Starting phenix.real_space_refine on Fri Mar 15 19:12:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f32_28829/03_2024/8f32_28829_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f32_28829/03_2024/8f32_28829.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f32_28829/03_2024/8f32_28829.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f32_28829/03_2024/8f32_28829.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f32_28829/03_2024/8f32_28829_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f32_28829/03_2024/8f32_28829_updated.pdb" } resolution = 3.71 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 8180 2.51 5 N 2085 2.21 5 O 2250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 30": "OE1" <-> "OE2" Residue "E PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 153": "OD1" <-> "OD2" Residue "E GLU 156": "OE1" <-> "OE2" Residue "E GLU 159": "OE1" <-> "OE2" Residue "E ASP 172": "OD1" <-> "OD2" Residue "E TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "D PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 153": "OD1" <-> "OD2" Residue "D GLU 156": "OE1" <-> "OE2" Residue "D GLU 159": "OE1" <-> "OE2" Residue "D ASP 172": "OD1" <-> "OD2" Residue "D TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 153": "OD1" <-> "OD2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C GLU 159": "OE1" <-> "OE2" Residue "C ASP 172": "OD1" <-> "OD2" Residue "C TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B GLU 159": "OE1" <-> "OE2" Residue "B ASP 172": "OD1" <-> "OD2" Residue "B TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 30": "OE1" <-> "OE2" Residue "A PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 153": "OD1" <-> "OD2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A ASP 172": "OD1" <-> "OD2" Residue "A TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12545 Number of models: 1 Model: "" Number of chains: 10 Chain: "E" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "D" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "C" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "B" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "A" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.68, per 1000 atoms: 0.53 Number of scatterers: 12545 At special positions: 0 Unit cell: (88.41, 88.41, 122.932, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 2250 8.00 N 2085 7.00 C 8180 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: 4.17 Conformation dependent library (CDL) restraints added in 2.3 seconds 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2910 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 20 sheets defined 28.0% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.54 Creating SS restraints... Processing helix chain 'E' and resid 63 through 69 Processing helix chain 'E' and resid 202 through 207 Processing helix chain 'E' and resid 210 through 224 removed outlier: 4.947A pdb=" N PHE E 223 " --> pdb=" O SER E 219 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N TRP E 224 " --> pdb=" O TRP E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 247 Processing helix chain 'E' and resid 261 through 285 Processing helix chain 'E' and resid 304 through 316 Processing helix chain 'D' and resid 63 through 69 Processing helix chain 'D' and resid 202 through 207 Processing helix chain 'D' and resid 210 through 224 removed outlier: 4.947A pdb=" N PHE D 223 " --> pdb=" O SER D 219 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N TRP D 224 " --> pdb=" O TRP D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 247 Processing helix chain 'D' and resid 261 through 285 Processing helix chain 'D' and resid 304 through 316 Processing helix chain 'C' and resid 63 through 69 Processing helix chain 'C' and resid 202 through 207 Processing helix chain 'C' and resid 210 through 224 removed outlier: 4.947A pdb=" N PHE C 223 " --> pdb=" O SER C 219 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N TRP C 224 " --> pdb=" O TRP C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 247 Processing helix chain 'C' and resid 261 through 285 Processing helix chain 'C' and resid 304 through 316 Processing helix chain 'B' and resid 63 through 69 Processing helix chain 'B' and resid 202 through 207 Processing helix chain 'B' and resid 210 through 224 removed outlier: 4.947A pdb=" N PHE B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N TRP B 224 " --> pdb=" O TRP B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 247 Processing helix chain 'B' and resid 261 through 285 Processing helix chain 'B' and resid 304 through 316 Processing helix chain 'A' and resid 63 through 69 Processing helix chain 'A' and resid 202 through 207 Processing helix chain 'A' and resid 210 through 224 removed outlier: 4.948A pdb=" N PHE A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N TRP A 224 " --> pdb=" O TRP A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 247 Processing helix chain 'A' and resid 261 through 285 Processing helix chain 'A' and resid 304 through 316 Processing sheet with id= A, first strand: chain 'E' and