Starting phenix.real_space_refine on Fri Feb 16 23:10:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ys5_10892/02_2024/6ys5_10892.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ys5_10892/02_2024/6ys5_10892.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ys5_10892/02_2024/6ys5_10892.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ys5_10892/02_2024/6ys5_10892.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ys5_10892/02_2024/6ys5_10892.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ys5_10892/02_2024/6ys5_10892.pdb" } resolution = 3.0 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 477 5.49 5 Mg 24 5.21 5 S 24 5.16 5 C 8718 2.51 5 N 3115 2.21 5 O 4506 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "d TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 41": "OE1" <-> "OE2" Residue "d ASP 83": "OD1" <-> "OD2" Residue "d GLU 118": "OE1" <-> "OE2" Residue "d GLU 125": "OE1" <-> "OE2" Residue "d GLU 166": "OE1" <-> "OE2" Residue "d TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 188": "NH1" <-> "NH2" Residue "d GLU 190": "OE1" <-> "OE2" Residue "d PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 10": "NH1" <-> "NH2" Residue "h GLU 11": "OE1" <-> "OE2" Residue "h PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 49": "NH1" <-> "NH2" Residue "h GLU 52": "OE1" <-> "OE2" Residue "h ASP 57": "OD1" <-> "OD2" Residue "h GLU 60": "OE1" <-> "OE2" Residue "h PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 63": "OE1" <-> "OE2" Residue "h GLU 67": "OE1" <-> "OE2" Residue "h ARG 70": "NH1" <-> "NH2" Residue "h ARG 102": "NH1" <-> "NH2" Residue "h ARG 111": "NH1" <-> "NH2" Residue "h ARG 119": "NH1" <-> "NH2" Residue "h GLU 123": "OE1" <-> "OE2" Residue "j TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 10": "NH1" <-> "NH2" Residue "j PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 54": "OE1" <-> "OE2" Residue "j TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 105": "OD1" <-> "OD2" Residue "j GLU 108": "OE1" <-> "OE2" Residue "j ARG 122": "NH1" <-> "NH2" Residue "k ASP 14": "OD1" <-> "OD2" Residue "k GLU 24": "OE1" <-> "OE2" Residue "k PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 75": "OD1" <-> "OD2" Residue "n TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 49": "OD1" <-> "OD2" Residue "n ASP 50": "OD1" <-> "OD2" Residue "n ASP 68": "OD1" <-> "OD2" Residue "n TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 10": "OE1" <-> "OE2" Residue "o GLU 39": "OE1" <-> "OE2" Residue "o GLU 40": "OE1" <-> "OE2" Residue "o PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16864 Number of models: 1 Model: "" Number of chains: 13 Chain: "3" Number of atoms: 9676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 9676 Classifications: {'RNA': 453} Modifications used: {'rna2p_pur': 35, 'rna2p_pyr': 39, 'rna3p_pur': 208, 'rna3p_pyr': 171} Link IDs: {'rna2p': 74, 'rna3p': 378} Chain breaks: 1 Chain: "7" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 428 Classifications: {'RNA': 20} Modifications used: {'rna3p_pur': 11, 'rna3p_pyr': 9} Link IDs: {'rna3p': 19} Chain: "9" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 80 Classifications: {'RNA': 4} Modifications used: {'rna3p_pyr': 4} Link IDs: {'rna3p': 3} Chain: "d" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1649 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 7, 'TRANS': 202} Chain: "h" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 871 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "j" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 995 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "k" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 797 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "n" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 903 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "o" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 791 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "t" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 650 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "3" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Unusual residues: {' MG': 22} Classifications: {'undetermined': 22} Link IDs: {None: 21} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.55, per 1000 atoms: 0.57 Number of scatterers: 16864 At special positions: 0 Unit cell: (116.63, 123.05, 128.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 24 16.00 P 477 15.00 Mg 24 11.99 O 4506 8.00 N 3115 7.00 C 8718 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.28 Conformation dependent library (CDL) restraints added in 1.3 seconds 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1574 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 7 sheets defined 45.8% alpha, 16.9% beta 135 base pairs and 251 stacking pairs defined. Time for finding SS restraints: 7.24 Creating SS restraints... Processing helix chain 'd' and resid 8 through 12 removed outlier: 3.903A pdb=" N LEU d 12 " --> pdb=" O GLY d 9 " (cutoff:3.500A) Processing helix chain 'd' and resid 28 through 47 removed outlier: 3.534A pdb=" N GLN d 38 " --> pdb=" O LEU d 34 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL d 39 " --> pdb=" O LYS d 35 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LYS d 45 " --> pdb=" O GLU d 41 " (cutoff:3.500A) Processing helix chain 'd' and resid 72 through 78 removed outlier: 3.810A pdb=" N VAL d 76 " --> pdb=" O ARG d 72 " (cutoff:3.500A) Processing helix chain 'd' and resid 83 through 96 removed outlier: 3.549A pdb=" N GLN d 88 " --> pdb=" O ILE d 84 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG d 89 " --> pdb=" O GLU d 85 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ASN d 93 " --> pdb=" O ARG d 89 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE d 94 " --> pdb=" O GLU d 90 " (cutoff:3.500A) Processing helix chain 'd' and resid 112 through 125 removed outlier: 3.523A pdb=" N VAL d 116 " --> pdb=" O ASP d 112 " (cutoff:3.500A) Processing helix chain 'd' and resid 129 through 143 removed outlier: 3.658A pdb=" N ARG d 143 " --> pdb=" O GLN d 139 " (cutoff:3.500A) Processing helix chain 'd' and resid 156 through 160 removed outlier: 3.524A pdb=" N GLY d 159 " --> pdb=" O ARG d 