Starting phenix.real_space_refine on Fri Mar 15 14:22:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5f_27911/03_2024/8e5f_27911_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5f_27911/03_2024/8e5f_27911.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5f_27911/03_2024/8e5f_27911.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5f_27911/03_2024/8e5f_27911.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5f_27911/03_2024/8e5f_27911_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5f_27911/03_2024/8e5f_27911_updated.pdb" } resolution = 3.8 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 ------------------------------------------------------------------------------- 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= 0.002 sd= 0.032 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: 5 Type Number sf(0) Gaussians Fe 20 7.16 5 S 70 5.16 5 C 7705 2.51 5 N 1920 2.21 5 O 2175 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 63": "OD1" <-> "OD2" Residue "A ASP 128": "OD1" <-> "OD2" Residue "A TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 156": "OD1" <-> "OD2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 257": "OE1" <-> "OE2" Residue "A GLU 258": "OE1" <-> "OE2" Residue "B ASP 63": "OD1" <-> "OD2" Residue "B ASP 128": "OD1" <-> "OD2" Residue "B TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 156": "OD1" <-> "OD2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "B PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 257": "OE1" <-> "OE2" Residue "B GLU 258": "OE1" <-> "OE2" Residue "C ASP 63": "OD1" <-> "OD2" Residue "C ASP 128": "OD1" <-> "OD2" Residue "C TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 156": "OD1" <-> "OD2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "C PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 257": "OE1" <-> "OE2" Residue "C GLU 258": "OE1" <-> "OE2" Residue "D ASP 63": "OD1" <-> "OD2" Residue "D ASP 128": "OD1" <-> "OD2" Residue "D TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 156": "OD1" <-> "OD2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "D PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 257": "OE1" <-> "OE2" Residue "D GLU 258": "OE1" <-> "OE2" Residue "E ASP 63": "OD1" <-> "OD2" Residue "E ASP 128": "OD1" <-> "OD2" Residue "E TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 156": "OD1" <-> "OD2" Residue "E GLU 187": "OE1" <-> "OE2" Residue "E PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 257": "OE1" <-> "OE2" Residue "E GLU 258": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11890 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2378 Unusual residues: {'HEC': 4} Classifications: {'peptide': 293, 'undetermined': 4} Link IDs: {'PTRANS': 19, 'TRANS': 273, None: 4} Not linked: pdbres="GLY A 316 " pdbres="HEC A 501 " Not linked: pdbres="HEC A 501 " pdbres="HEC A 502 " Not linked: pdbres="HEC A 502 " pdbres="HEC A 503 " Not linked: pdbres="HEC A 503 " pdbres="HEC A 504 " Chain: "B" Number of atoms: 2378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2378 Unusual residues: {'HEC': 4} Classifications: {'peptide': 293, 'undetermined': 4} Link IDs: {'PTRANS': 19, 'TRANS': 273, None: 4} Not linked: pdbres="GLY B 316 " pdbres="HEC B 501 " Not linked: pdbres="HEC B 501 " pdbres="HEC B 502 " Not linked: pdbres="HEC B 502 " pdbres="HEC B 503 " Not linked: pdbres="HEC B 503 " pdbres="HEC B 504 " Chain: "C" Number of atoms: 2378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2378 Unusual residues: {'HEC': 4} Classifications: {'peptide': 293, 'undetermined': 4} Link IDs: {'PTRANS': 19, 'TRANS': 273, None: 4} Not linked: pdbres="GLY C 316 " pdbres="HEC C 501 " Not linked: pdbres="HEC C 501 " pdbres="HEC C 502 " Not linked: pdbres="HEC C 502 " pdbres="HEC C 503 " Not linked: pdbres="HEC C 503 " pdbres="HEC C 504 " Chain: "D" Number of atoms: 2378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2378 Unusual residues: {'HEC': 4} Classifications: {'peptide': 293, 'undetermined': 4} Link IDs: {'PTRANS': 