" O LYS N 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 52 through 56 Processing helix chain 'N' and resid 82 through 90 Processing helix chain 'S' and resid 12 through 25 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 31 through 35 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: 5.722A 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: 6.453A 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: 6.400A pdb=" N HIS C 69 " --> pdb=" O SER C 53 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE C 55 " --> pdb=" O THR C 67 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N THR C 67 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE C 57 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ARG C 65 " --> pdb=" O ILE C 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 166 through 170 removed outlier: 5.953A pdb=" N ASP C 181 " --> pdb=" O LYS C 204 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 73 through 75 Processing sheet with id=AA6, first strand: chain 'I' and resid 6 through 11 removed outlier: 3.738A pdb=" N GLY I 10 " --> pdb=" O ALA I 17 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N VAL I 29 " --> pdb=" O ILE I 65 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N VAL I 67 " --> pdb=" O VAL I 29 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 40 through 51 removed outlier: 4.678A pdb=" N LEU J 71 " --> pdb=" O LEU J 42 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR J 44 " --> pdb=" O THR J 69 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N THR J 69 " --> pdb=" O THR J 44 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS J 46 " --> pdb=" O ILE J 67 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE J 67 " --> pdb=" O LYS J 46 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ARG J 48 " --> pdb=" O TYR J 65 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TYR J 65 " --> pdb=" O ARG J 48 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N THR J 50 " --> pdb=" O ASP J 63 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ASP J 63 " --> pdb=" O THR J 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 40 through 51 removed outlier: 4.678A pdb=" N LEU J 71 " --> pdb=" O LEU J 42 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR J 44 " --> pdb=" O THR J 69 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N THR J 69 " --> pdb=" O THR J 44 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS J 46 " --> pdb=" O ILE J 67 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE J 67 " --> pdb=" O LYS J 46 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ARG J 48 " --> pdb=" O TYR J 65 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TYR J 65 " --> pdb=" O ARG J 48 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N THR J 50 " --> pdb=" O ASP J 63 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ASP J 63 " --> pdb=" O THR J 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 31 through 33 removed outlier: 5.808A pdb=" N LEU S 31 " --> pdb=" O ALA S 50 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N HIS S 52 " --> pdb=" O LEU S 31 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N THR S 33 " --> pdb=" O HIS S 52 " (cutoff:3.500A) 442 hydrogen bonds defined for protein. 1251 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 299 hydrogen bonds 378 hydrogen bond angles 0 basepair planarities 130 basepair parallelities 210 stacking parallelities Total time for adding SS restraints: 9.13 Time building geometry restraints manager: 14.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2703 1.32 - 1.45: 7435 1.45 - 1.57: 8660 1.57 - 1.69: 911 1.69 - 1.81: 53 Bond restraints: 19762 Sorted by residual: bond pdb=" C5 2MG 1 966 " pdb=" C4 2MG 1 966 " ideal model delta sigma weight residual 1.382 1.457 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" N VAL M 65 " pdb=" CA VAL M 65 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.11e-02 8.12e+03 1.24e+01 bond pdb=" N ILE J 40 " pdb=" CA ILE J 40 " ideal model delta sigma weight residual 1.460 1.493 -0.033 9.30e-03 1.16e+04 1.23e+01 bond pdb=" N VAL J 51 " pdb=" CA VAL J 51 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.14e-02 7.69e+03 1.21e+01 bond pdb=" C6 2MG 11207 " pdb=" N1 2MG 11207 " ideal model delta sigma weight residual 1.399 1.329 0.070 2.00e-02 2.50e+03 1.21e+01 ... (remaining 19757 not shown) Histogram of bond angle deviations from ideal: 98.99 - 106.55: 2805 106.55 - 114.12: 12384 114.12 - 121.69: 9322 121.69 - 129.25: 3914 129.25 - 136.82: 472 Bond angle restraints: 28897 Sorted by residual: angle pdb=" C HIS M 14 " pdb=" CA HIS M 14 " pdb=" CB HIS M 14 " ideal model delta sigma weight residual 109.62 118.70 -9.08 1.79e+00 3.12e-01 2.57e+01 angle pdb=" CA GLY