resid 140 through 142 removed outlier: 5.804A pdb=" N VAL E 12 " --> pdb=" O ARG E 141 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ASP E 13 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR E 44 " --> pdb=" O ASP E 13 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASP E 36 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ILE E 23 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LYS E 34 " --> pdb=" O ILE E 23 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 16 through 18 removed outlier: 3.638A pdb=" N ILE E 18 " --> pdb=" O GLN E 146 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 76 through 78 Processing sheet with id= D, first strand: chain 'E' and resid 166 through 173 Processing sheet with id= E, first strand: chain 'D' and resid 140 through 142 removed outlier: 5.804A pdb=" N VAL D 12 " --> pdb=" O ARG D 141 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ASP D 13 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR D 44 " --> pdb=" O ASP D 13 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASP D 36 " --> pdb=" O ASN D 21 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ILE D 23 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LYS D 34 " --> pdb=" O ILE D 23 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 16 through 18 removed outlier: 3.637A pdb=" N ILE D 18 " --> pdb=" O GLN D 146 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 76 through 78 Processing sheet with id= H, first strand: chain 'D' and resid 166 through 173 Processing sheet with id= I, first strand: chain 'C' and resid 140 through 142 removed outlier: 5.804A pdb=" N VAL C 12 " --> pdb=" O ARG C 141 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ASP C 13 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR C 44 " --> pdb=" O ASP C 13 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASP C 36 " --> pdb=" O ASN C 21 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ILE C 23 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LYS C 34 " --> pdb=" O ILE C 23 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 16 through 18 removed outlier: 3.637A pdb=" N ILE C 18 " --> pdb=" O GLN C 146 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 76 through 78 Processing sheet with id= L, first strand: chain 'C' and resid 166 through 173 Processing sheet with id= M, first strand: chain 'B' and resid 140 through 142 removed outlier: 5.804A pdb=" N VAL B 12 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ASP B 13 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR B 44 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASP B 36 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ILE B 23 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LYS B 34 " --> pdb=" O ILE B 23 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 16 through 18 removed outlier: 3.639A pdb=" N ILE B 18 " --> pdb=" O GLN B 146 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 76 through 78 Processing sheet with id= P, first strand: chain 'B' and resid 166 through 173 Processing sheet with id= Q, first strand: chain 'A' and resid 140 through 142 removed outlier: 5.804A pdb=" N VAL A 12 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ASP A 13 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR A 44 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASP A 36 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ILE A 23 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LYS A 34 " --> pdb=" O ILE A 23 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 16 through 18 removed outlier: 3.501A pdb=" N GLN A 146 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE A 18 " --> pdb=" O GLN A 146 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'A' and resid 76 through 78 Processing sheet with id= T, first strand: chain 'A' and resid 166 through 173 539 hydrogen bonds defined for protein. 1587 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.85 Time building geometry restraints manager: 4.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3475 1.33 - 1.45: 2400 1.45 - 1.57: 6955 1.57 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 12880 Sorted by residual: bond pdb=" CB GLU B 150 " pdb=" CG GLU B 150 " ideal model delta sigma weight residual 1.520 1.566 -0.046 3.00e-02 1.11e+03 2.40e+00 bond pdb=" CB GLU C 150 " pdb=" CG GLU C 150 " ideal model delta sigma weight residual 1.520 1.566 -0.046 3.00e-02 1.11e+03 2.39e+00 bond pdb=" CB GLU E 150 " pdb=" CG GLU E 150 " ideal model delta sigma weight residual 1.520 1.566 -0.046 3.00e-02 1.11e+03 2.38e+00 bond pdb=" CB GLU D 150 " pdb=" CG GLU D 150 " ideal model delta sigma weight residual 1.520 1.566 -0.046 3.00e-02 1.11e+03 2.37e+00 bond pdb=" CB GLU A 150 " pdb=" CG GLU A 150 " ideal model delta sigma weight residual 1.520 1.566 -0.046 3.00e-02 1.11e+03 2.37e+00 ... (remaining 12875 not shown) Histogram of bond angle deviations from ideal: 100.42 - 107.14: 396 107.14 - 113.87: 7003 113.87 - 120.59: 5109 120.59 - 127.31: 4872 127.31 - 134.03: 165 Bond angle restraints: 17545 Sorted by residual: angle