19, 'TRANS': 273, None: 4} Not linked: pdbres="GLY D 316 " pdbres="HEC D 501 " Not linked: pdbres="HEC D 501 " pdbres="HEC D 502 " Not linked: pdbres="HEC D 502 " pdbres="HEC D 503 " Not linked: pdbres="HEC D 503 " pdbres="HEC D 504 " Chain: "E" Number of atoms: 2378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2378 Unusual residues: {'HEC': 4} Classifications: {'peptide': 293, 'undetermined': 4} Link IDs: {'PTRANS': 19, 'TRANS': 273, None: 4} Not linked: pdbres="GLY E 316 " pdbres="HEC E 501 " Not linked: pdbres="HEC E 501 " pdbres="HEC E 502 " Not linked: pdbres="HEC E 502 " pdbres="HEC E 503 " Not linked: pdbres="HEC E 503 " pdbres="HEC E 504 " Time building chain proxies: 6.54, per 1000 atoms: 0.55 Number of scatterers: 11890 At special positions: 0 Unit cell: (71.28, 75.6, 204.12, 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) Fe 20 26.01 S 70 16.00 O 2175 8.00 N 1920 7.00 C 7705 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 69 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 163 " distance=2.03 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 69 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 163 " distance=2.03 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 69 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 163 " distance=2.03 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 69 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 163 " distance=2.03 Simple disulfide: pdb=" SG CYS E 62 " - pdb=" SG CYS E 69 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 163 " distance=2.03 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=65, symmetry=0 Number of additional bonds: simple=65, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.90 Conformation dependent library (CDL) restraints added in 2.1 seconds 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2640 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 35 helices and 20 sheets defined 15.0% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.29 Creating SS restraints... Processing helix chain 'A' and resid 79 through 85 Processing helix chain 'A' and resid 90 through 96 Processing helix chain 'A' and resid 102 through 111 removed outlier: 4.254A pdb=" N GLY A 106 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 108 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN A 109 " --> pdb=" O GLY A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 189 Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 289 through 291 No H-bonds generated for 'chain 'A' and resid 289 through 291' Processing helix chain 'A' and resid 303 through 306 Processing helix chain 'B' and resid 79 through 85 Processing helix chain 'B' and resid 90 through 96 Processing helix chain 'B' and resid 102 through 111 removed outlier: 4.254A pdb=" N GLY B 106 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU B 108 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN B 109 " --> pdb=" O GLY B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 189 Processing helix chain 'B' and resid 284 through 286 No H-bonds generated for 'chain 'B' and resid 284 through 286' Processing helix chain 'B' and resid 289 through 291 No H-bonds generated for 'chain 'B' and resid 289 through 291' Processing helix chain 'B' and resid 303 through 306 Processing helix chain 'C' and resid 79 through 85 Processing helix chain 'C' and resid 90 through 96 Processing helix chain 'C' and resid 102 through 111 removed outlier: 4.253A pdb=" N GLY C 106 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU C 108 " --> pdb=" O SER C 105 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN C 109 " --> pdb=" O GLY C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 189 Processing helix chain 'C' and resid 284 through 286 No H-bonds generated for 'chain 'C' and resid 284 through 286' Processing helix chain 'C' and resid 289 through 291 No H-bonds generated for 'chain 'C' and resid 289 through 291' Processing helix chain 'C' and resid 303 through 306 Processing helix chain 