156 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA d 160 " --> pdb=" O LEU d 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 156 through 160' Processing helix chain 'h' and resid 20 through 31 removed outlier: 3.884A pdb=" N ALA h 24 " --> pdb=" O SER h 20 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS h 29 " --> pdb=" O LYS h 25 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL h 30 " --> pdb=" O PHE h 26 " (cutoff:3.500A) Processing helix chain 'h' and resid 35 through 53 removed outlier: 3.531A pdb=" N ALA h 39 " --> pdb=" O LYS h 35 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU h 52 " --> pdb=" O GLU h 48 " (cutoff:3.500A) Processing helix chain 'h' and resid 57 through 70 removed outlier: 3.692A pdb=" N GLU h 63 " --> pdb=" O VAL h 59 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU h 67 " --> pdb=" O GLU h 63 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS h 68 " --> pdb=" O THR h 64 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL h 69 " --> pdb=" O THR h 65 " (cutoff:3.500A) Processing helix chain 'h' and resid 98 through 108 Processing helix chain 'h' and resid 115 through 129 removed outlier: 3.661A pdb=" N ALA h 121 " --> pdb=" O ALA h 117 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU h 123 " --> pdb=" O ARG h 119 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU h 125 " --> pdb=" O ALA h 121 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU h 129 " --> pdb=" O LEU h 125 " (cutoff:3.500A) Processing helix chain 'h' and resid 138 through 144 removed outlier: 3.525A pdb=" N MET h 144 " --> pdb=" O ASP h 140 " (cutoff:3.500A) Processing helix chain 'j' and resid 32 through 37 Processing helix chain 'j' and resid 39 through 47 removed outlier: 3.825A pdb=" N ARG j 43 " --> pdb=" O ARG j 39 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N MET j 44 " --> pdb=" O GLU j 40 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL j 45 " --> pdb=" O THR j 41 " (cutoff:3.500A) Processing helix chain 'j' and resid 47 through 53 removed outlier: 3.542A pdb=" N GLU j 51 " --> pdb=" O ARG j 47 " (cutoff:3.500A) Processing helix chain 'j' and resid 69 through 89 removed outlier: 3.671A pdb=" N ALA j 88 " --> pdb=" O ALA j 84 " (cutoff:3.500A) Processing helix chain 'j' and resid 92 through 99 Processing helix chain 'k' and resid 14 through 32 removed outlier: 3.689A pdb=" N GLN k 20 " --> pdb=" O ARG k 16 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU k 27 " --> pdb=" O GLN k 23 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR k 28 " --> pdb=" O GLU k 24 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR k 32 " --> pdb=" O THR k 28 " (cutoff:3.500A) Processing helix chain 'k' and resid 82 through 89 Processing helix chain 'n' and resid 14 through 19 Processing helix chain 'n' and resid 20 through 22 No H-bonds generated for 'chain 'n' and resid 20 through 22' Processing helix chain 'n' and resid 26 through 38 removed outlier: 3.641A pdb=" N ALA n 30 " --> pdb=" O GLY n 26 " (cutoff:3.500A) Processing helix chain 'n' and resid 44 through 48 removed outlier: 3.524A pdb=" N LEU n 48 " --> pdb=" O ILE n 45 " (cutoff:3.500A) Processing helix chain 'n' and resid 51 through 61 removed outlier: 4.126A pdb=" N ALA n 55 " --> pdb=" O ALA n 51 " (cutoff:3.500A) Processing helix chain 'n' and resid 65 through 84 removed outlier: 3.507A pdb=" N ASN n 76 " --> pdb=" O GLU n 72 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE n 77 " --> pdb=" O ILE n 73 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS n 78 " --> pdb=" O SER n 74 " (cutoff:3.500A) Processing helix chain 'n' and resid 85 through 93 Processing helix chain 'o' and resid 3 through 20 removed outlier: 3.727A pdb=" N ILE o 7 " --> pdb=" O LYS o 3 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN o 8 " --> pdb=" O LYS o 4 " (cutoff:3.500A) Processing helix chain 'o' and resid 20 through 32 removed outlier: 3.688A pdb=" N ARG o 24 " --> pdb=" O TYR o 20 " (cutoff:3.500A) Processing helix chain 'o' and resid 37 through 49 removed outlier: 3.676A pdb=" N MET o 45 " --> pdb=" O ARG o 41 " (cutoff:3.500A) Processing helix chain 'o' and resid 50 through 51 No H-bonds generated for 'chain 'o' and resid 50 through 51' Processing helix chain 'o' and resid 52 through 60 Proline residue: o 57 - end of helix removed outlier: 3.591A pdb=" N LEU o 60 " --> pdb=" O PRO o 57 " (cutoff:3.500A) Processing helix chain 'o' and resid 80 through 90 removed outlier: 3.515A pdb=" N ASP o 86 " --> pdb=" O ASN o 82 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN o 90 " --> pdb=" O ASP o 86 " (cutoff:3.500A) Processing helix chain 't' and resid 12 through 26 removed outlier: 3.538A pdb=" N ALA t 24 " --> pdb=" O GLU t 20 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER t 25 " --> pdb=" O ALA t 21 " (cutoff:3.500A) Processing helix chain 't' and resid 70 through 75 removed outlier: 3.537A pdb=" N ALA t 75 " --> pdb=" O GLY t 72 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'd' and resid 20 through 21 removed outlier: 3.637A pdb=" N ASN d 54 " --> pdb=" O SER d 69 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA d 64 " --> pdb=" O GLN d 100 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N SER d 102 " --> pdb=" O ALA d 64 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL d 66 " --> pdb=" O SER d 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'd' and resid 165 through 171 removed outlier: 3.617A pdb=" N GLY d 148 " --> pdb=" O PHE d 203 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG d 204 " --> pdb=" O ASP d 181 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASP d 181 " --> pdb=" O ARG d 204 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'j' and resid 4 through 7 removed outlier: 6.439A pdb=" N LYS j 25 " --> pdb=" O LEU j 61 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ILE j 63 " --> pdb=" O LYS j 25 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N VAL j 27 " --> pdb=" O ILE j 63 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'k' and resid 40 through 52 removed outlier: 6.824A pdb=" N LEU k 73 " --> pdb=" O PRO k 41 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LYS k 71 " --> pdb=" O PRO k 43 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'k' and resid 40 through 52 removed outlier: 6.824A pdb=" N LEU k 73 " --> pdb=" O PRO k 41 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LYS k 71 " --> pdb=" O PRO k 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'n' and resid 3 through 4 Processing sheet with id=AA7, first strand: chain 't' and resid 31 through 33 284 hydrogen bonds defined for protein. 