Starting phenix.real_space_refine on Thu Feb 15 11:05:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fya_29562/02_2024/8fya_29562.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fya_29562/02_2024/8fya_29562.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fya_29562/02_2024/8fya_29562.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fya_29562/02_2024/8fya_29562.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fya_29562/02_2024/8fya_29562.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fya_29562/02_2024/8fya_29562.pdb" } resolution = 2.91 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= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 611 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 57 5.49 5 S 31 5.16 5 C 7056 2.51 5 N 2060 2.21 5 O 2229 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 18": "OD1" <-> "OD2" Residue "A TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 65": "OD1" <-> "OD2" Residue "B TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 174": "OD1" <-> "OD2" Residue "C ASP 224": "OD1" <-> "OD2" Residue "C ASP 227": "OD1" <-> "OD2" Residue "C PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 284": "OE1" <-> "OE2" Residue "D ASP 81": "OD1" <-> "OD2" Residue "D TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 76": "OD1" <-> "OD2" Residue "E GLU 110": "OE1" <-> "OE2" Residue "F TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 261": "OD1" <-> "OD2" Residue "F ASP 265": "OD1" <-> "OD2" Residue "F ASP 275": "OD1" <-> "OD2" Residue "F GLU 281": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11433 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 746 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain: "B" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2295 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 11, 'TRANS': 280} Chain: "C" Number of atoms: 2388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2388 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 13, 'TRANS': 291} Chain breaks: 1 Chain: "D" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 746 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain: "E" Number of atoms: 1865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1865 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 8, 'TRANS': 232} Chain breaks: 1 Chain: "F" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2186 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain: "G" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 573 Classifications: {'DNA': 28} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 27} Chain: "H" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 634 Classifications: {'DNA': 31} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 30} Time building chain proxies: 6.73, per 1000 atoms: 0.59 Number of scatterers: 11433 At special positions: 0 Unit cell: (93.66, 90.315, 142.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 31 16.00 P 57 15.00 O 2229 8.00 N 2060 7.00 C 7056 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: 4.96 Conformation dependent library (CDL) restraints added in 2.0 seconds 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2410 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 8 sheets defined 51.2% alpha, 15.4% beta 20 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 4.54 Creating SS restraints... Processing helix chain 'A' and resid 12 through 19 Processing helix chain 'A' and resid 20 through 22 No H-bonds generated for 'chain 'A' and resid 20 through 22' Processing helix chain 'A' and resid 36 through 49 removed outlier: 3.823A pdb=" N GLU A 49 " --> pdb=" O ARG A 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 55 Processing helix chain 'B' and resid 67 through 77 Processing helix chain 'B' and resid 86 through 89 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 102 through 114 removed outlier: 3.982A pdb=" N ASN B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 129 Processing helix chain 'B' and resid 139 through 163 Processing helix chain 'B' and resid 180 through 205 Processing helix chain 'B' and resid 219 through 231 removed outlier: 3.872A pdb=" N LEU B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N TYR B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ALA B 231 " --> pdb=" O ASP B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 244 Processing helix chain 'B' and resid 250 through 265 removed outlier: 4.343A pdb=" N ASP B 265 " --> pdb=" O ASP B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 280 Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'C' and resid 17 through 21 removed outlier: 3.871A pdb=" N ARG C 21 " --> pdb=" O