'D' and resid 79 through 85 Processing helix chain 'D' and resid 90 through 96 Processing helix chain 'D' and resid 102 through 111 removed outlier: 4.253A pdb=" N GLY D 106 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN D 109 " --> pdb=" O GLY D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 189 Processing helix chain 'D' and resid 284 through 286 No H-bonds generated for 'chain 'D' and resid 284 through 286' Processing helix chain 'D' and resid 289 through 291 No H-bonds generated for 'chain 'D' and resid 289 through 291' Processing helix chain 'D' and resid 303 through 306 Processing helix chain 'E' and resid 79 through 85 Processing helix chain 'E' and resid 90 through 96 Processing helix chain 'E' and resid 102 through 111 removed outlier: 4.253A pdb=" N GLY E 106 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU E 108 " --> pdb=" O SER E 105 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN E 109 " --> pdb=" O GLY E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 189 Processing helix chain 'E' and resid 284 through 286 No H-bonds generated for 'chain 'E' and resid 284 through 286' Processing helix chain 'E' and resid 289 through 291 No H-bonds generated for 'chain 'E' and resid 289 through 291' Processing helix chain 'E' and resid 303 through 306 Processing sheet with id= A, first strand: chain 'A' and resid 50 through 52 Processing sheet with id= B, first strand: chain 'A' and resid 265 through 268 removed outlier: 3.737A pdb=" N GLY A 166 " --> pdb=" O TYR A 130 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 193 through 195 removed outlier: 3.528A pdb=" N LYS A 195 " --> pdb=" O PHE A 277 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 201 through 203 Processing sheet with id= E, first strand: chain 'B' and resid 50 through 52 Processing sheet with id= F, first strand: chain 'B' and resid 265 through 268 removed outlier: 3.736A pdb=" N GLY B 166 " --> pdb=" O TYR B 130 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 193 through 195 removed outlier: 3.528A pdb=" N LYS B 195 " --> pdb=" O PHE B 277 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 201 through 203 Processing sheet with id= I, first strand: chain 'C' and resid 50 through 52 Processing sheet with id= J, first strand: chain 'C' and resid 265 through 268 removed outlier: 3.737A pdb=" N GLY C 166 " --> pdb=" O TYR C 130 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 193 through 195 removed outlier: 3.527A pdb=" N LYS C 195 " --> pdb=" O PHE C 277 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 201 through 203 Processing sheet with id= M, first strand: chain 'D' and resid 50 through 52 Processing sheet with id= N, first strand: chain 'D' and resid 265 through 268 removed outlier: 3.736A pdb=" N GLY D 166 " --> pdb=" O TYR D 130 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 193 through 195 removed outlier: 3.529A pdb=" N LYS D 195 " --> pdb=" O PHE D 277 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 201 through 203 Processing sheet with id= Q, first strand: chain 'E' and resid 50 through 52 Processing sheet with id= R, first strand: chain 'E' and resid 265 through 268 removed outlier: 3.737A pdb=" N GLY E 166 " --> pdb=" O TYR E 130 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 193 through 195 removed outlier: 3.528A pdb=" N LYS E 195 " --> pdb=" O PHE E 277 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 201 through 203 225 hydrogen bonds defined for protein. 540 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: 2.90 Time building geometry restraints manager: 5.