813 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 345 hydrogen bonds 578 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 251 stacking parallelities Total time for adding SS restraints: 8.00 Time building geometry restraints manager: 8.80 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: 2376 1.32 - 1.45: 7110 1.45 - 1.57: 7656 1.57 - 1.69: 950 1.69 - 1.81: 45 Bond restraints: 18137 Sorted by residual: bond pdb=" CA ARG n 107 " pdb=" C ARG n 107 " ideal model delta sigma weight residual 1.522 1.487 0.035 1.72e-02 3.38e+03 4.04e+00 bond pdb=" C ALA n 106 " pdb=" N ARG n 107 " ideal model delta sigma weight residual 1.333 1.309 0.024 1.56e-02 4.11e+03 2.39e+00 bond pdb=" CG ARG j 120 " pdb=" CD ARG j 120 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.36e+00 bond pdb=" CB GLU o 14 " pdb=" CG GLU o 14 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.05e+00 bond pdb=" CB ARG j 122 " pdb=" CG ARG j 122 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.01e+00 ... (remaining 18132 not shown) Histogram of bond angle deviations from ideal: 98.91 - 105.96: 2660 105.96 - 113.01: 10411 113.01 - 120.06: 6696 120.06 - 127.12: 5973 127.12 - 134.17: 1072 Bond angle restraints: 26812 Sorted by residual: angle pdb=" C PRO k 55 " pdb=" N HIS k 56 " pdb=" CA HIS k 56 " ideal model delta sigma weight residual 122.44 116.36 6.08 1.19e+00 7.06e-01 2.61e+01 angle pdb=" N HIS k 56 " pdb=" CA HIS k 56 " pdb=" C HIS k 56 " ideal model delta sigma weight residual 111.02 117.89 -6.87 1.52e+00 4.33e-01 2.04e+01 angle pdb=" CA ARG n 107 " pdb=" C ARG n 107 " pdb=" N THR n 108 " ideal model delta sigma weight residual 118.59 124.29 -5.70 1.63e+00 3.76e-01 1.22e+01 angle pdb=" C2' A 3 955 " pdb=" C1' A 3 955 " pdb=" N9 A 3 955 " ideal model delta sigma weight residual 112.00 117.21 -5.21 1.50e+00 4.44e-01 1.21e+01 angle pdb=" C2' G 31353 " pdb=" C1' G 31353 " pdb=" N9 G 31353 " ideal model delta sigma weight residual 112.00 116.98 -4.98 1.50e+00 4.44e-01 1.10e+01 ... (remaining 26807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.83: 10385 34.83 - 69.65: 1080 69.65 - 104.48: 137 104.48 - 139.30: 3 139.30 - 174.13: 7 Dihedral angle restraints: 11612 sinusoidal: 9176 harmonic: 2436 Sorted by residual: dihedral pdb=" O4' C 3 964 " pdb=" C1' C 3 964 " pdb=" N1 C 3 964 " pdb=" C2 C 3 964 " ideal model delta sinusoidal sigma weight residual 200.00 40.76 159.24 1 1.50e+01 4.44e-03 8.26e+01 dihedral pdb=" O4' U 31156 " pdb=" C1' U 31156 " pdb=" N1 U 31156 " pdb=" C2 U 31156 " ideal model delta sinusoidal sigma weight residual -128.00 46.13 -174.13 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' U 3 957 " pdb=" C1' U 3 957 " pdb=" N1 U 3 957 " pdb=" C2 U 3 957 " ideal model delta sinusoidal sigma weight residual 232.00 58.17 173.83 1 1.70e+01 3.46e-03 6.62e+01 ... (remaining 11609 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2592 0.047 - 0.095: 638 0.095 - 0.142: 151 0.142 - 0.189: 26 0.189 - 0.236: 6 Chirality restraints: 3413 Sorted by residual: chirality pdb=" C1' G 31353 " pdb=" O4' G 31353 " pdb=" C2' G 31353 " pdb=" N9 G 31353 " both_signs ideal model delta sigma weight residual False 2.46 2.22 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" C3' U 7 27 " pdb=" C4' U 7 27 " pdb=" O3' U 7 27 " pdb=" C2' U 7 27 " both_signs ideal model delta sigma weight residual False -2.48 -2.26 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" C1' C 31155 " pdb=" O4' C 31155 " pdb=" C2' C 31155 " pdb=" N1 C 31155 " both_signs ideal model delta sigma weight residual False 2.47 2.25 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 3410 not shown) Planarity restraints: 1645 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A 3 955 " 0.047 2.00e-02 2.50e+03 2.20e-02 1.33e+01 pdb=" N9 A 3 955 " -0.052 2.00e-02 2.50e+03 pdb=" C8 A 3 955 " -0.005 2.00e-02 2.50e+03 pdb=" N7 A 3 955 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A 3 955 " 0.004 2.00e-02 2.50e+03 pdb=" C6 A 3 955 " 0.007 2.00e-02 2.50e+03 pdb=" N6 A 3 955 " 0.014 2.00e-02 2.50e+03 pdb=" N1 A 3 955 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A 3 955 " -0.008 2.00e-02 2.50e+03 pdb=" N3 A 3 955 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A 3 955 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 31354 " -0.042 2.00e-02 2.50e+03 1.94e-02 1.03e+01 pdb=" N9 A 31354 " 0.045 2.00e-02 2.50e+03 pdb=" C8 A 31354 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A 31354 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A 31354 " -0.004 2.00e-02 2.50e+03 pdb=" C6 A 31354 " -0.001 2.00e-02 2.50e+03 pdb=" N6 A 31354 " -0.013 2.00e-02 2.50e+03 pdb=" N1 A 31354 " -0.005 2.00e-02 2.50e+03 pdb=" C2 A 31354 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A 31354 " 0.011 2.00e-02 2.50e+03 pdb=" C4 A 31354 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 31353 " -0.038 2.00e-02 2.50e+03 1.71e-02 8.82e+00 pdb=" N9 G 31353 " 0.041 2.00e-02 2.50e+03 pdb=" C8 G 31353 " 0.005 2.00e-02 2.50e+03 pdb=" N7 G 31353 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G 31353 " 0.006 2.00e-02 2.50e+03 pdb=" C6 G 31353 " -0.009 2.00e-02 2.50e+03 pdb=" O6 G 31353 " -0.011 2.00e-02 2.50e+03 pdb=" N1 G 31353 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G 31353 " -0.006 2.00e-02 2.50e+03 pdb=" N2 G 31353 " 0.006 2.00e-02 2.50e+03 pdb=" N3 G 31353 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G 31353 " 0.001 2.00e-02 2.50e+03 ... (remaining 1642 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 59 2.48 - 3.09: 10419 3.09 - 3.69: 28528 3.69 - 4.30: 45757 4.30 - 4.90: 62981 Nonbonded interactions: 147744 Sorted by model distance: nonbonded pdb=" O6 G 31105 " pdb="MG MG 31608 " model vdw 1.880 2.170 nonbonded pdb=" OP1 U 31196 " pdb="MG MG 31606 " model vdw 1.981 2.170 nonbonded pdb=" O LYS h 114 " pdb=" NH1 ARG h 119 " model