pdb=" N ILE C 157 " pdb=" CA ILE C 157 " pdb=" C ILE C 157 " ideal model delta sigma weight residual 113.71 106.87 6.84 9.50e-01 1.11e+00 5.19e+01 angle pdb=" N ILE D 157 " pdb=" CA ILE D 157 " pdb=" C ILE D 157 " ideal model delta sigma weight residual 113.71 106.87 6.84 9.50e-01 1.11e+00 5.18e+01 angle pdb=" N ILE B 157 " pdb=" CA ILE B 157 " pdb=" C ILE B 157 " ideal model delta sigma weight residual 113.71 106.88 6.83 9.50e-01 1.11e+00 5.18e+01 angle pdb=" N ILE E 157 " pdb=" CA ILE E 157 " pdb=" C ILE E 157 " ideal model delta sigma weight residual 113.71 106.88 6.83 9.50e-01 1.11e+00 5.17e+01 angle pdb=" N ILE A 157 " pdb=" CA ILE A 157 " pdb=" C ILE A 157 " ideal model delta sigma weight residual 113.71 106.89 6.82 9.50e-01 1.11e+00 5.16e+01 ... (remaining 17540 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.33: 6455 14.33 - 28.66: 855 28.66 - 42.99: 185 42.99 - 57.32: 20 57.32 - 71.65: 15 Dihedral angle restraints: 7530 sinusoidal: 3025 harmonic: 4505 Sorted by residual: dihedral pdb=" CA SER D 227 " pdb=" C SER D 227 " pdb=" N PHE D 228 " pdb=" CA PHE D 228 " ideal model delta harmonic sigma weight residual 180.00 -154.17 -25.83 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA SER A 227 " pdb=" C SER A 227 " pdb=" N PHE A 228 " pdb=" CA PHE A 228 " ideal model delta harmonic sigma weight residual -180.00 -154.17 -25.83 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA SER B 227 " pdb=" C SER B 227 " pdb=" N PHE B 228 " pdb=" CA PHE B 228 " ideal model delta harmonic sigma weight residual -180.00 -154.19 -25.81 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 7527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1184 0.043 - 0.086: 515 0.086 - 0.130: 206 0.130 - 0.173: 40 0.173 - 0.216: 5 Chirality restraints: 1950 Sorted by residual: chirality pdb=" CB ILE B 39 " pdb=" CA ILE B 39 " pdb=" CG1 ILE B 39 " pdb=" CG2 ILE B 39 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB ILE D 39 " pdb=" CA ILE D 39 " pdb=" CG1 ILE D 39 " pdb=" CG2 ILE D 39 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CB ILE C 39 " pdb=" CA ILE C 39 " pdb=" CG1 ILE C 39 " pdb=" CG2 ILE C 39 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1947 not shown) Planarity restraints: 2235 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE D 119 " -0.033 5.00e-02 4.00e+02 4.98e-02 3.96e+00 pdb=" N PRO D 120 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO D 120 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 120 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 119 " 0.033 5.00e-02 4.00e+02 4.97e-02 3.95e+00 pdb=" N PRO E 120 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO E 120 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 120 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 119 " 0.033 5.00e-02 4.00e+02 4.95e-02 3.93e+00 pdb=" N PRO A 120 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 120 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 120 " 0.028 5.00e-02 4.00e+02 ... (remaining 2232 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 970 2.74 - 3.28: 12164 3.28 - 3.82: 20445 3.82 - 4.36: 24895 4.36 - 4.90: 43280 Nonbonded interactions: 101754 Sorted by model distance: nonbonded pdb=" OG SER D 227 " pdb=" OE2 GLU D 230 " model vdw 2.201 2.440 nonbonded pdb=" OG SER C 227 " pdb=" OE2 GLU C 230 " model vdw 2.201 2.440 nonbonded pdb=" OG SER E 227 " pdb=" OE2 GLU E 230 " model vdw 2.202 2.440 nonbonded pdb=" OG SER A 227 " pdb=" OE2 GLU A 230 " model vdw 2.202 2.440 nonbonded pdb=" OG SER B 227 " pdb=" OE2 GLU B 230 " model vdw 2.202 2.440 ... (remaining 101749 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 0.490 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: 2.960 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 33.990 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.100 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 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 : 0.005 0.049 12880 Z= 0.311 Angle : 0.837 7.926 17545 Z= 0.467 Chirality : 0.056 0.216 1950 Planarity : 0.006 0.050 2235 Dihedral : 13.435 71.655 4620 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % 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: -1.60 (0.21), residues: 1525 helix: -0.87 (0.22), residues: 525 sheet: -0.04 (0.23), residues: 490 loop : -2.13 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 43 HIS 0.013 0.003 HIS C 169 PHE 0.018 0.002 PHE B 308 TYR 0.020 0.002 TYR D 245 ARG 0.003 0.000 ARG C 286 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 1.357 Fit side-chains revert: symmetry clash REVERT: E 187 GLU cc_start: 0.6904 (tm-30) cc_final: 0.6593 (tm-30) REVERT: D 86 ASP cc_start: 0.6982 (t70) cc_final: 0.6574 (t0) REVERT: C 86 ASP cc_start: 0.7052 (t70) cc_final: 0.6644 (t0) REVERT: C 115 ASP cc_start: 0.6719 (t0) cc_final: 0.5810 (t0) REVERT: C 117 ARG cc_start: 0.7805 (mmt180) cc_final: 0.7204 (mmt180) REVERT: C 187 GLU cc_start: 0.6966 (tm-30) cc_final: 0.6710 (tm-30) REVERT: B 86 ASP cc_start: 0.6869 (t70) cc_final: 0.6406 (t0) REVERT: B 187 GLU cc_start: 0.6932 (tm-30) cc_final: 0.6651 (tm-30) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.2482 time to fit residues: 97.8415 Evaluate side-chains 202 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 38 optimal weight: 0.8980 chunk 76 optimal weight: 9.9990 chunk 60 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 87 optimal weight: 20.0000 chunk 136 optimal weight: 0.