VAL C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 53 No H-bonds generated for 'chain 'C' and resid 51 through 53' Processing helix chain 'C' and resid 68 through 77 Processing helix chain 'C' and resid 102 through 114 removed outlier: 3.517A pdb=" N ASN C 114 " --> pdb=" O GLU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 130 Processing helix chain 'C' and resid 139 through 163 Processing helix chain 'C' and resid 180 through 205 Processing helix chain 'C' and resid 219 through 231 removed outlier: 3.722A pdb=" N LEU C 228 " --> pdb=" O ASP C 224 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TYR C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA C 231 " --> pdb=" O ASP C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 245 Processing helix chain 'C' and resid 250 through 267 removed outlier: 3.507A pdb=" N LEU C 254 " --> pdb=" O ASP C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 280 removed outlier: 3.539A pdb=" N LEU C 280 " --> pdb=" O LEU C 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 19 Processing helix chain 'D' and resid 20 through 22 No H-bonds generated for 'chain 'D' and resid 20 through 22' Processing helix chain 'D' and resid 36 through 49 Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing helix chain 'E' and resid 68 through 77 Processing helix chain 'E' and resid 86 through 89 Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 102 through 114 removed outlier: 3.999A pdb=" N ASN E 114 " --> pdb=" O GLU E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 129 removed outlier: 3.581A pdb=" N ARG E 118 " --> pdb=" O ASN E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 205 Processing helix chain 'E' and resid 219 through 231 removed outlier: 3.806A pdb=" N LEU E 228 " --> pdb=" O ASP E 224 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR E 229 " --> pdb=" O VAL E 225 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ALA E 231 " --> pdb=" O ASP E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 245 Processing helix chain 'E' and resid 250 through 265 removed outlier: 4.451A pdb=" N ASP E 265 " --> pdb=" O ASP E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 280 removed outlier: 3.648A pdb=" N LEU E 280 " --> pdb=" O LEU E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 303 Processing helix chain 'F' and resid 51 through 53 No H-bonds generated for 'chain 'F' and resid 51 through 53' Processing helix chain 'F' and resid 68 through 78 Processing helix chain 'F' and resid 102 through 114 removed outlier: 3.881A pdb=" N ASN F 114 " --> pdb=" O GLU F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 130 Processing helix chain 'F' and resid 139 through 163 Processing helix chain 'F' and resid 180 through 205 Processing helix chain 'F' and resid 219 through 231 removed outlier: 3.758A pdb=" N LEU F 228 " --> pdb=" O ASP F 224 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TYR F 229 " --> pdb=" O VAL F 225 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ALA F 231 " --> pdb=" O ASP F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 245 Processing helix chain 'F' and resid 250 through 267 Processing helix chain 'F' and resid 267 through 280 removed outlier: 3.868A pdb=" N LEU F 280 " --> pdb=" O LEU F 276 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27 removed outlier: 5.798A pdb=" N GLU A 25 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL A 32 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA A 27 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N MET A 3 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA A 61 " --> pdb=" O MET A 3 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 56 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 81 removed outlier: 5.461A pdb=" N ILE A 88 " --> pdb=" O ARG F 49 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG F 49 " --> pdb=" O ILE A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 289 through 291 removed outlier: 8.105A pdb=" N VAL B 57 " --> pdb=" O ARG B 21 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR B 23 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LEU B 59 " --> pdb=" O THR B 23 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE B 25 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU B 58 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL B 84 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LEU B 60 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU B 81 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N SER B 94 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP B 83 " --> pdb=" O TYR B 92 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR C 91 " --> pdb=" O TRP C 83 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR C 23 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N LEU C 59 " --> pdb=" O THR C 23 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE C 25 " --> pdb=" O LEU C 59 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 308 through 310 removed outlier: 3.901A pdb=" N ASN B 308 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ALA B 30 " --> pdb=" O ASP B 65 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG C 34 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ARG C 49 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ILE D 88 " --> pdb=" O ARG C 49 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 214 through 215 Processing sheet with id=AA6, first strand: chain 'D' and resid 24 through 27 removed outlier: 7.287A pdb=" N VAL D 30 " --> pdb=" O ILE D 26 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N MET D 3 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA D 61 " --> pdb=" O MET D 3 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 289 through 291 removed outlier: 7.715A pdb=" N VAL E 57 " --> pdb=" O ARG E 21 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N THR E 23 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LEU E 59 " --> pdb=" O THR E 23 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE E 25 " --> pdb=" O LEU E 59 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR F 91 " --> pdb=" O TRP F 83 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR F 23 " --> pdb=" O VAL F 57 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU F 59 " --> pdb=" O THR F 23 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE F 25 " --> pdb=" O LEU F 59 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 308 through 310 removed outlier: 7.598A pdb=" N ILE E 32 " --> pdb=" O SER E 67 " (cutoff:3.500A) 574 hydrogen bonds defined for protein. 1638 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 86 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 3.77 Time building geometry restraints manager: 5.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3360 1.34 - 1.45: 2039 1.45 - 1.57: 6193 1.57 - 1.69: 114 1.69 - 1.81: 60 Bond restraints: 11766 Sorted by residual: bond pdb=" CB ILE A 26 " pdb=" CG2 ILE A 26 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.59e+00 bond pdb=" C3' DC G 8 " pdb=" O3' DC G 8 " ideal model delta sigma weight residual 1.422 1.457 -0.035 3.00e-02 1.11e+03 1.36e+00 bond pdb=" C4' DG G 24 " pdb=" O4' DG G 24 " ideal model delta sigma weight residual 1.450 1.431 0.019 2.00e-02 2.50e+03 9.49e-01 bond pdb=" C3' DT H 9 " pdb=" C2' DT H 9 " ideal model delta sigma weight residual 1.525 1.544 -0.019 2.00e-02 2.50e+03 8.78e-01 bond pdb=" CA GLN C 87 " pdb=" CB GLN C 87 " ideal model delta sigma weight residual 1.527 1.542 -0.015 1.70e-02 3.46e+03 7.95e-01 ... (remaining 11761 not shown) Histogram of bond angle deviations from ideal: 98.49 - 105.60: 455 105.60 - 112.72: 6371 112.72 - 119.83: 3816 119.83 - 126.94: 5271 126.94 - 134.05: 261 Bond angle restraints: 16174 Sorted by residual: angle pdb=" CA GLN C 87 " pdb=" CB GLN C 87 " pdb=" CG GLN C 87 " ideal model delta sigma weight residual 114.10 119.22 -5.12 2.00e+00 2.50e-01 6.55e+00 angle pdb=" CA GLN F 87 " pdb=" CB GLN F 87 " pdb=" CG GLN F 87 " ideal model delta sigma weight residual 114.10 118.53 -4.43 2.00e+00 2.50e-01 4.90e+00 angle pdb=" C ALA E 99 " pdb=" N ARG E 100 " pdb=" CA ARG E 100 " ideal model delta sigma weight residual 121.54 125.35 -3.81 1.91e+00 2.74e-01 3.97e+00 angle pdb=" N VAL E 35 " pdb=" CA VAL E 35 " pdb=" C VAL E 35 " ideal model delta sigma weight residual 109.17 106.16 3.01 1.54e+00 4.22e-01 3.81e+00 angle pdb=" CA GLY B 179 " pdb=" C GLY B 179 " pdb=" N ASP B 180 " ideal model delta sigma weight residual 114.48 116.79 -2.31 1.19e+00 7.06e-01 3.77e+00 ... (remaining 16169 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 6645 35.99 - 71.98: 279 71.98 - 107.97: 9 107.97 - 143.96: 0 143.96 - 179.96: 1 Dihedral angle restraints: 6934 sinusoidal: 3177 harmonic: 3757 Sorted by residual: dihedral pdb=" C4' DC G 8 " pdb=" C3' DC G 8 " pdb=" O3' DC G 8 " pdb=" P DT G 9 " ideal model delta sinusoidal sigma weight residual -140.00 39.96 -179.96 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA ARG E 34 " pdb=" C ARG E 34 " pdb=" N VAL E 35 " pdb=" CA VAL E 35 " ideal model delta harmonic sigma weight residual 180.00 160.93 19.07 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA GLU F 19 " pdb=" C GLU F 19 " pdb=" N ASP F 20 " pdb=" CA ASP F 20 " ideal model delta harmonic sigma weight residual -180.00 -161.21 -18.79 