vdw 2.056 2.520 nonbonded pdb=" OP2 G 31301 " pdb="MG MG 31620 " model vdw 2.056 2.170 nonbonded pdb=" OP1 G 3 990 " pdb="MG MG 31614 " model vdw 2.064 2.170 ... (remaining 147739 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.220 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: 13.380 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 53.290 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 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 0.048 18137 Z= 0.454 Angle : 0.721 7.502 26812 Z= 0.392 Chirality : 0.046 0.236 3413 Planarity : 0.005 0.042 1645 Dihedral : 22.533 174.129 10038 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 7.15 % Allowed : 18.10 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.24), residues: 836 helix: -2.42 (0.22), residues: 344 sheet: 0.17 (0.44), residues: 125 loop : -2.42 (0.26), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP o 101 HIS 0.007 0.001 HIS k 15 PHE 0.012 0.002 PHE d 42 TYR 0.014 0.002 TYR d 29 ARG 0.004 0.001 ARG j 107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 170 time to evaluate : 1.107 Fit side-chains REVERT: d 11 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8635 (ptp-170) REVERT: d 110 ASP cc_start: 0.8014 (m-30) cc_final: 0.7761 (m-30) REVERT: d 152 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7468 (tm-30) REVERT: d 187 MET cc_start: 0.8303 (mmm) cc_final: 0.7661 (tpt) REVERT: h 3 ARG cc_start: 0.6482 (mtm-85) cc_final: 0.6222 (mtm-85) REVERT: h 10 ARG cc_start: 0.7570 (ttm110) cc_final: 0.7360 (ttm110) REVERT: h 62 PHE cc_start: 0.8326 (t80) cc_final: 0.8018 (t80) REVERT: j 40 GLU cc_start: 0.7673 (pp20) cc_final: 0.7391 (pp20) REVERT: k 47 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7275 (pt0) REVERT: n 79 ARG cc_start: 0.7445 (ttm110) cc_final: 0.7223 (ttm110) REVERT: n 107 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.7649 (mmp80) REVERT: o 85 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8081 (ttt180) outliers start: 49 outliers final: 26 residues processed: 204 average time/residue: 1.5923 time to fit residues: 357.0460 Evaluate side-chains 182 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 151 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 11 ARG Chi-restraints excluded: chain d residue 34 LEU Chi-restraints excluded: chain d residue 75 ILE Chi-restraints excluded: chain d residue 93 ASN Chi-restraints excluded: chain d residue 152 GLU Chi-restraints excluded: chain h residue 6 VAL Chi-restraints excluded: chain h residue 27 MET Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 64 THR Chi-restraints excluded: chain h residue 69 VAL Chi-restraints excluded: chain h residue 97 THR Chi-restraints excluded: chain j residue 26 LEU Chi-restraints excluded: chain j residue 50 LEU Chi-restraints excluded: chain j residue 51 GLU Chi-restraints excluded: chain j residue 56 THR Chi-restraints excluded: chain j residue 85 LEU Chi-restraints excluded: chain k residue 47 GLU Chi-restraints excluded: chain k residue 77 VAL Chi-restraints excluded: chain k residue 80 THR Chi-restraints excluded: chain n residue 40 THR Chi-restraints excluded: chain n residue 42 THR Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain n residue 65 THR Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain n residue 107 ARG Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain o residue 85 ARG Chi-restraints excluded: chain o residue 100 SER Chi-restraints excluded: chain t residue 23 VAL Chi-restraints excluded: chain t residue 50 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 118 optimal weight: 0.0040 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 6 HIS d 54 ASN d 104 ASN d 176 HIS h 29 HIS j 4 ASN j 30 ASN j 35 GLN j 73 GLN j 79 HIS j 124 GLN k 15 HIS k 50 ASN k 58 ASN k 64 GLN k 99 GLN n 76 ASN n 105 ASN o 8 ASN o 71 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18137 Z= 0.175 Angle : 0.534 6.884 26812 Z= 0.285 Chirality : 0.036 0.203 3413 Planarity : 0.004 0.038 1645 Dihedral : 22.405 176.299 8429 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.65 % Allowed : 24.38 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.27), residues: 836 helix: -0.87 (0.28), residues: 337 sheet: 0.99 (0.46), residues: 123 loop : -1.95 (0.27), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP o 101 HIS 0.007 0.001 HIS k 15 PHE 0.010 0.001 PHE h 61 TYR 0.008 0.001 TYR d 29 ARG 0.004 0.000 ARG d 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 163 time to evaluate : 1.082 Fit side-chains REVERT: h 10 ARG cc_start: 0.7560 (ttm110) cc_final: 0.7357 (ttm110) REVERT: j 27 VAL cc_start: 0.8947 (m) cc_final: 0.8724 (t) REVERT: k 47 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7299 (pt0) outliers start: 25 outliers final: 17 residues processed: 182 average time/residue: 1.4392 time to fit residues: 289.1822 Evaluate side-chains 169 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 151 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 69 SER Chi-restraints excluded: chain d residue 102 SER Chi-restraints excluded: chain d residue 110 ASP Chi-restraints excluded: chain d residue 192 THR Chi-restraints excluded: chain d residue 196 ILE Chi-restraints excluded: chain h residue 7 VAL Chi-restraints excluded: chain h residue 13 LEU Chi-restraints excluded: chain h residue 41 SER Chi-restraints excluded: chain h residue 69 VAL Chi-restraints excluded: chain h residue 110 LYS Chi-restraints excluded: chain j residue 26 LEU Chi-restraints excluded: chain j residue 85 LEU Chi-restraints excluded: chain k residue 47 GLU Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain n residue 68 ASP Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain t residue 23 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 118 optimal weight: 0.3980 chunk 127 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 117 optimal weight: 0.2980 chunk 40 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 3 GLN k 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 18137 Z= 0.300 Angle : 0.601 7.069 26812 Z= 0.315 Chirality : 0.040 0.217 3413 Planarity : 0.005 0.039 1645 Dihedral : 22.389 175.596 8386 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 5.99 % Allowed : 24.53 % Favored : 69.49 % 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: -1.12 (0.28), residues: 836 helix: -0.44 (0.28), residues: 335 sheet: 1.24 (0.47), residues: 123 loop : -1.69 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP o 101 HIS 0.005 0.001 HIS k 15 PHE 0.011 0.002 PHE h 61 TYR 0.012 0.002 TYR d 29 ARG 0.003 0.000 ARG n 113 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 155 time to evaluate : 1.173 Fit side-chains REVERT: d 152 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7655 (tm-30) REVERT: h 5 ARG cc_start: 0.6377 (OUTLIER) cc_final: 0.5120 (mmt90) REVERT: h 10 ARG cc_start: 0.7599 (ttm110) cc_final: 0.7265 (ttm110) REVERT: k 7 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7498 (mtm-85) REVERT: k 47 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7264 (pt0) outliers start: 41 outliers final: 28 residues processed: 178 average time/residue: 1.3990 time to fit residues: 275.3942 Evaluate side-chains 182 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 150 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain d residue 51 MET Chi-restraints excluded: chain d residue 69 SER Chi-restraints excluded: chain d residue 75 ILE Chi-restraints excluded: chain d residue 102 SER Chi-restraints excluded: chain d residue 110 ASP Chi-restraints excluded: chain d residue 122 SER Chi-restraints excluded: chain d residue 152 GLU Chi-restraints excluded: chain d residue 165 THR Chi-restraints excluded: chain d residue 192 THR Chi-restraints excluded: chain d residue 196 ILE Chi-restraints excluded: chain h residue 5 ARG Chi-restraints excluded: chain h residue 6 VAL Chi-restraints excluded: chain h residue 7 VAL Chi-restraints excluded: chain h residue 41 SER Chi-restraints excluded: chain h residue 64 THR Chi-restraints excluded: chain h residue 69 VAL Chi-restraints excluded: chain h residue 110 LYS Chi-restraints excluded: chain j residue 85 LEU Chi-restraints excluded: chain k residue 7 ARG Chi-restraints excluded: chain k residue 47 GLU Chi-restraints excluded: chain k residue 75 ASP Chi-restraints excluded: chain n residue 42 THR Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain n residue 65 THR Chi-restraints excluded: chain n residue 68 ASP Chi-restraints excluded: chain n residue 75 MET Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain t residue 23 VAL Chi-restraints excluded: chain t residue 50 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 2.9990 chunk 88 optimal weight: 0.4980 chunk 61 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 125 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 112 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 123 GLN h 54 ASN k 64 GLN k 99 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18137 Z= 0.182 Angle : 0.542 7.651 26812 Z= 0.286 Chirality : 0.037 0.203 3413 Planarity : 0.004 0.037 1645 Dihedral : 22.336 176.234 8384 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 5.55 % Allowed : 24.82 % Favored : 69.64 % 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: -0.81 (0.28), residues: 836 helix: -0.20 (0.29), residues: 341 sheet: 1.44 (0.48), residues: 123 loop : -1.54 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP o 101 HIS 0.003 0.001 HIS k 15 PHE 0.011 0.001 PHE h 61 TYR 0.008 0.001 TYR d 29 ARG 0.002 0.000 ARG d 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 153 time to evaluate : 1.130 Fit side-chains revert: symmetry clash REVERT: d 152 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7608 (tm-30) REVERT: h 5 ARG cc_start: 0.6257 (OUTLIER) cc_final: 0.5045 (mmt90) REVERT: h 10 ARG cc_start: 0.7584 (ttm110) cc_final: 0.7257 (ttm110) REVERT: j 27 VAL cc_start: 0.8968 (m) cc_final: 0.8719 (t) REVERT: j 40 GLU cc_start: 0.7441 (tm-30) cc_final: 0.7231 (tm-30) REVERT: j 51 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7226 (pp20) REVERT: k 7 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.7384 (mtm-85) REVERT: k 47 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7211 (pt0) REVERT: k 99 GLN cc_start: 0.8808 (mm-40) cc_final: 0.8550 (mm110) REVERT: t 18 LYS cc_start: 0.8974 (mttt) cc_final: 0.8765 (mttm) outliers start: 38 outliers final: 24 residues processed: 175 average time/residue: 1.4487 time to fit residues: 280.4897 Evaluate side-chains 177 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 148 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 75 ILE Chi-restraints excluded: chain d residue 102 SER Chi-restraints excluded: chain d residue 122 SER Chi-restraints excluded: chain d residue 152 GLU Chi-restraints excluded: chain d residue 165 THR Chi-restraints excluded: chain d residue 196 ILE Chi-restraints excluded: chain h residue 5 ARG Chi-restraints excluded: chain h residue 6 VAL Chi-restraints excluded: chain h residue 7 VAL Chi-restraints excluded: chain h residue 13 LEU Chi-restraints excluded: chain h residue 41 SER Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 64 THR Chi-restraints excluded: chain h residue 65 THR Chi-restraints excluded: chain h residue 69 VAL Chi-restraints excluded: chain h residue 110 LYS Chi-restraints excluded: chain j residue 51 GLU Chi-restraints excluded: chain j residue 85 LEU Chi-restraints excluded: chain k residue 7 ARG Chi-restraints excluded: chain k residue 47 GLU Chi-restraints excluded: chain k residue 75 ASP Chi-restraints excluded: chain n residue 42 THR Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain n residue 68 ASP Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain o residue 100 SER Chi-restraints excluded: chain t residue 23 VAL Chi-restraints excluded: chain t residue 50 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 107 optimal weight: 0.0070 chunk 86 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 123 GLN k 64 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 18137 Z= 0.272 Angle : 0.581 7.005 26812 Z= 0.305 Chirality : 0.039 0.212 3413 Planarity : 0.005 0.060 1645 Dihedral : 22.319 175.800 8384 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 5.99 % Allowed : 24.96 % Favored : 69.05 % 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: -0.69 (0.29), residues: 836 helix: -0.13 (0.29), residues: 345 sheet: 1.50 (0.48), residues: 123 loop : -1.44 