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 42 GLN E 177 HIS D 21 ASN D 169 HIS D 177 HIS C 60 ASN C 177 HIS B 21 ASN B 62 GLN B 139 GLN B 177 HIS A 21 ASN A 42 GLN A 139 GLN A 146 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12880 Z= 0.316 Angle : 0.585 5.393 17545 Z= 0.310 Chirality : 0.047 0.136 1950 Planarity : 0.004 0.045 2235 Dihedral : 5.095 22.684 1690 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.75 % Allowed : 11.05 % Favored : 87.20 % 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: -0.68 (0.21), residues: 1525 helix: 0.60 (0.24), residues: 495 sheet: 0.19 (0.24), residues: 455 loop : -1.90 (0.24), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 43 HIS 0.007 0.001 HIS B 169 PHE 0.024 0.002 PHE B 19 TYR 0.015 0.002 TYR B 258 ARG 0.002 0.000 ARG E 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 215 time to evaluate : 1.355 Fit side-chains REVERT: D 86 ASP cc_start: 0.6987 (t70) cc_final: 0.6553 (t0) REVERT: B 264 GLN cc_start: 0.7356 (mp10) cc_final: 0.7103 (mp10) outliers start: 24 outliers final: 19 residues processed: 221 average time/residue: 0.2349 time to fit residues: 75.5415 Evaluate side-chains 198 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 179 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 266 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 113 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 147 optimal weight: 9.9990 chunk 121 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 146 GLN D 89 ASN D 139 GLN D 146 GLN D 264 GLN C 146 GLN B 146 GLN B 151 ASN A 89 ASN A 151 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 12880 Z= 0.345 Angle : 0.588 5.637 17545 Z= 0.312 Chirality : 0.047 0.133 1950 Planarity : 0.004 0.046 2235 Dihedral : 5.012 23.097 1690 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.58 % Allowed : 12.95 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.22), residues: 1525 helix: 1.09 (0.24), residues: 495 sheet: -0.05 (0.23), residues: 465 loop : -1.79 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 43 HIS 0.007 0.001 HIS B 169 PHE 0.021 0.002 PHE A 19 TYR 0.015 0.002 TYR D 258 ARG 0.003 0.000 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 197 time to evaluate : 1.304 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 outliers start: 63 outliers final: 47 residues processed: 232 average time/residue: 0.2415 time to fit residues: 81.7926 Evaluate side-chains 224 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 177 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 264 GLN Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain A residue 266 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 144 optimal weight: 20.0000 chunk 71 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 285 HIS D 285 HIS C 60 ASN A 151 ASN A 177 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 12880 Z= 0.422 Angle : 0.620 6.138 17545 Z= 0.328 Chirality : 0.049 0.138 1950 Planarity : 0.004 0.043 2235 Dihedral : 5.173 26.393 1690 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 6.04 % Allowed : 13.67 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.22), residues: 1525 helix: 1.12 (0.24), residues: 495 sheet: -0.14 (0.23), residues: 465 loop : -1.91 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 43 HIS 0.006 0.002 HIS B 169 PHE 0.023 0.002 PHE B 19 TYR 0.015 0.002 TYR D 258 ARG 0.004 0.000 ARG E 117 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 203 time to evaluate : 1.535 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 outliers start: 83 outliers final: 57 residues processed: 252 average time/residue: 0.2219 time to fit residues: 83.4477 Evaluate side-chains 227 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 170 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 251 ASN Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 251 ASN Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 251 ASN Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 264 GLN Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 264 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 74 optimal weight: 0.0980 chunk 130 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 GLN C 21 ASN C 60 ASN B 42 GLN A 151 ASN A 169 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12880 Z= 0.176 Angle : 0.488 4.625 17545 Z= 0.258 Chirality : 0.045 0.137 1950 Planarity : 0.003 0.037 2235 Dihedral : 4.497 18.229 1690 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.65 % Allowed : 15.93 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.22), residues: 1525 helix: 1.75 (0.25), residues: 485 sheet: 0.14 (0.23), residues: 455 loop : -1.93 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 43 HIS 0.006 0.001 HIS B 169 