B 124 " pdb=" C GLY B 124 " pdb=" O GLY B 124 " ideal model delta sigma weight residual 121.30 116.92 4.38 9.80e-01 1.04e+00 1.99e+01 angle pdb=" N SER I 93 " pdb=" CA SER I 93 " pdb=" C SER I 93 " ideal model delta sigma weight residual 112.90 107.06 5.84 1.31e+00 5.83e-01 1.99e+01 angle pdb=" C GLU M 66 " pdb=" CA GLU M 66 " pdb=" CB GLU M 66 " ideal model delta sigma weight residual 116.63 111.47 5.16 1.16e+00 7.43e-01 1.98e+01 angle pdb=" CA GLY M 26 " pdb=" C GLY M 26 " pdb=" O GLY M 26 " ideal model delta sigma weight residual 122.28 117.92 4.36 1.00e+00 1.00e+00 1.90e+01 ... (remaining 28892 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.21: 11300 35.21 - 70.41: 1162 70.41 - 105.62: 157 105.62 - 140.82: 5 140.82 - 176.03: 4 Dihedral angle restraints: 12628 sinusoidal: 9473 harmonic: 3155 Sorted by residual: dihedral pdb=" C4' G 11279 " pdb=" C3' G 11279 " pdb=" C2' G 11279 " pdb=" C1' G 11279 " ideal model delta sinusoidal sigma weight residual -35.00 35.37 -70.37 1 8.00e+00 1.56e-02 9.96e+01 dihedral pdb=" C5' G 11279 " pdb=" C4' G 11279 " pdb=" C3' G 11279 " pdb=" O3' G 11279 " ideal model delta sinusoidal sigma weight residual 147.00 81.41 65.59 1 8.00e+00 1.56e-02 8.80e+01 dihedral pdb=" O4' U 11008 " pdb=" C1' U 11008 " pdb=" N1 U 11008 " pdb=" C2 U 11008 " ideal model delta sinusoidal sigma weight residual -160.00 16.03 -176.03 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 12625 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3092 0.066 - 0.131: 417 0.131 - 0.197: 75 0.197 - 0.263: 17 0.263 - 0.328: 3 Chirality restraints: 3604 Sorted by residual: chirality pdb=" C3' G 11279 " pdb=" C4' G 11279 " pdb=" O3' G 11279 " pdb=" C2' G 11279 " both_signs ideal model delta sigma weight residual False -2.74 -2.42 -0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CA THR B 125 " pdb=" N THR B 125 " pdb=" C THR B 125 " pdb=" CB THR B 125 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA HIS M 14 " pdb=" N HIS M 14 " pdb=" C HIS M 14 " pdb=" CB HIS M 14 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 3601 not shown) Planarity restraints: 1988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' 2MG 1 966 " -0.062 2.00e-02 2.50e+03 1.14e-01 4.23e+02 pdb=" N9 2MG 1 966 " -0.010 2.00e-02 2.50e+03 pdb=" C8 2MG 1 966 " 0.056 2.00e-02 2.50e+03 pdb=" N7 2MG 1 966 " 0.077 2.00e-02 2.50e+03 pdb=" C5 2MG 1 966 " 0.024 2.00e-02 2.50e+03 pdb=" C6 2MG 1 966 " 0.010 2.00e-02 2.50e+03 pdb=" O6 2MG 1 966 " 0.058 2.00e-02 2.50e+03 pdb=" N1 2MG 1 966 " -0.056 2.00e-02 2.50e+03 pdb=" C2 2MG 1 966 " -0.112 2.00e-02 2.50e+03 pdb=" N2 2MG 1 966 " -0.166 2.00e-02 2.50e+03 pdb=" N3 2MG 1 966 " -0.097 2.00e-02 2.50e+03 pdb=" C4 2MG 1 966 " -0.034 2.00e-02 2.50e+03 pdb=" CM2 2MG 1 966 " 0.313 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' 2MG 11207 " 0.027 2.00e-02 2.50e+03 3.94e-02 5.05e+01 pdb=" N9 2MG 11207 " -0.006 2.00e-02 2.50e+03 pdb=" C8 2MG 11207 " -0.018 2.00e-02 2.50e+03 pdb=" N7 2MG 11207 " -0.024 2.00e-02 2.50e+03 pdb=" C5 2MG 11207 " -0.005 2.00e-02 2.50e+03 pdb=" C6 2MG 11207 " -0.006 2.00e-02 2.50e+03 pdb=" O6 2MG 11207 " -0.020 2.00e-02 2.50e+03 pdb=" N1 2MG 11207 " 0.018 2.00e-02 2.50e+03 pdb=" C2 2MG 11207 " 0.038 2.00e-02 2.50e+03 pdb=" N2 2MG 11207 " 0.058 2.00e-02 2.50e+03 pdb=" N3 2MG 11207 " 0.035 2.00e-02 2.50e+03 pdb=" C4 2MG 11207 " 0.010 2.00e-02 2.50e+03 pdb=" CM2 2MG 11207 " -0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN N 60 " 0.012 2.00e-02 2.50e+03 2.50e-02 6.23e+00 pdb=" C GLN N 60 " -0.043 2.00e-02 2.50e+03 pdb=" O GLN N 60 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG N 61 " 0.015 2.00e-02 2.50e+03 ... (remaining 1985 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 267 2.38 - 3.01: 11503 3.01 - 3.64: 38143 3.64 - 4.27: 54012 4.27 - 4.90: 74536 Nonbonded interactions: 178461 Sorted by model distance: nonbonded pdb=" O3' G 11365 " pdb="MG MG 11606 " model vdw 1.752 2.170 nonbonded pdb=" O3' G 11242 " pdb="MG MG 11610 " model vdw 1.796 2.170 nonbonded pdb=" OP1 U 11199 " pdb="MG MG 11609 " model vdw 1.842 2.170 nonbonded pdb=" OP1 C 11054 " pdb="MG MG 11608 " model vdw 1.849 2.170 nonbonded pdb=" OP1 A 1 964 " pdb="MG MG 11609 " model vdw 1.857 2.170 ... (remaining 178456 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.600 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: 0.010 Extract box with map and model: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 75.340 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 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 : 0.009 0.075 19762 Z= 0.538 Angle : 0.894 9.586 28897 Z= 0.539 Chirality : 0.050 0.328 3604 Planarity : 0.005 0.114 1988 Dihedral : 22.890 176.029 10586 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 32.