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 6931 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1317 0.037 - 0.074: 375 0.074 - 0.110: 100 0.110 - 0.147: 29 0.147 - 0.184: 2 Chirality restraints: 1823 Sorted by residual: chirality pdb=" CB VAL C 191 " pdb=" CA VAL C 191 " pdb=" CG1 VAL C 191 " pdb=" CG2 VAL C 191 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.44e-01 chirality pdb=" CA ILE B 50 " pdb=" N ILE B 50 " pdb=" C ILE B 50 " pdb=" CB ILE B 50 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" CB THR E 113 " pdb=" CA THR E 113 " pdb=" OG1 THR E 113 " pdb=" CG2 THR E 113 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.98e-01 ... (remaining 1820 not shown) Planarity restraints: 1879 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 172 " -0.025 5.00e-02 4.00e+02 3.91e-02 2.44e+00 pdb=" N PRO B 173 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 173 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 173 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 85 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO D 86 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO D 86 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 86 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 31 " -0.009 2.00e-02 2.50e+03 9.37e-03 1.76e+00 pdb=" CG TYR A 31 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR A 31 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 31 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 31 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 31 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 31 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 31 " 0.000 2.00e-02 2.50e+03 ... (remaining 1876 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 492 2.72 - 3.26: 11148 3.26 - 3.81: 20453 3.81 - 4.35: 25083 4.35 - 4.90: 41575 Nonbonded interactions: 98751 Sorted by model distance: nonbonded pdb=" OH TYR F 229 " pdb=" OD2 ASP F 275 " model vdw 2.172 2.440 nonbonded pdb=" OH TYR E 229 " pdb=" OD2 ASP E 275 " model vdw 2.174 2.440 nonbonded pdb=" OG1 THR A 7 " pdb=" OG SER A 57 " model vdw 2.201 2.440 nonbonded pdb=" O LEU E 295 " pdb=" OH TYR E 309 " model vdw 2.207 2.440 nonbonded pdb=" O GLY D 17 " pdb=" OG1 THR D 20 " model vdw 2.213 2.440 ... (remaining 98746 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 'D' } ncs_group { reference = (chain 'B' and resid 20 through 283) selection = (chain 'C' and resid 20 through 283) selection = (chain 'F' and resid 20 through 283) } 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 3.580 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 38.170 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.040 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:11.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 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 : 0.003 0.042 11766 Z= 0.196 Angle : 0.511 6.016 16174 Z= 0.279 Chirality : 0.040 0.184 1823 Planarity : 0.003 0.047 1879 Dihedral : 16.989 179.956 4524 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.09 % Allowed : 0.00 % Favored : 99.91 % 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: 1.24 (0.24), residues: 1288 helix: 2.15 (0.21), residues: 601 sheet: 0.05 (0.40), residues: 201 loop : -0.49 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 83 HIS 0.010 0.001 HIS B 29 PHE 0.008 0.001 PHE A 35 TYR 0.022 0.001 TYR A 31 ARG 0.008 0.000 ARG F 124 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 244 time to evaluate : 1.206 Fit side-chains REVERT: A 58 MET cc_start: 0.8838 (ttp) cc_final: 0.8525 (ttp) REVERT: C 257 LEU cc_start: 0.8442 (tt) cc_final: 0.7867 (tp) REVERT: F 254 LEU cc_start: 0.8294 (tt) cc_final: 0.8082 (tt) outliers start: 1 outliers final: 1 residues processed: 244 average time/residue: 1.2009 time to fit residues: 316.9343 Evaluate side-chains 181 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 180 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 254 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 0.6980 chunk 101 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 34 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 105 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN B 183 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11766 Z= 0.223 Angle : 0.532 7.769 16174 Z= 0.292 Chirality : 0.041 0.162 1823 Planarity : 0.004 0.036 1879 Dihedral : 18.248 177.224 2097 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.72 % Allowed : 12.01 % Favored : 85.27 % 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: 1.25 (0.24), residues: 1288 helix: 2.23 (0.21), residues: 607 sheet: -0.18 (0.38), residues: 206 loop : -0.53 