PHE 0.017 0.001 PHE B 19 TYR 0.009 0.001 TYR A 258 ARG 0.003 0.000 ARG C 299 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 205 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 ASN cc_start: 0.7916 (t0) cc_final: 0.7674 (m-40) outliers start: 64 outliers final: 51 residues processed: 240 average time/residue: 0.2265 time to fit residues: 79.8124 Evaluate side-chains 233 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 182 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 264 GLN Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 264 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 8.9990 chunk 130 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 120 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 76 optimal weight: 8.9990 chunk 139 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 12880 Z= 0.407 Angle : 0.616 9.565 17545 Z= 0.323 Chirality : 0.048 0.138 1950 Planarity : 0.004 0.036 2235 Dihedral : 5.010 25.666 1690 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 6.18 % Allowed : 14.76 % Favored : 79.05 % 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: -0.36 (0.22), residues: 1525 helix: 1.46 (0.25), residues: 490 sheet: 0.03 (0.23), residues: 455 loop : -1.97 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 43 HIS 0.008 0.001 HIS E 169 PHE 0.024 0.002 PHE A 19 TYR 0.018 0.002 TYR B 258 ARG 0.003 0.000 ARG E 117 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 189 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 ASN cc_start: 0.8010 (t0) cc_final: 0.7777 (m-40) outliers start: 85 outliers final: 73 residues processed: 247 average time/residue: 0.2371 time to fit residues: 84.8949 Evaluate side-chains 247 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 174 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 251 ASN Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 230 GLU Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 264 GLN Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 264 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 105 optimal weight: 0.5980 chunk 122 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 144 optimal weight: 0.2980 chunk 90 optimal weight: 8.9990 chunk 88 optimal weight: 20.0000 chunk 66 optimal weight: 0.7980 chunk 89 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 ASN A 151 ASN A 169 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12880 Z= 0.180 Angle : 0.504 6.752 17545 Z= 0.262 Chirality : 0.045 0.125 1950 Planarity : 0.003 0.037 2235 Dihedral : 4.437 17.389 1690 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 5.45 % Allowed : 16.00 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.23), residues: 1525 helix: 1.91 (0.26), residues: 485 sheet: 0.06 (0.23), residues: 465 loop : -1.83 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP C 220 HIS 0.008 0.001 HIS E 169 PHE 0.021 0.001 PHE A 19 TYR 0.011 0.001 TYR E 258 ARG 0.002 0.000 ARG C 299 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 202 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 ASN cc_start: 0.7948 (t0) cc_final: 0.7704 (m-40) outliers start: 75 outliers final: 60 residues processed: 252 average time/residue: 0.2243 time to fit residues: 83.0440 Evaluate side-chains 246 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 186 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 251 ASN Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 251 ASN Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 251 ASN Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 264 GLN Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 264 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 91 optimal weight: 0.0030 chunk 98 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 131 optimal weight: 8.9990 chunk 138 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 ASN C 60 ASN A 151 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12880 Z= 0.178 Angle : 0.502 6.263 17545 Z= 0.258 Chirality : 0.045 0.127 1950 Planarity : 0.003 0.035 2235 Dihedral : 4.320 16.961 1690 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 5.31 % Allowed : 16.51 % Favored : 78.18 % 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: 0.07 (0.23), residues: 1525 helix: 1.94 (0.26), residues: 485 sheet: 0.19 (0.24), residues: 465 loop : -1.77 (0.27), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 220 HIS 0.009 0.001 HIS E 169 PHE 0.020 0.001 PHE A 19 TYR 0.010 0.001 TYR E 258 ARG 0.002 0.000 ARG C 299 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 209 time to evaluate : 1.250 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: E 237 THR cc_start: 0.8615 (m) cc_final: 0.8355 (m) REVERT: B 69 ASN cc_start: 0.7979 (t0) cc_final: 0.7733 (m-40) REVERT: B 117 ARG cc_start: 0.7643 (mpt180) cc_final: 0.7367 (mmt180) outliers start: 73 outliers final: 66 residues processed: 259 average time/residue: 0.2330 time to fit residues: 87.8105 Evaluate side-chains 256 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 190 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 251 