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.24), residues: 1087 helix: -1.42 (0.22), residues: 478 sheet: -1.84 (0.36), residues: 162 loop : -1.82 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 201 HIS 0.006 0.001 HIS M 14 PHE 0.016 0.002 PHE C 37 TYR 0.016 0.002 TYR I 64 ARG 0.013 0.001 ARG I 99 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 1.291 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 TRP cc_start: 0.8038 (t-100) cc_final: 0.7647 (t-100) REVERT: B 101 LEU cc_start: 0.8609 (mt) cc_final: 0.8377 (mt) REVERT: C 183 ASP cc_start: 0.8739 (t0) cc_final: 0.8406 (t0) REVERT: J 91 ASP cc_start: 0.8062 (p0) cc_final: 0.7779 (p0) REVERT: J 97 ASP cc_start: 0.8734 (t70) cc_final: 0.8515 (t0) REVERT: M 34 LEU cc_start: 0.9321 (tp) cc_final: 0.9050 (tp) REVERT: M 81 MET cc_start: 0.9185 (mtp) cc_final: 0.8705 (ttm) REVERT: N 67 THR cc_start: 0.8772 (p) cc_final: 0.8094 (t) REVERT: S 66 MET cc_start: 0.8908 (mtp) cc_final: 0.8613 (mtp) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.3560 time to fit residues: 125.1528 Evaluate side-chains 138 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.284 ------------------------------------------------------------------------------- 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: 5.9990 chunk 115 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 61 optimal weight: 9.9990 chunk 119 optimal weight: 0.8980 chunk 46 optimal weight: 30.0000 chunk 72 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 GLN ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 GLN ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 GLN ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN N 66 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19762 Z= 0.205 Angle : 0.679 14.021 28897 Z= 0.346 Chirality : 0.038 0.260 3604 Planarity : 0.005 0.053 1988 Dihedral : 23.597 179.258 8369 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.40 % Allowed : 16.56 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.24), residues: 1087 helix: -0.49 (0.22), residues: 498 sheet: -1.38 (0.37), residues: 157 loop : -1.27 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 201 HIS 0.003 0.001 HIS S 14 PHE 0.027 0.002 PHE B 198 TYR 0.016 0.002 TYR C 168 ARG 0.015 0.001 ARG S 3 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 188 time to evaluate : 1.267 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 GLN cc_start: 0.8467 (tt0) cc_final: 0.8202 (tt0) REVERT: B 120 GLN cc_start: 0.9037 (tp-100) cc_final: 0.8605 (tp-100) REVERT: B 184 PHE cc_start: 0.7561 (OUTLIER) cc_final: 0.6251 (m-80) REVERT: B 192 ASP cc_start: 0.7100 (OUTLIER) cc_final: 0.6510 (t0) REVERT: C 36 ASP cc_start: 0.8392 (m-30) cc_final: 0.7715 (m-30) REVERT: C 183 ASP cc_start: 0.8578 (t0) cc_final: 0.8330 (t0) REVERT: I 50 GLN cc_start: 0.9242 (mm-40) cc_final: 0.8901 (mm-40) REVERT: I 88 MET cc_start: 0.8981 (ttm) cc_final: 0.8658 (mmt) REVERT: J 46 LYS cc_start: 0.8769 (mmmm) cc_final: 0.8378 (mmtp) REVERT: J 97 ASP cc_start: 0.8806 (t70) cc_final: 0.8540 (p0) REVERT: J 99 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8435 (mm110) REVERT: M 20 THR cc_start: 0.9386 (m) cc_final: 0.8905 (p) REVERT: M 81 MET cc_start: 0.9040 (mtp) cc_final: 0.8611 (ttm) REVERT: M 95 LEU cc_start: 0.9376 (mt) cc_final: 0.9044 (mp) REVERT: N 62 ASN cc_start: 0.8856 (m-40) cc_final: 0.8407 (t0) REVERT: N 67 THR cc_start: 0.8987 (p) cc_final: 0.8388 (t) REVERT: N 86 GLU cc_start: 0.9082 (mp0) cc_final: 0.8758 (mp0) REVERT: S 66 MET cc_start: 0.8809 (mtp) cc_final: 0.8510 (mtp) outliers start: 22 outliers final: 12 residues processed: 200 average time/residue: 0.3408 time to fit residues: 102.0098 Evaluate side-chains 161 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 147 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain M residue 31 LYS Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 71 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 138 optimal weight: 4.9990 chunk 149 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 HIS C 8 ASN C 140 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 HIS ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 66 GLN N 71 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19762 Z= 0.278 Angle : 0.653 12.993 28897 Z= 0.332 Chirality : 0.038 0.261 3604 Planarity : 0.005 0.056 1988 Dihedral : 23.518 179.709 8369 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 18.