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 296 HIS 0.011 0.001 HIS B 29 PHE 0.012 0.001 PHE D 89 TYR 0.013 0.001 TYR A 31 ARG 0.006 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 194 time to evaluate : 1.205 Fit side-chains REVERT: A 58 MET cc_start: 0.8906 (ttp) cc_final: 0.8637 (ttp) REVERT: C 65 ASP cc_start: 0.7299 (OUTLIER) cc_final: 0.7011 (m-30) REVERT: C 257 LEU cc_start: 0.8385 (tt) cc_final: 0.8063 (tp) REVERT: D 65 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7526 (mt-10) REVERT: E 31 LYS cc_start: 0.7957 (mtpm) cc_final: 0.7674 (mttp) REVERT: F 253 GLN cc_start: 0.8064 (tm-30) cc_final: 0.7855 (tm-30) outliers start: 29 outliers final: 14 residues processed: 209 average time/residue: 1.2109 time to fit residues: 274.9411 Evaluate side-chains 192 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 176 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 102 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 5.9990 chunk 37 optimal weight: 0.4980 chunk 101 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 33 optimal weight: 0.4980 chunk 121 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11766 Z= 0.218 Angle : 0.513 5.928 16174 Z= 0.280 Chirality : 0.041 0.193 1823 Planarity : 0.003 0.033 1879 Dihedral : 18.288 177.820 2095 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.66 % Allowed : 14.35 % Favored : 81.99 % 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: 1.35 (0.24), residues: 1288 helix: 2.37 (0.21), residues: 608 sheet: -0.28 (0.37), residues: 206 loop : -0.48 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 296 HIS 0.010 0.001 HIS B 29 PHE 0.011 0.001 PHE D 89 TYR 0.009 0.001 TYR B 229 ARG 0.006 0.000 ARG C 258 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 180 time to evaluate : 1.396 Fit side-chains REVERT: A 58 MET cc_start: 0.8927 (ttp) cc_final: 0.8621 (ttp) REVERT: B 156 ARG cc_start: 0.7538 (tpp-160) cc_final: 0.7313 (ttm-80) REVERT: C 65 ASP cc_start: 0.7182 (m-30) cc_final: 0.6927 (m-30) REVERT: C 257 LEU cc_start: 0.8522 (tt) cc_final: 0.8212 (tp) REVERT: D 23 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8265 (ptm) REVERT: D 65 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7524 (mt-10) REVERT: E 31 LYS cc_start: 0.7895 (mtpm) cc_final: 0.7583 (mtpp) REVERT: E 33 ASN cc_start: 0.7739 (OUTLIER) cc_final: 0.7483 (m-40) REVERT: E 289 GLU cc_start: 0.6345 (OUTLIER) cc_final: 0.5337 (pp20) REVERT: F 43 GLU cc_start: 0.6632 (OUTLIER) cc_final: 0.6392 (mt-10) REVERT: F 138 LEU cc_start: 0.6924 (OUTLIER) cc_final: 0.6018 (tt) outliers start: 39 outliers final: 18 residues processed: 199 average time/residue: 1.1667 time to fit residues: 252.5020 Evaluate side-chains 188 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 165 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain D residue 23 MET Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 138 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.8980 chunk 91 optimal weight: 8.9990 chunk 63 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 58 optimal weight: 0.2980 chunk 81 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN D 10 ASN E 29 HIS E 277 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11766 Z= 0.211 Angle : 0.505 5.859 16174 Z= 0.275 Chirality : 0.041 0.168 1823 Planarity : 0.003 0.031 1879 Dihedral : 18.305 177.876 2095 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.03 % Allowed : 15.29 % Favored : 80.68 % 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: 1.36 (0.24), residues: 1288 helix: 2.42 (0.21), residues: 608 sheet: -0.31 (0.37), residues: 202 loop : -0.52 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 296 HIS 0.009 0.001 HIS B 29 PHE 0.010 0.001 PHE D 89 TYR 0.007 0.001 TYR B 229 ARG 0.006 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 183 time to evaluate : 1.468 Fit side-chains REVERT: A 58 MET cc_start: 0.8942 (ttp) cc_final: 0.8627 (ttp) REVERT: B 156 ARG cc_start: 0.7549 (tpp-160) cc_final: 0.7321 (ttm-80) REVERT: C 65 ASP cc_start: 0.7097 (m-30) cc_final: 0.6867 (m-30) REVERT: C 232 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7496 (pp20) REVERT: C 257 LEU cc_start: 0.8543 (tt) cc_final: 0.8280 (tp) REVERT: D 23 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8285 (ptm) REVERT: E 31 LYS cc_start: 0.7917 (mtpm) cc_final: 0.7639 (mtpp) REVERT: E 33 ASN cc_start: 0.7728 (OUTLIER) cc_final: 0.7466 (m-40) REVERT: E 289 GLU cc_start: 0.6315 (OUTLIER) cc_final: 0.5263 (pp20) REVERT: F 43 GLU cc_start: 0.6576 (OUTLIER) cc_final: 0.6350 (mt-10) REVERT: F 138 LEU cc_start: 0.6937 (OUTLIER) cc_final: 0.6077 (tt) outliers start: 43 outliers final: 21 residues processed: 