ASN Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 251 ASN Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 251 ASN Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 264 GLN Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain A residue 294 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 20.0000 chunk 138 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 142 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 ASN B 151 ASN A 151 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12880 Z= 0.228 Angle : 0.528 6.576 17545 Z= 0.271 Chirality : 0.045 0.129 1950 Planarity : 0.003 0.035 2235 Dihedral : 4.383 18.874 1690 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 5.60 % Allowed : 16.15 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.23), residues: 1525 helix: 1.80 (0.25), residues: 490 sheet: 0.23 (0.24), residues: 465 loop : -1.72 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 220 HIS 0.009 0.001 HIS E 169 PHE 0.019 0.001 PHE A 19 TYR 0.012 0.001 TYR E 258 ARG 0.004 0.000 ARG A 255 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 189 time to evaluate : 1.348 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: E 237 THR cc_start: 0.8648 (m) cc_final: 0.8396 (m) REVERT: E 264 GLN cc_start: 0.7463 (OUTLIER) cc_final: 0.7097 (mm110) REVERT: B 69 ASN cc_start: 0.7954 (t0) cc_final: 0.7726 (m-40) REVERT: A 54 LYS cc_start: 0.7612 (mmtt) cc_final: 0.7312 (tppt) outliers start: 77 outliers final: 69 residues processed: 242 average time/residue: 0.2364 time to fit residues: 83.5074 Evaluate side-chains 258 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 188 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 251 ASN Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 251 ASN Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 251 ASN Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 264 GLN Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain A residue 294 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 149 optimal weight: 20.0000 chunk 137 optimal weight: 7.9990 chunk 118 optimal weight: 0.0020 chunk 12 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 overall best weight: 2.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 139 GLN C 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12880 Z= 0.298 Angle : 0.567 7.813 17545 Z= 0.291 Chirality : 0.046 0.140 1950 Planarity : 0.003 0.035 2235 Dihedral : 4.586 21.914 1690 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 5.31 % Allowed : 16.36 % Favored : 78.33 % 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: -0.00 (0.23), residues: 1525 helix: 1.70 (0.25), residues: 490 sheet: 0.34 (0.24), residues: 455 loop : -1.83 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 220 HIS 0.009 0.001 HIS E 169 PHE 0.018 0.002 PHE A 19 TYR 0.014 0.002 TYR E 258 ARG 0.004 0.000 ARG A 255 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 189 time to evaluate : 1.394 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: E 264 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.7110 (mm110) REVERT: B 69 ASN cc_start: 0.7989 (t0) cc_final: 0.7756 (m-40) REVERT: A 54 LYS cc_start: 0.7635 (mmtt) cc_final: 0.7326 (tppt) REVERT: A 117 ARG cc_start: 0.7934 (tpt170) cc_final: 0.7379 (mmt180) outliers start: 73 outliers final: 69 residues processed: 240 average time/residue: 0.2315 time to fit residues: 81.3703 Evaluate side-chains 255 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 185 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 251 ASN Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 251 ASN Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 251 ASN Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 264 GLN Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain A residue 294 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 7.9990 chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 8.9990 chunk 119 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 104 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 ASN A 151 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.147787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.116704 restraints weight = 17110.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.120412 restraints weight = 11040.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.122931 restraints weight = 8265.385| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12880 Z= 0.265 Angle : 0.553 7.485 17545 Z= 0.283 Chirality : 0.046 0.132 1950 Planarity : 0.003 0.035 2235 Dihedral : 4.556 20.939 1690 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 5.38 % Allowed : 16.65 % Favored : 77.96 % 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: -0.01 (0.23), residues: 1525 helix: 1.72 (0.25), residues: 490 sheet: 0.19 (0.24), residues: 465 loop : -1.76 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 220 HIS 0.009 0.001 HIS E 169 PHE 0.018 0.001 PHE A 19 TYR 0.013 0.001 TYR E 258 ARG 0.003 0.000 ARG A 255 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2464.83 seconds wall clock time: 47 minutes 20.76 seconds (2840.76 seconds total)