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.70 % Allowed : 17.86 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.24), residues: 1087 helix: -0.13 (0.22), residues: 502 sheet: -1.21 (0.37), residues: 167 loop : -1.22 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 103 HIS 0.009 0.001 HIS S 14 PHE 0.022 0.002 PHE B 184 TYR 0.018 0.002 TYR I 6 ARG 0.004 0.001 ARG S 3 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 168 time to evaluate : 1.287 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: symmetry clash REVERT: B 113 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7605 (mtm180) REVERT: B 120 GLN cc_start: 0.9064 (tp-100) cc_final: 0.8840 (tp-100) REVERT: B 184 PHE cc_start: 0.7691 (OUTLIER) cc_final: 0.6575 (m-10) REVERT: B 192 ASP cc_start: 0.6830 (OUTLIER) cc_final: 0.6432 (t70) REVERT: C 36 ASP cc_start: 0.8630 (m-30) cc_final: 0.7929 (m-30) REVERT: C 102 ASN cc_start: 0.9024 (m-40) cc_final: 0.8804 (m-40) REVERT: C 183 ASP cc_start: 0.8573 (t0) cc_final: 0.8246 (t0) REVERT: G 21 GLU cc_start: 0.8877 (pp20) cc_final: 0.8307 (tp30) REVERT: G 113 ASP cc_start: 0.8822 (t0) cc_final: 0.8596 (t0) REVERT: I 42 GLU cc_start: 0.8401 (tp30) cc_final: 0.8134 (tp30) REVERT: I 46 MET cc_start: 0.8937 (mtt) cc_final: 0.7883 (mtt) REVERT: I 50 GLN cc_start: 0.9202 (mm-40) cc_final: 0.8866 (mm-40) REVERT: I 88 MET cc_start: 0.9057 (ttm) cc_final: 0.8696 (mmt) REVERT: J 97 ASP cc_start: 0.8839 (t70) cc_final: 0.8588 (t0) REVERT: J 99 GLN cc_start: 0.8811 (mm-40) cc_final: 0.8293 (mm110) REVERT: M 27 LYS cc_start: 0.9573 (tptm) cc_final: 0.9290 (tptt) REVERT: M 42 ASP cc_start: 0.7720 (m-30) cc_final: 0.7493 (t0) REVERT: M 81 MET cc_start: 0.9076 (mtp) cc_final: 0.8720 (ttm) REVERT: N 62 ASN cc_start: 0.8861 (m-40) cc_final: 0.8598 (t0) REVERT: N 67 THR cc_start: 0.9055 (p) cc_final: 0.8506 (t) REVERT: N 93 ILE cc_start: 0.9474 (mm) cc_final: 0.9272 (mp) REVERT: S 66 MET cc_start: 0.8866 (mtp) cc_final: 0.8625 (mtt) outliers start: 34 outliers final: 19 residues processed: 187 average time/residue: 0.3105 time to fit residues: 87.5274 Evaluate side-chains 160 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 138 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 113 ARG Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain N residue 14 VAL Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 71 optimal weight: 0.0970 chunk 15 optimal weight: 10.0000 chunk 65 optimal weight: 30.0000 chunk 92 optimal weight: 0.7980 chunk 138 optimal weight: 0.6980 chunk 146 optimal weight: 0.0470 chunk 72 optimal weight: 0.9980 chunk 131 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 HIS C 8 ASN G 122 ASN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 19762 Z= 0.157 Angle : 0.605 11.836 28897 Z= 0.309 Chirality : 0.036 0.227 3604 Planarity : 0.004 0.045 1988 Dihedral : 23.312 177.889 8369 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.27 % Allowed : 19.93 % Favored : 76.80 % 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: -0.86 (0.25), residues: 1087 helix: 0.03 (0.22), residues: 511 sheet: -1.08 (0.38), residues: 162 loop : -0.93 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP G 103 HIS 0.012 0.001 HIS B 18 PHE 0.016 0.001 PHE B 184 TYR 0.013 0.002 TYR I 6 ARG 0.005 0.001 ARG I 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 173 time to evaluate : 1.320 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.7401 (mtm180) REVERT: B 184 PHE cc_start: 0.7613 (OUTLIER) cc_final: 0.6736 (m-10) REVERT: B 190 ASN cc_start: 0.7063 (OUTLIER) cc_final: 0.5130 (p0) REVERT: B 192 ASP cc_start: 0.6639 (OUTLIER) cc_final: 0.6008 (t70) REVERT: C 102 ASN cc_start: 0.8936 (m-40) cc_final: 0.8685 (m-40) REVERT: C 112 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.7824 (p0) REVERT: C 183 ASP cc_start: 0.8568 (t0) cc_final: 0.8284 (t0) REVERT: I 22 LYS cc_start: 0.9082 (tppt) cc_final: 0.8831 (mmmt) REVERT: I 42 GLU cc_start: 0.8366 (tp30) cc_final: 0.7894 (tp30) REVERT: I 46 MET cc_start: 0.8833 (mtt) cc_final: 0.7604 (mtt) REVERT: I 50 GLN cc_start: 0.9253 (mm-40) cc_final: 0.8943 (mm-40) REVERT: I 88 MET cc_start: 0.8986 (ttm) cc_final: 0.8509 (mmm) REVERT: I 115 LYS cc_start: 0.9076 (mttt) cc_final: 0.8728 (mmtt) REVERT: J 63 ASP cc_start: 0.8144 (t70) cc_final: 0.7915 (t0) REVERT: J 82 LYS cc_start: 0.9313 (mmmm) cc_final: 0.9111 (mmmm) REVERT: J 97 ASP cc_start: 0.8769 (t70) cc_final: 0.7972 (p0) REVERT: M 27 LYS cc_start: 0.9509 (tptm) cc_final: 0.9289 (tptt) REVERT: M 42 ASP cc_start: 0.7639 (m-30) cc_final: 0.7414 (t0) REVERT: M 81 MET cc_start: 0.9059 (mtp) cc_final: 0.8746 (ttm) REVERT: M 95 LEU cc_start: 0.9418 (mm) cc_final: 0.9207 (mp) REVERT: N 62 ASN cc_start: 0.8837 (m-40) cc_final: 0.8503 (t0) REVERT: N 67 THR cc_start: 0.8950 (p) cc_final: 0.8407 (t) REVERT: N 89 MET cc_start: 0.9008 (mmm) cc_final: 0.8543 (mmm) REVERT: S 66 MET cc_start: 0.8873 (mtp) cc_final: 0.8664 (mtt) outliers start: 30 outliers final: 16 residues processed: 197 average time/residue: 0.3314 time to fit residues: 96.9261 Evaluate side-chains 170 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 149 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 113 ARG Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 190 ASN Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 56 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 chunk 125 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 8 ASN G 122 ASN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 19762 Z= 0.420 Angle : 0.748 12.737 28897 Z= 0.377 Chirality : 0.041 0.256 3604 Planarity : 0.005 0.049 1988 Dihedral : 23.529 178.698 8369 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 23.