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP o 101 HIS 0.005 0.001 HIS k 15 PHE 0.013 0.002 PHE h 61 TYR 0.011 0.001 TYR d 29 ARG 0.014 0.001 ARG d 143 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 147 time to evaluate : 1.114 Fit side-chains REVERT: d 152 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7613 (tm-30) REVERT: h 5 ARG cc_start: 0.6315 (OUTLIER) cc_final: 0.4957 (mmt90) REVERT: h 10 ARG cc_start: 0.7602 (ttm110) cc_final: 0.7252 (ttm110) REVERT: j 51 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7241 (pp20) REVERT: k 7 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.7455 (mtm-85) REVERT: k 47 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7272 (pt0) REVERT: k 99 GLN cc_start: 0.8813 (mm-40) cc_final: 0.8609 (mm110) REVERT: n 113 ARG cc_start: 0.7226 (OUTLIER) cc_final: 0.7025 (mtt180) outliers start: 41 outliers final: 28 residues processed: 172 average time/residue: 1.3612 time to fit residues: 259.9098 Evaluate side-chains 180 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 146 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain d residue 75 ILE Chi-restraints excluded: chain d residue 102 SER Chi-restraints excluded: chain d residue 122 SER Chi-restraints excluded: chain d residue 152 GLU Chi-restraints excluded: chain d residue 165 THR Chi-restraints excluded: chain d residue 192 THR Chi-restraints excluded: chain d residue 196 ILE Chi-restraints excluded: chain h residue 5 ARG Chi-restraints excluded: chain h residue 6 VAL Chi-restraints excluded: chain h residue 7 VAL Chi-restraints excluded: chain h residue 27 MET Chi-restraints excluded: chain h residue 41 SER Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 64 THR Chi-restraints excluded: chain h residue 65 THR Chi-restraints excluded: chain h residue 69 VAL Chi-restraints excluded: chain h residue 110 LYS Chi-restraints excluded: chain j residue 51 GLU Chi-restraints excluded: chain j residue 85 LEU Chi-restraints excluded: chain k residue 7 ARG Chi-restraints excluded: chain k residue 47 GLU Chi-restraints excluded: chain k residue 75 ASP Chi-restraints excluded: chain n residue 42 THR Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain n residue 68 ASP Chi-restraints excluded: chain n residue 75 MET Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain n residue 113 ARG Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain o residue 100 SER Chi-restraints excluded: chain t residue 23 VAL Chi-restraints excluded: chain t residue 50 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18137 Z= 0.205 Angle : 0.558 7.255 26812 Z= 0.294 Chirality : 0.037 0.201 3413 Planarity : 0.005 0.040 1645 Dihedral : 22.314 176.042 8384 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 4.96 % Allowed : 26.13 % Favored : 68.91 % 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: -0.56 (0.29), residues: 836 helix: 0.03 (0.29), residues: 344 sheet: 1.48 (0.48), residues: 123 loop : -1.39 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP o 101 HIS 0.004 0.001 HIS k 15 PHE 0.016 0.001 PHE h 61 TYR 0.009 0.001 TYR d 29 ARG 0.012 0.000 ARG d 143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 148 time to evaluate : 1.187 Fit side-chains REVERT: d 152 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7603 (tm-30) REVERT: h 5 ARG cc_start: 0.6296 (OUTLIER) cc_final: 0.5025 (mmt90) REVERT: j 40 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7447 (tp30) REVERT: j 51 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7230 (pp20) REVERT: k 7 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.7403 (mtm-85) REVERT: k 47 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7262 (pt0) REVERT: n 113 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.7023 (mtt180) REVERT: t 18 LYS cc_start: 0.8968 (mttt) cc_final: 0.8746 (mttm) outliers start: 34 outliers final: 24 residues processed: 167 average time/residue: 1.4008 time to fit residues: 258.9739 Evaluate side-chains 174 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 144 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 51 MET Chi-restraints excluded: chain d residue 75 ILE Chi-restraints excluded: chain d residue 102 SER Chi-restraints excluded: chain d residue 152 GLU Chi-restraints excluded: chain d residue 165 THR Chi-restraints excluded: chain d residue 196 ILE Chi-restraints excluded: chain h residue 5 ARG Chi-restraints excluded: chain h residue 6 VAL Chi-restraints excluded: chain h residue 7 VAL Chi-restraints excluded: chain h residue 27 MET Chi-restraints excluded: chain h residue 41 SER Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 64 THR Chi-restraints excluded: chain h residue 69 VAL Chi-restraints excluded: chain h residue 110 LYS Chi-restraints excluded: chain j residue 51 GLU Chi-restraints excluded: chain j residue 85 LEU Chi-restraints excluded: chain k residue 7 ARG Chi-restraints excluded: chain k residue 47 GLU Chi-restraints excluded: chain k residue 75 ASP Chi-restraints excluded: chain n residue 42 THR Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain n residue 68 ASP Chi-restraints excluded: chain n residue 75 MET Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain n residue 113 ARG Chi-restraints excluded: chain o residue 100 SER Chi-restraints excluded: chain t residue 23 VAL Chi-restraints excluded: chain t residue 50 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 125 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 123 GLN k 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18137 Z= 0.220 Angle : 0.561 11.213 26812 Z= 0.294 Chirality : 0.037 0.203 3413 Planarity : 0.005 0.039 1645 Dihedral : 22.287 176.019 8384 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 6.86 % Allowed : 24.82 % Favored : 68.32 % 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: -0.47 (0.29), residues: 836 helix: 0.11 (0.29), residues: 344 sheet: 1.53 (0.48), residues: 123 loop : -1.35 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP o 101 HIS 0.004 0.001 HIS k 15 PHE 0.014 0.001 PHE h 61 TYR 0.009 0.001 TYR d 29 ARG 0.010 0.000 ARG d 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 149 time to evaluate : 1.017 Fit side-chains REVERT: d 152 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7606 (tm-30) REVERT: h 5 ARG cc_start: 0.6239 (OUTLIER) cc_final: 0.4889 (mmt90) REVERT: j 51 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7225 (pp20) REVERT: k 7 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7393 (mtm-85) REVERT: k 47 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7242 (pt0) REVERT: n 113 ARG cc_start: 0.7237 (OUTLIER) cc_final: 0.7014 (mtt180) REVERT: t 18 LYS cc_start: 0.8961 (mttt) cc_final: 0.8746 (mttm) REVERT: t 29 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7619 (mttm) REVERT: t 63 THR cc_start: 0.9160 (m) cc_final: 0.8957 (m) outliers start: 47 outliers final: 32 residues processed: 178 average time/residue: 1.3750 time to fit residues: 271.5508 Evaluate side-chains 184 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 145 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain d residue 51 MET Chi-restraints excluded: chain d residue 75 ILE Chi-restraints excluded: chain d residue 76 VAL Chi-restraints excluded: chain d residue 102 SER Chi-restraints excluded: chain d residue 122 SER Chi-restraints excluded: chain d residue 152 GLU Chi-restraints excluded: chain d residue 165 THR Chi-restraints excluded: chain d residue 192 THR Chi-restraints excluded: chain d residue 196 ILE Chi-restraints excluded: chain h residue 5 ARG Chi-restraints excluded: chain h residue 6 VAL Chi-restraints excluded: chain h residue 7 VAL Chi-restraints excluded: chain h residue 27 MET Chi-restraints excluded: chain h residue 41 SER Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 64 THR Chi-restraints excluded: chain h residue 65 THR Chi-restraints excluded: chain h residue 69 VAL Chi-restraints excluded: chain h residue 110 LYS Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 51 GLU Chi-restraints excluded: chain j residue 85 LEU Chi-restraints excluded: chain k residue 7 ARG Chi-restraints excluded: chain k residue 47 GLU Chi-restraints excluded: chain k residue 75 ASP Chi-restraints excluded: chain k residue 80 THR Chi-restraints excluded: chain n residue 42 THR Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain n residue 68 ASP Chi-restraints excluded: chain n residue 75 MET Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain n residue 113 ARG Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain o residue 100 SER Chi-restraints excluded: chain t residue 23 VAL Chi-restraints excluded: chain t residue 29 LYS Chi-restraints excluded: chain t residue 50 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 123 GLN k 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 18137 Z= 0.374 Angle : 0.659 9.560 26812 Z= 0.341 Chirality : 0.043 0.225 3413 Planarity : 0.005 0.042 1645 Dihedral : 22.369 174.659 8384 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 6.42 % Allowed : 25.84 % Favored : 67.74 % 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: -0.62 (0.29), residues: 836 helix: -0.04 (0.29), residues: 344 sheet: 1.48 (0.48), residues: 123 loop : -1.41 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP o 101 HIS 0.006 0.001 HIS k 15 PHE 0.018 0.002 PHE h 61 TYR 0.012 0.002 TYR d 29 ARG 0.008 0.001 ARG d 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 146 time to evaluate : 1.206 Fit side-chains REVERT: d 152 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7630 (tm-30) REVERT: h 5 ARG cc_start: 0.6513 (OUTLIER) cc_final: 0.5051 (mmt90) REVERT: h 48 GLU cc_start: 0.6949 (pt0) cc_final: 0.6688 (pm20) REVERT: h 68 LYS cc_start: 0.7653 (tppt) cc_final: 0.7374 (tptm) REVERT: j 51 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7256 (pp20) REVERT: k 7 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.7486 (mtm-85) REVERT: n 113 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.7118 (mtt180) REVERT: t 63 THR cc_start: 0.9160 (m) cc_final: 0.8930 (m) outliers start: 44 outliers final: 33 residues processed: 173 average time/residue: 1.4202 time to fit residues: 271.7019 Evaluate side-chains 179 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 141 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain d residue 51 MET Chi-restraints excluded: chain d residue 75 ILE Chi-restraints excluded: chain d residue 76 VAL Chi-restraints excluded: chain d residue 93 ASN Chi-restraints excluded: chain d residue 102 SER Chi-restraints excluded: chain d residue 122 SER Chi-restraints excluded: chain d residue 141 THR Chi-restraints excluded: chain d residue 152 GLU Chi-restraints excluded: chain d residue 165 THR Chi-restraints excluded: chain d residue 192 THR Chi-restraints excluded: chain d residue 196 ILE Chi-restraints excluded: chain h residue 5 ARG Chi-restraints excluded: chain h residue 6 VAL Chi-restraints excluded: chain h residue 27 MET Chi-restraints excluded: chain h residue 41 SER Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 64 THR Chi-restraints excluded: chain h residue 65 THR Chi-restraints excluded: chain h residue 69 VAL Chi-restraints excluded: chain h residue 110 LYS Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 51 GLU Chi-restraints excluded: chain j residue 85 LEU Chi-restraints excluded: chain k residue 7 ARG Chi-restraints excluded: chain k residue 75 ASP Chi-restraints excluded: chain k residue 80 THR Chi-restraints excluded: chain n residue 42 THR Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain n residue 68 ASP Chi-restraints excluded: chain n residue 75 MET Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain n residue 113 ARG Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain o residue 100 SER Chi-restraints excluded: chain t residue 23 VAL Chi-restraints excluded: chain t residue 50 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 chunk 120 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 110 optimal weight: 0.5980 chunk 76 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: k 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18137 Z= 0.172 Angle : 0.569 11.277 26812 Z= 0.300 Chirality : 0.037 0.199 3413 Planarity : 0.004 0.038 1645 Dihedral : 22.327 175.480 8381 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 4.53 % Allowed : 27.30 % Favored : 68.18 % 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: -0.45 (0.29), residues: 836 helix: 0.12 (0.29), residues: 349 sheet: 1.53 (0.48), residues: 123 loop : -1.34 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP o 101 HIS 0.003 0.001 HIS k 15 PHE 0.022 0.001 PHE h 61 TYR 0.010 0.001 TYR j 59 ARG 0.007 0.000 ARG d 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 145 time to evaluate : 1.136 Fit side-chains REVERT: d 152 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7596 (tm-30) REVERT: h 5 ARG cc_start: 0.6412 (OUTLIER) cc_final: 0.5000 (mmt90) REVERT: h 68 LYS cc_start: 0.7599 (tppt) cc_final: 0.7315 (tptm) REVERT: j 51 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7216 (pp20) REVERT: k 7 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.7444 (mtm-85) REVERT: n 113 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.7036 (mtt180) REVERT: t 63 THR cc_start: 0.9126 (m) cc_final: 0.8917 (m) outliers start: 31 outliers final: 24 residues processed: 164 average time/residue: 1.4262 time to fit residues: 258.1204 Evaluate side-chains 172 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 143 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 75 ILE Chi-restraints excluded: chain d residue 76 VAL Chi-restraints excluded: chain d residue 139 GLN Chi-restraints excluded: chain d residue 152 GLU Chi-restraints excluded: chain d residue 165 THR Chi-restraints excluded: chain d residue 196 ILE Chi-restraints excluded: chain h residue 5 ARG Chi-restraints excluded: chain h residue 6 VAL Chi-restraints excluded: chain h residue 13 LEU Chi-restraints excluded: chain h residue 27 MET Chi-restraints excluded: chain h residue 41 SER Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 64 THR Chi-restraints excluded: chain h residue 110 LYS Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 51 GLU Chi-restraints excluded: chain j residue 85 LEU Chi-restraints excluded: chain k residue 7 ARG Chi-restraints excluded: chain k residue 75 ASP Chi-restraints excluded: chain k residue 80 THR Chi-restraints excluded: chain n residue 42 THR Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain n residue 68 ASP Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain n residue 113 ARG Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain o residue 92 ASP Chi-restraints excluded: chain t residue 23 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 119 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: k 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18137 Z= 0.197 Angle : 0.560 11.290 26812 Z= 0.294 Chirality : 0.037 0.201 3413 Planarity : 0.005 0.039 1645 Dihedral : 22.246 175.656 8380 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 4.38 % Allowed : 27.45 % Favored : 68.18 % 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: -0.28 (0.29), residues: 836 helix: 0.24 (0.29), residues: 349 sheet: 1.63 (0.46), residues: 133 loop : -1.32 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP o 101 HIS 0.004 0.001 HIS k 15 PHE 0.022 0.001 PHE h 61 TYR 0.009 0.001 TYR d 29 ARG 0.007 0.000 ARG n 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 144 time to evaluate : 1.058 Fit side-chains REVERT: d 152 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7606 (tm-30) REVERT: h 5 ARG cc_start: 0.6276 (OUTLIER) cc_final: 0.4819 (mmt90) REVERT: h 48 GLU cc_start: 0.6876 (pt0) cc_final: 0.6633 (pm20) REVERT: h 68 LYS cc_start: 0.7582 (tppt) cc_final: 0.7303 (tptm) REVERT: j 51 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7233 (pp20) REVERT: k 7 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.7416 (mtm-85) REVERT: n 113 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.7138 (mtt180) REVERT: t 63 THR cc_start: 0.9139 (m) cc_final: 0.8929 (m) outliers start: 30 outliers final: 25 residues processed: 162 average time/residue: 1.4358 time to fit residues: 257.3085 Evaluate side-chains 173 residues out of total 698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 143 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 75 ILE Chi-restraints excluded: chain d residue 76 VAL Chi-restraints excluded: chain d residue 102 SER Chi-restraints excluded: chain d residue 139 GLN Chi-restraints excluded: chain d residue 152 GLU Chi-restraints excluded: chain d residue 165 THR Chi-restraints excluded: chain d residue 196 ILE Chi-restraints excluded: chain h residue 5 ARG Chi-restraints excluded: chain h residue 6 VAL Chi-restraints excluded: chain h residue 7 VAL Chi-restraints excluded: chain h residue 13 LEU Chi-restraints excluded: chain h residue 27 MET Chi-restraints excluded: chain h residue 41 SER Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 64 THR Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 51 GLU Chi-restraints excluded: chain j residue 85 LEU Chi-restraints excluded: chain k residue 7 ARG Chi-restraints excluded: chain k residue 75 ASP Chi-restraints excluded: chain k residue 80 THR Chi-restraints excluded: chain n residue 42 THR Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain n residue 68 ASP Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain n residue 113 ARG Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain o residue 92 ASP Chi-restraints excluded: chain t residue 23 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: k 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.126261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.093744 restraints weight = 20404.328| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 0.78 r_work: 0.2676 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2573 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 18137 Z= 0.298 Angle : 0.609 11.319 26812 Z= 0.317 Chirality : 0.040 0.215 3413 Planarity : 0.005 0.039 1645 Dihedral : 22.269 175.143 8380 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 4.53 % Allowed : 27.45 % Favored : 68.03 % 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: -0.36 (0.29), residues: 836 helix: 0.15 (0.28), residues: 349 sheet: 1.60 (0.46), residues: 133 loop : -1.34 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP o 101 HIS 0.005 0.001 HIS k 15 PHE 0.023 0.002 PHE h 61 TYR 0.011 0.002 TYR j 59 ARG 0.007 0.001 ARG d 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5066.93 seconds wall clock time: 91 minutes 23.38 seconds (5483.38 seconds total)