204 average time/residue: 1.1530 time to fit residues: 256.1730 Evaluate side-chains 195 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 168 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain D residue 23 MET Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 140 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 66 optimal weight: 0.0030 chunk 116 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 HIS E 277 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11766 Z= 0.220 Angle : 0.507 5.822 16174 Z= 0.275 Chirality : 0.041 0.166 1823 Planarity : 0.003 0.030 1879 Dihedral : 18.356 177.728 2095 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.41 % Allowed : 15.95 % Favored : 79.64 % 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: 1.35 (0.24), residues: 1288 helix: 2.42 (0.21), residues: 607 sheet: -0.39 (0.36), residues: 203 loop : -0.50 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 296 HIS 0.008 0.001 HIS B 29 PHE 0.010 0.001 PHE F 263 TYR 0.015 0.001 TYR F 223 ARG 0.005 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 180 time to evaluate : 1.460 Fit side-chains REVERT: A 58 MET cc_start: 0.8972 (ttp) cc_final: 0.8653 (ttp) REVERT: B 33 ASN cc_start: 0.8169 (OUTLIER) cc_final: 0.7967 (m-40) REVERT: B 156 ARG cc_start: 0.7522 (tpp-160) cc_final: 0.7287 (ttm-80) REVERT: C 65 ASP cc_start: 0.7099 (m-30) cc_final: 0.6866 (m-30) REVERT: C 126 TYR cc_start: 0.7848 (t80) cc_final: 0.7604 (t80) REVERT: C 232 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7747 (pp20) REVERT: D 3 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.7281 (ttt) REVERT: D 23 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.8276 (ptm) REVERT: E 31 LYS cc_start: 0.7927 (mtpm) cc_final: 0.7641 (mtpp) REVERT: E 33 ASN cc_start: 0.7719 (OUTLIER) cc_final: 0.7453 (m-40) REVERT: E 289 GLU cc_start: 0.6308 (OUTLIER) cc_final: 0.5246 (pp20) REVERT: F 43 GLU cc_start: 0.6666 (OUTLIER) cc_final: 0.6439 (mt-10) REVERT: F 138 LEU cc_start: 0.6924 (OUTLIER) cc_final: 0.6060 (tt) outliers start: 47 outliers final: 27 residues processed: 204 average time/residue: 1.1818 time to fit residues: 261.6048 Evaluate side-chains 196 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 161 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 23 MET Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 254 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 31 optimal weight: 0.4980 chunk 129 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 ASN E 29 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11766 Z= 0.223 Angle : 0.508 5.836 16174 Z= 0.276 Chirality : 0.041 0.169 1823 Planarity : 0.003 0.030 1879 Dihedral : 18.416 177.558 2095 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.88 % Allowed : 16.23 % Favored : 78.89 % 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: 1.31 (0.24), residues: 1288 helix: 2.40 (0.21), residues: 607 sheet: -0.44 (0.36), residues: 203 loop : -0.52 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 296 HIS 0.007 0.001 HIS B 29 PHE 0.009 0.001 PHE D 89 TYR 0.016 0.001 TYR F 223 ARG 0.006 0.000 ARG F 17 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 185 time to evaluate : 1.624 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.8978 (ttp) cc_final: 0.8644 (ttp) REVERT: B 33 ASN cc_start: 0.8157 (OUTLIER) cc_final: 0.7945 (m-40) REVERT: B 156 ARG cc_start: 0.7539 (tpp-160) cc_final: 0.7314 (ttm-80) REVERT: C 65 ASP cc_start: 0.7109 (m-30) cc_final: 0.6864 (m-30) REVERT: C 126 TYR cc_start: 0.7797 (t80) cc_final: 0.7584 (t80) REVERT: C 232 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7760 (pp20) REVERT: D 3 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7332 (ttt) REVERT: D 23 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8224 (ptm) REVERT: D 35 PHE cc_start: 0.8273 (OUTLIER) cc_final: 0.7686 (m-80) REVERT: E 31 LYS cc_start: 0.7879 (mtpm) cc_final: 0.7612 (mtpp) REVERT: E 33 ASN cc_start: 0.7689 (OUTLIER) cc_final: 0.7409 (m-40) REVERT: E 261 ASP cc_start: 0.6915 (m-30) cc_final: 0.6692 (m-30) REVERT: E 289 GLU cc_start: 0.6402 (OUTLIER) cc_final: 0.5388 (pp20) REVERT: F 43 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.6459 (mt-10) REVERT: F 138 LEU cc_start: 0.6970 (OUTLIER) cc_final: 0.6092 (tt) outliers start: 52 outliers final: 27 residues processed: 212 average time/residue: 1.1384 time to fit residues: 263.8568 Evaluate side-chains 197 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 162 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 23 MET Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 35 PHE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 54 MET Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 254 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 109 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 51 optimal weight: 9.