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 4.03 % Allowed : 21.79 % Favored : 74.18 % 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: -0.97 (0.24), residues: 1087 helix: -0.12 (0.22), residues: 515 sheet: -0.94 (0.38), residues: 164 loop : -1.00 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP G 103 HIS 0.008 0.002 HIS C 6 PHE 0.014 0.002 PHE B 184 TYR 0.031 0.002 TYR I 90 ARG 0.009 0.001 ARG C 132 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 150 time to evaluate : 1.316 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 PHE cc_start: 0.7076 (m-80) cc_final: 0.6815 (m-80) REVERT: B 154 MET cc_start: 0.7910 (tpp) cc_final: 0.7631 (tpt) REVERT: B 184 PHE cc_start: 0.7729 (m-80) cc_final: 0.6865 (m-10) REVERT: B 192 ASP cc_start: 0.6907 (OUTLIER) cc_final: 0.6059 (t70) REVERT: C 36 ASP cc_start: 0.8908 (m-30) cc_final: 0.8356 (m-30) REVERT: C 102 ASN cc_start: 0.9034 (m-40) cc_final: 0.8805 (m-40) REVERT: C 183 ASP cc_start: 0.8646 (t0) cc_final: 0.8374 (t0) REVERT: I 42 GLU cc_start: 0.8485 (tp30) cc_final: 0.8075 (tp30) REVERT: I 46 MET cc_start: 0.8948 (mtt) cc_final: 0.7810 (mtt) REVERT: I 50 GLN cc_start: 0.9195 (mm-40) cc_final: 0.8851 (mm-40) REVERT: I 88 MET cc_start: 0.9082 (ttm) cc_final: 0.8878 (tpp) REVERT: J 63 ASP cc_start: 0.8201 (t70) cc_final: 0.7666 (t70) REVERT: J 97 ASP cc_start: 0.8129 (t70) cc_final: 0.7912 (t0) REVERT: J 99 GLN cc_start: 0.6442 (mp10) cc_final: 0.6110 (mp10) REVERT: M 27 LYS cc_start: 0.9568 (tptm) cc_final: 0.9115 (mmtt) REVERT: M 42 ASP cc_start: 0.7695 (m-30) cc_final: 0.7395 (t0) REVERT: M 81 MET cc_start: 0.9117 (mtp) cc_final: 0.8814 (mtt) REVERT: N 62 ASN cc_start: 0.8868 (m-40) cc_final: 0.8551 (t0) REVERT: N 67 THR cc_start: 0.9212 (p) cc_final: 0.8725 (t) REVERT: N 86 GLU cc_start: 0.9183 (mp0) cc_final: 0.8808 (mp0) REVERT: N 89 MET cc_start: 0.9059 (mmm) cc_final: 0.8830 (mmm) outliers start: 37 outliers final: 29 residues processed: 174 average time/residue: 0.3086 time to fit residues: 81.6521 Evaluate side-chains 168 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 138 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 190 ASN Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain M residue 31 LYS Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain N residue 14 VAL Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 20 GLU Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 71 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 7.9990 chunk 132 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 86 optimal weight: 7.9990 chunk 36 optimal weight: 8.9990 chunk 147 optimal weight: 0.9980 chunk 122 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 8 ASN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19762 Z= 0.194 Angle : 0.628 12.435 28897 Z= 0.320 Chirality : 0.037 0.237 3604 Planarity : 0.004 0.052 1988 Dihedral : 23.448 178.790 8369 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.59 % Allowed : 22.55 % Favored : 73.86 % 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: -0.83 (0.25), residues: 1087 helix: -0.05 (0.22), residues: 511 sheet: -1.03 (0.39), residues: 165 loop : -0.78 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP G 103 HIS 0.004 0.001 HIS B 18 PHE 0.014 0.001 PHE B 184 TYR 0.010 0.002 TYR I 7 ARG 0.008 0.000 ARG C 132 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 161 time to evaluate : 1.274 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 137 ARG cc_start: 0.8445 (ttt180) cc_final: 0.8211 (ttt180) REVERT: B 154 MET cc_start: 0.7626 (tpp) cc_final: 0.7204 (tpt) REVERT: B 161 LEU cc_start: 0.8360 (tp) cc_final: 0.8071 (tt) REVERT: B 184 PHE cc_start: 0.7672 (m-80) cc_final: 0.6772 (m-10) REVERT: B 192 ASP cc_start: 0.6464 (OUTLIER) cc_final: 0.6066 (t70) REVERT: C 36 ASP cc_start: 0.8738 (m-30) cc_final: 0.8185 (m-30) REVERT: C 102 ASN cc_start: 0.8969 (m-40) cc_final: 0.8728 (m-40) REVERT: C 183 ASP cc_start: 0.8593 (t0) cc_final: 0.8333 (t0) REVERT: C 211 MET cc_start: 0.7184 (mmm) cc_final: 0.6981 (mmm) REVERT: I 42 GLU cc_start: 0.8399 (tp30) cc_final: 0.7881 (tp30) REVERT: I 46 MET cc_start: 0.8877 (mtt) cc_final: 0.7608 (mtt) REVERT: I 50 GLN cc_start: 0.9231 (mm-40) cc_final: 0.8900 (mm-40) REVERT: I 88 MET cc_start: 0.8971 (ttm) cc_final: 0.8439 (mmm) REVERT: I 115 LYS cc_start: 0.9041 (mttt) cc_final: 0.8654 (mmtt) REVERT: J 63 ASP cc_start: 0.8287 (t70) cc_final: 0.7754 (t70) REVERT: M 27 LYS cc_start: 0.9532 (tptm) cc_final: 0.9144 (tptt) REVERT: M 42 ASP cc_start: 0.7719 (m-30) cc_final: 0.7439 (t0) REVERT: M 81 MET cc_start: 0.9094 (mtp) cc_final: 0.8791 (mtt) REVERT: N 62 ASN cc_start: 0.8796 (m-40) cc_final: 0.8461 (t0) REVERT: N 67 THR cc_start: 0.9109 (p) cc_final: 0.8602 (t) REVERT: N 86 GLU cc_start: 0.9136 (mp0) cc_final: 0.8755 (mp0) outliers start: 33 outliers final: 25 residues processed: 185 average time/residue: 0.3055 time to fit residues: 86.6731 Evaluate side-chains 165 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 139 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 190 ASN Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 71 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 89 optimal weight: 0.3980 chunk 67 optimal weight: 0.0570 chunk 90 optimal weight: 1.9990 overall best weight: 1.8904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 8 ASN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19762 Z= 0.199 Angle : 0.629 11.989 28897 Z= 0.320 Chirality : 0.036 0.237 3604 Planarity : 0.004 0.055 1988 Dihedral : 23.404 178.658 8369 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.81 % Allowed : 23.53 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.25), residues: 1087 helix: 0.01 (0.22), residues: 500 sheet: -0.82 (0.38), residues: 171 loop : -0.72 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP G 103 HIS 0.004 0.001 HIS S 14 PHE 0.011 0.001 PHE B 184 TYR 0.015 0.002 TYR C 42 ARG 0.008 0.000 ARG B 222 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 149 time to evaluate : 1.183 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: symmetry clash revert: symmetry clash REVERT: B 154 MET cc_start: 0.7763 (tpp) cc_final: 0.7533 (tpt) REVERT: B 161 LEU cc_start: 0.8349 (tp) cc_final: 0.8055 (tt) REVERT: B 184 PHE cc_start: 0.7659 (m-80) cc_final: 0.6856 (m-80) REVERT: B 192 ASP cc_start: 0.6433 (OUTLIER) cc_final: 0.6085 (t70) REVERT: C 36 ASP cc_start: 0.8676 (m-30) cc_final: 0.8192 (m-30) REVERT: C 183 ASP cc_start: 0.8603 (t0) cc_final: 0.8341 (t0) REVERT: G 53 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7540 (ptt-90) REVERT: I 42 GLU cc_start: 0.8448 (tp30) cc_final: 0.7914 (tp30) REVERT: I 46 MET cc_start: 0.8909 (mtt) cc_final: 0.7708 (mtt) REVERT: I 50 GLN cc_start: 0.9219 (mm-40) cc_final: 0.8811 (mm-40) REVERT: I 88 MET cc_start: 0.8974 (ttm) cc_final: 0.8731 (mmm) REVERT: I 115 LYS cc_start: 0.9029 (mttt) cc_final: 0.8637 (mmtt) REVERT: J 63 ASP cc_start: 0.8275 (t70) cc_final: 0.7696 (t70) REVERT: M 27 LYS cc_start: 0.9526 (tptm) cc_final: 0.9140 (tptt) REVERT: M 42 ASP cc_start: 0.7769 (m-30) cc_final: 0.7516 (t0) REVERT: M 81 MET cc_start: 0.9138 (mtp) cc_final: 0.8825 (mtt) REVERT: N 62 ASN cc_start: 0.8801 (m-40) cc_final: 0.8472 (t0) REVERT: N 67 THR cc_start: 0.9151 (p) cc_final: 0.8636 (t) outliers start: 35 outliers final: 27 residues processed: 173 average time/residue: 0.3192 time to fit residues: 82.9361 Evaluate side-chains 164 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 135 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain M residue 31 LYS Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain N residue 60 GLN Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 71 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 93 optimal weight: 0.5980 chunk 99 optimal weight: 20.0000 chunk 72 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 140 optimal weight: 1.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 ASN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 GLN N 60 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19762 Z= 0.254 Angle : 0.651 11.046 28897 Z= 0.333 Chirality : 0.037 0.238 3604 Planarity : 0.005 0.057 1988 Dihedral : 23.435 179.330 8369 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 4.25 % Allowed : 23.86 % Favored : 71.90 % 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: -0.78 (0.24), residues: 1087 helix: -0.08 (0.22), residues: 504 sheet: -0.65 (0.40), residues: 169 loop : -0.81 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP G 103 HIS 0.004 0.001 HIS S 14 PHE 0.017 0.001 PHE B 90 TYR 0.018 0.002 TYR I 90 ARG 0.009 0.001 ARG B 222 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 145 time to evaluate : 1.423 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: symmetry clash REVERT: B 161 LEU cc_start: 0.8326 (tp) cc_final: 0.8045 (tt) REVERT: B 184 PHE cc_start: 0.7629 (m-80) cc_final: 0.6849 (m-80) REVERT: B 192 ASP cc_start: 0.7000 (OUTLIER) cc_final: 0.6279 (t0) REVERT: C 36 ASP cc_start: 0.8696 (m-30) cc_final: 0.8206 (m-30) REVERT: C 183 ASP cc_start: 0.8620 (t0) cc_final: 0.8345 (t0) REVERT: G 53 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.7486 (ptt-90) REVERT: I 42 GLU cc_start: 0.8501 (tp30) cc_final: 0.8027 (tp30) REVERT: I 46 MET cc_start: 0.8900 (mtt) cc_final: 0.7732 (mtt) REVERT: I 50 GLN cc_start: 0.9231 (mm-40) cc_final: 0.8822 (mm-40) REVERT: I 115 LYS cc_start: 0.9043 (mttt) cc_final: 0.8622 (mmtt) REVERT: J 63 ASP cc_start: 0.8250 (t70) cc_final: 0.7689 (t70) REVERT: M 27 LYS cc_start: 0.9531 (tptm) cc_final: 0.9150 (tptt) REVERT: M 42 ASP cc_start: 0.7722 (m-30) cc_final: 0.7428 (t0) REVERT: M 81 MET cc_start: 0.9153 (mtp) cc_final: 0.8840 (mtt) REVERT: N 62 ASN cc_start: 0.8773 (m-40) cc_final: 0.8439 (t0) REVERT: N 67 THR cc_start: 0.9185 (p) cc_final: 0.8699 (t) outliers start: 39 outliers final: 30 residues processed: 173 average time/residue: 0.3281 time to fit residues: 86.3410 Evaluate side-chains 170 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 138 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 19 ASN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain M residue 31 LYS Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain N residue 14 VAL Chi-restraints excluded: chain N residue 60 GLN Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 71 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 140 optimal weight: 0.0020 chunk 82 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 ASN ** C 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19762 Z= 0.165 Angle : 0.627 11.620 28897 Z= 0.320 Chirality : 0.036 0.239 3604 Planarity : 0.004 0.055 1988 Dihedral : 23.341 177.473 8369 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.94 % Allowed : 24.84 % Favored : 72.22 % 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: -0.84 (0.24), residues: 1087 helix: -0.14 (0.22), residues: 499 sheet: -0.51 (0.41), residues: 164 loop : -0.89 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP G 103 HIS 0.002 0.001 HIS B 18 PHE 0.011 0.001 PHE B 184 TYR 0.016 0.001 TYR I 90 ARG 0.010 0.000 ARG N 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 157 time to evaluate : 1.280 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 184 PHE cc_start: 0.7561 (m-80) cc_final: 0.6755 (m-80) REVERT: B 192 ASP cc_start: 0.6835 (OUTLIER) cc_final: 0.6166 (t0) REVERT: C 36 ASP cc_start: 0.8611 (m-30) cc_final: 0.8184 (m-30) REVERT: C 183 ASP cc_start: 0.8577 (t0) cc_final: 0.8327 (t0) REVERT: C 211 MET cc_start: 0.7067 (mmm) cc_final: 0.6779 (mmm) REVERT: G 53 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7632 (ptt-90) REVERT: I 42 GLU cc_start: 0.8493 (tp30) cc_final: 0.8024 (tp30) REVERT: I 46 MET cc_start: 0.8848 (mtt) cc_final: 0.7620 (mtt) REVERT: I 50 GLN cc_start: 0.9237 (mm-40) cc_final: 0.8900 (mm-40) REVERT: I 115 LYS cc_start: 0.9015 (mttt) cc_final: 0.8639 (mmtt) REVERT: J 63 ASP cc_start: 0.8331 (t70) cc_final: 0.7750 (t70) REVERT: J 88 MET cc_start: 0.8635 (mtm) cc_final: 0.8281 (mmm) REVERT: M 27 LYS cc_start: 0.9483 (tptm) cc_final: 0.9084 (tptt) REVERT: M 42 ASP cc_start: 0.7801 (m-30) cc_final: 0.7502 (t0) REVERT: M 81 MET cc_start: 0.9181 (mtp) cc_final: 0.8944 (ttm) REVERT: N 62 ASN cc_start: 0.8750 (m-40) cc_final: 0.8362 (t0) REVERT: N 67 THR cc_start: 0.9114 (p) cc_final: 0.8556 (t) REVERT: N 86 GLU cc_start: 0.9183 (pt0) cc_final: 0.8931 (pt0) REVERT: S 5 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9073 (mm) outliers start: 27 outliers final: 19 residues processed: 176 average time/residue: 0.3372 time to fit residues: 89.0366 Evaluate side-chains 159 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 137 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 19 ASN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain N residue 60 GLN Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 71 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 20.0000 chunk 68 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 chunk 139 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 93 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 HIS ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4600 Sorry: Reduce crashed with command 'molprobity.reduce -oh -his -flip -keep -allalt -limit120 -pen9999 -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: Processing file: --standard input-- Building His ring NH Hydrogens. Building or keeping OH & SH Hydrogens. Rotating existing OH & SH Hydrogens WARNING: atom HM21 from 2MG will be treated as hydrogen WARNING: atom HM21 from 2MG will be treated as hydrogen WARNING: atom HM22 from 2MG will be treated as