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11766 Z= 0.268 Angle : 0.539 7.544 16174 Z= 0.291 Chirality : 0.042 0.189 1823 Planarity : 0.004 0.030 1879 Dihedral : 18.462 177.373 2095 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.32 % Allowed : 18.01 % Favored : 77.67 % 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: 1.23 (0.24), residues: 1288 helix: 2.32 (0.21), residues: 608 sheet: -0.51 (0.36), residues: 203 loop : -0.54 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 296 HIS 0.007 0.001 HIS B 29 PHE 0.009 0.001 PHE D 89 TYR 0.017 0.001 TYR F 223 ARG 0.006 0.000 ARG F 17 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 166 time to evaluate : 1.355 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.8987 (ttp) cc_final: 0.8774 (ttp) REVERT: B 33 ASN cc_start: 0.8165 (OUTLIER) cc_final: 0.7947 (m-40) REVERT: B 156 ARG cc_start: 0.7541 (tpp-160) cc_final: 0.7315 (ttm-80) REVERT: C 65 ASP cc_start: 0.7190 (m-30) cc_final: 0.6922 (m-30) REVERT: C 232 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7705 (pp20) REVERT: D 23 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8270 (ptm) REVERT: D 35 PHE cc_start: 0.8298 (OUTLIER) cc_final: 0.7724 (m-80) REVERT: E 33 ASN cc_start: 0.7734 (OUTLIER) cc_final: 0.7445 (m-40) REVERT: E 289 GLU cc_start: 0.6470 (OUTLIER) cc_final: 0.5469 (pp20) REVERT: F 43 GLU cc_start: 0.6723 (OUTLIER) cc_final: 0.6499 (mt-10) outliers start: 46 outliers final: 27 residues processed: 192 average time/residue: 1.1658 time to fit residues: 243.2801 Evaluate side-chains 190 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 157 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 23 MET Chi-restraints excluded: chain D residue 35 PHE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 54 MET Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 234 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 5.9990 chunk 38 optimal weight: 0.0770 chunk 25 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 87 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 12 optimal weight: 0.0980 chunk 101 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 chunk 123 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11766 Z= 0.228 Angle : 0.528 7.743 16174 Z= 0.285 Chirality : 0.041 0.189 1823 Planarity : 0.004 0.048 1879 Dihedral : 18.429 177.200 2095 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.75 % Allowed : 18.57 % Favored : 77.67 % 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: 1.23 (0.24), residues: 1288 helix: 2.33 (0.21), residues: 608 sheet: -0.53 (0.36), residues: 203 loop : -0.53 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 296 HIS 0.006 0.001 HIS B 29 PHE 0.009 0.001 PHE D 89 TYR 0.017 0.001 TYR F 223 ARG 0.006 0.000 ARG F 17 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 168 time to evaluate : 1.319 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.8977 (ttp) cc_final: 0.8758 (ttp) REVERT: B 33 ASN cc_start: 0.8153 (OUTLIER) cc_final: 0.7951 (m-40) REVERT: C 65 ASP cc_start: 0.7149 (m-30) cc_final: 0.6890 (m-30) REVERT: C 254 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8296 (tt) REVERT: D 3 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7369 (ttt) REVERT: D 23 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.8271 (ptm) REVERT: D 35 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.7767 (m-80) REVERT: E 31 LYS cc_start: 0.7884 (mtpp) cc_final: 0.7606 (mtpp) REVERT: E 33 ASN cc_start: 0.7673 (OUTLIER) cc_final: 0.7423 (m-40) REVERT: E 289 GLU cc_start: 0.6480 (OUTLIER) cc_final: 0.5423 (pp20) REVERT: F 43 GLU cc_start: 0.6702 (OUTLIER) cc_final: 0.6475 (mt-10) outliers start: 40 outliers final: 24 residues processed: 192 average time/residue: 1.2208 time to fit residues: 253.9977 Evaluate side-chains 203 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 171 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 23 MET Chi-restraints excluded: chain D residue 35 PHE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 234 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.6980 chunk 123 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 127 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11766 Z= 0.260 Angle : 0.550 7.874 16174 Z= 0.295 Chirality : 0.042 0.187 1823 Planarity : 0.004 0.030 1879 Dihedral : 18.469 177.172 2095 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.66 % Allowed : 18.95 % Favored : 77.39 % 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: 