hydrogen WARNING: atom HM23 from 2MG will be treated as hydrogen WARNING: atom HM22 from 2MG will be treated as hydrogen WARNING: atom HM21 from 2MG will be treated as hydrogen WARNING: atom HM22 from 2MG will be treated as hydrogen WARNING: atom HM23 from 2MG will be treated as hydrogen WARNING: atom HM23 from 2MG will be treated as hydrogen WARNING: atom HM21 from 2MG will be treated as hydrogen WARNING: atom HM22 from 2MG will be treated as hydrogen WARNING: atom HM23 from 2MG will be treated as hydrogen WARNING: atom HM23 from 2MG will be treated as hydrogen WARNING: atom HM23 from 2MG will be treated as hydrogen WARNING: atom HM22 from 2MG will be treated as hydrogen WARNING: atom HM21 from 2MG will be treated as hydrogen WARNING: atom HM22 from 2MG will be treated as hydrogen WARNING: atom HM23 from 2MG will be treated as hydrogen WARNING: atom HM22 from 2MG will be treated as hydrogen WARNING: atom HM21 from 2MG will be treated as hydrogen WARNING: atom HM21 from 2MG will be treated as hydrogen WARNING: atom HM23 from 2MG will be treated as hydrogen WARNING: atom HM22 from 2MG will be treated as hydrogen WARNING: atom HM21 from 2MG will be treated as hydrogen WARNING: atom HM51 from 5MC will be treated as hydrogen WARNING: atom HM51 from 5MC will be treated as hydrogen WARNING: atom HM52 from 5MC will be treated as hydrogen WARNING: atom HM53 from 5MC will be treated as hydrogen WARNING: atom HM52 from 5MC will be treated as hydrogen WARNING: atom HM51 from 5MC will be treated as hydrogen WARNING: atom HM52 from 5MC will be treated as hydrogen WARNING: atom HM53 from 5MC will be treated as hydrogen WARNING: atom HM53 from 5MC will be treated as hydrogen WARNING: atom HM51 from 5MC will be treated as hydrogen WARNING: atom HM52 from 5MC will be treated as hydrogen WARNING: atom HM53 from 5MC will be treated as hydrogen WARNING: atom HN41 from 5MC will be treated as hydrogen WARNING: atom HN41 from 5MC will be treated as hydrogen WARNING: atom HN42 from 5MC will be treated as hydrogen WARNING: atom HN42 from 5MC will be treated as hydrogen WARNING: atom HN41 from 5MC will be treated as hydrogen WARNING: atom HN42 from 5MC will be treated as hydrogen WARNING: atom HN42 from 5MC will be treated as hydrogen WARNING: atom HN41 from 5MC will be treated as hydrogen WARNING: atom HM53 from 5MC will be treated as hydrogen WARNING: atom HM53 from 5MC will be treated as hydrogen WARNING: atom HM52 from 5MC will be treated as hydrogen WARNING: atom HM51 from 5MC will be treated as hydrogen WARNING: atom HM52 from 5MC will be treated as hydrogen WARNING: atom HM53 from 5MC will be treated as hydrogen WARNING: atom HM52 from 5MC will be treated as hydrogen WARNING: atom HM51 from 5MC will be treated as hydrogen WARNING: atom HM51 from 5MC will be treated as hydrogen WARNING: atom HM53 from 5MC will be treated as hydrogen WARNING: atom HM52 from 5MC will be treated as hydrogen WARNING: atom HM51 from 5MC will be treated as hydrogen WARNING: atom HM21 from 2MG will be treated as hydrogen WARNING: atom HM21 from 2MG will be treated as hydrogen WARNING: atom HM22 from 2MG will be treated as hydrogen WARNING: atom HM23 from 2MG will be treated as hydrogen WARNING: atom HM22 from 2MG will be treated as hydrogen WARNING: atom HM21 from 2MG will be treated as hydrogen WARNING: atom HM22 from 2MG will be treated as hydrogen WARNING: atom HM23 from 2MG will be treated as hydrogen WARNING: atom HM23 from 2MG will be treated as hydrogen WARNING: atom HM21 from 2MG will be treated as hydrogen WARNING: atom HM22 from 2MG will be treated as hydrogen WARNING: atom HM23 from 2MG will be treated as hydrogen WARNING: atom HM23 from 2MG will be treated as hydrogen WARNING: atom HM23 from 2MG will be treated as hydrogen WARNING: atom HM22 from 2MG will be treated as hydrogen WARNING: atom HM21 from 2MG will be treated as hydrogen WARNING: atom HM22 from 2MG will be treated as hydrogen WARNING: atom HM23 from 2MG will be treated as hydrogen WARNING: atom HM22 from 2MG will be treated as hydrogen WARNING: atom HM21 from 2MG will be treated as hydrogen WARNING: atom HM21 from 2MG will be treated as hydrogen WARNING: atom HM23 from 2MG will be treated as hydrogen WARNING: atom HM22 from 2MG will be treated as hydrogen WARNING: atom HM21 from 2MG will be treated as hydrogen VDW dot density = 16/A^2 Orientation penalty scale = 9999 (999900%) Eliminate contacts within 3 bonds. Ignore atoms with |occupancy| <= 0.01 during adjustments. Waters ignored if B-Factor >= 40 or |occupancy| < 0.66 Aromatic rings in amino acids accept hydrogen bonds. Flipping Asn, Gln and His groups. For each flip state, bumps where gap is more than 0.4A are indicated with '!'. Rotating NH3 Hydrogens. Not processing Met methyls.