1.16 (0.24), residues: 1288 helix: 2.27 (0.21), residues: 608 sheet: -0.54 (0.36), residues: 203 loop : -0.58 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 296 HIS 0.007 0.001 HIS B 29 PHE 0.010 0.001 PHE D 89 TYR 0.016 0.001 TYR F 223 ARG 0.007 0.000 ARG C 124 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 169 time to evaluate : 1.344 Fit side-chains REVERT: B 33 ASN cc_start: 0.8161 (OUTLIER) cc_final: 0.7949 (m-40) REVERT: B 156 ARG cc_start: 0.7528 (tpp-160) cc_final: 0.7310 (ttm-80) REVERT: C 65 ASP cc_start: 0.7192 (m-30) cc_final: 0.6918 (m-30) REVERT: C 254 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8264 (tt) REVERT: D 23 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8279 (ptm) REVERT: D 35 PHE cc_start: 0.8301 (OUTLIER) cc_final: 0.7727 (m-80) REVERT: E 31 LYS cc_start: 0.7895 (mtpp) cc_final: 0.7626 (mtpp) REVERT: E 33 ASN cc_start: 0.7688 (OUTLIER) cc_final: 0.7416 (m-40) REVERT: E 289 GLU cc_start: 0.6512 (OUTLIER) cc_final: 0.5493 (pp20) REVERT: F 43 GLU cc_start: 0.6719 (OUTLIER) cc_final: 0.6494 (mt-10) REVERT: F 103 ARG cc_start: 0.7492 (ptm160) cc_final: 0.7264 (ttp-170) outliers start: 39 outliers final: 23 residues processed: 190 average time/residue: 1.2020 time to fit residues: 247.6585 Evaluate side-chains 200 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 170 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 23 MET Chi-restraints excluded: chain D residue 35 PHE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 234 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 88 optimal weight: 10.0000 chunk 133 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 106 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 11766 Z= 0.296 Angle : 0.580 8.074 16174 Z= 0.309 Chirality : 0.043 0.199 1823 Planarity : 0.004 0.043 1879 Dihedral : 18.552 176.912 2095 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.47 % Allowed : 19.61 % Favored : 76.92 % 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: 1.07 (0.24), residues: 1288 helix: 2.20 (0.21), residues: 607 sheet: -0.55 (0.35), residues: 208 loop : -0.64 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 296 HIS 0.008 0.001 HIS B 29 PHE 0.011 0.001 PHE D 89 TYR 0.018 0.002 TYR F 223 ARG 0.007 0.000 ARG C 124 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 172 time to evaluate : 1.327 Fit side-chains REVERT: A 58 MET cc_start: 0.8965 (ttp) cc_final: 0.8501 (ttp) REVERT: B 33 ASN cc_start: 0.8163 (OUTLIER) cc_final: 0.7939 (m-40) REVERT: B 156 ARG cc_start: 0.7544 (tpp-160) cc_final: 0.7341 (ttm-80) REVERT: C 65 ASP cc_start: 0.7231 (m-30) cc_final: 0.6963 (m-30) REVERT: C 254 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8230 (tt) REVERT: D 23 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8320 (ptm) REVERT: D 35 PHE cc_start: 0.8354 (OUTLIER) cc_final: 0.7799 (m-80) REVERT: E 31 LYS cc_start: 0.7898 (mtpp) cc_final: 0.7619 (mtpp) REVERT: E 33 ASN cc_start: 0.7711 (OUTLIER) cc_final: 0.7419 (m-40) REVERT: E 261 ASP cc_start: 0.6868 (m-30) cc_final: 0.6641 (m-30) REVERT: E 289 GLU cc_start: 0.6551 (OUTLIER) cc_final: 0.5521 (pp20) REVERT: F 43 GLU cc_start: 0.6737 (OUTLIER) cc_final: 0.6514 (mt-10) outliers start: 37 outliers final: 23 residues processed: 194 average time/residue: 1.1451 time to fit residues: 242.0844 Evaluate side-chains 197 residues out of total 1066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 167 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 3 MET Chi-restraints excluded: chain D residue 23 MET Chi-restraints excluded: chain D residue 35 PHE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 234 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 109 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.157784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.125827 restraints weight = 12292.113| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.76 r_work: 0.3342 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11766 Z= 0.229 Angle : 0.553 8.596 16174 Z= 0.296 Chirality : 0.043 0.258 1823 Planarity : 0.004 0.041 1879 Dihedral : 18.478 176.609 2095 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.00 % Allowed : 20.26 % Favored : 76.74 % 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: 1.16 (0.24), residues: 1288 helix: 2.28 (0.21), residues: 607 sheet: -0.56 (0.36), residues: 203 loop : -0.58 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 296 HIS 0.006 0.001 HIS B 29 PHE 0.009 0.001 PHE D 89 TYR 0.016 0.001 TYR F 223 ARG 0.007 0.000 ARG C 124 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4451.68 seconds wall clock time: 79 minutes 56.76 seconds (4796.76 seconds total)