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 5340 1.39 - 1.56: 6860 1.56 - 1.73: 10 1.73 - 1.89: 80 1.89 - 2.06: 80 Bond restraints: 12370 Sorted by residual: bond pdb=" C2D HEC D 502 " pdb=" C3D HEC D 502 " ideal model delta sigma weight residual 1.544 1.331 0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C2D HEC B 502 " pdb=" C3D HEC B 502 " ideal model delta sigma weight residual 1.544 1.332 0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C2D HEC A 502 " pdb=" C3D HEC A 502 " ideal model delta sigma weight residual 1.544 1.332 0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C2D HEC E 502 " pdb=" C3D HEC E 502 " ideal model delta sigma weight residual 1.544 1.332 0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C2D HEC C 502 " pdb=" C3D HEC C 502 " ideal model delta sigma weight residual 1.544 1.332 0.212 2.00e-02 2.50e+03 1.12e+02 ... (remaining 12365 not shown) Histogram of bond angle deviations from ideal: 88.49 - 106.71: 576 106.71 - 124.94: 15551 124.94 - 143.16: 1023 143.16 - 161.38: 0 161.38 - 179.61: 40 Bond angle restraints: 17190 Sorted by residual: angle pdb=" CA PRO C 260 " pdb=" N PRO C 260 " pdb=" CD PRO C 260 " ideal model delta sigma weight residual 112.00 95.43 16.57 1.40e+00 5.10e-01 1.40e+02 angle pdb=" CA PRO B 260 " pdb=" N PRO B 260 " pdb=" CD PRO B 260 " ideal model delta sigma weight residual 112.00 95.44 16.56 1.40e+00 5.10e-01 1.40e+02 angle pdb=" CA PRO D 260 " pdb=" N PRO D 260 " pdb=" CD PRO D 260 " ideal model delta sigma weight residual 112.00 95.44 16.56 1.40e+00 5.10e-01 1.40e+02 angle pdb=" CA PRO A 260 " pdb=" N PRO A 260 " pdb=" CD PRO A 260 " ideal model delta sigma weight residual 112.00 95.45 16.55 1.40e+00 5.10e-01 1.40e+02 angle pdb=" CA PRO E 260 " pdb=" N PRO E 260 " pdb=" CD PRO E 260 " ideal model delta sigma weight residual 112.00 95.45 16.55 1.40e+00 5.10e-01 1.40e+02 ... (remaining 17185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 6020 17.96 - 35.93: 507 35.93 - 53.89: 113 53.89 - 71.85: 45 71.85 - 89.82: 35 Dihedral angle restraints: 6720 sinusoidal: 2530 harmonic: 4190 Sorted by residual: dihedral pdb=" C2C HEC B 502 " pdb=" C3C HEC B 502 " pdb=" CAC HEC B 502 " pdb=" CBC HEC B 502 " ideal model delta sinusoidal sigma weight residual 240.00 150.18 89.82 2 1.00e+01 1.00e-02 4.80e+01 dihedral pdb=" C2C HEC E 502 " pdb=" C3C HEC E 502 " pdb=" CAC HEC E 502 " pdb=" CBC HEC E 502 " ideal model delta sinusoidal sigma weight residual 240.00 150.19 89.81 2 1.00e+01 1.00e-02 4.80e+01 dihedral pdb=" C2C HEC C 502 " pdb=" C3C HEC C 502 " pdb=" CAC HEC C 502 " pdb=" CBC HEC C 502 " ideal model delta sinusoidal sigma weight residual 240.00 150.19 89.81 2 1.00e+01 1.00e-02 4.80e+01 ... (remaining 6717 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1451 0.079 - 0.159: 219 0.159 - 0.238: 0 0.238 - 0.318: 10 0.318 - 0.397: 5 Chirality restraints: 1685 Sorted by residual: chirality pdb=" CA ARG D 234 " pdb=" N ARG D 234 " pdb=" C ARG D 234 " pdb=" CB ARG D 234 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CA ARG E 234 " pdb=" N ARG E 234 " pdb=" C ARG E 234 " pdb=" CB ARG E 234 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.92e+00 chirality pdb=" CA ARG A 234 " pdb=" N ARG A 234 " pdb=" C ARG A 234 " pdb=" CB ARG A 234 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.40 2.00e-01 2.50e+01 3.91e+00 ... (remaining 1682 not shown) Planarity restraints: 2145 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 259 " 0.072 5.00e-02 4.00e+02 9.68e-02 1.50e+01 pdb=" N PRO D 260 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO D 260 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO D 260 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 259 " 0.072 5.00e-02 4.00e+02 9.68e-02 1.50e+01 pdb=" N PRO A 260 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO A 260 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 260 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 259 " 0.072 5.00e-02 4.00e+02 9.67e-02 1.50e+01 pdb=" N PRO E 260 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO E 260 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 260 " 0.052 5.00e-02 4.00e+02 ... (remaining 2142 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 134 2.60 - 3.18: 10324 3.18 - 3.75: 18231 3.75 - 4.33: 24805 4.33 - 4.90: 41796 Nonbonded interactions: 95290 Sorted by model distance: nonbonded pdb=" NE2 HIS C 89 " pdb="FE HEC C 502 " model vdw 2.029 3.080 nonbonded pdb=" NE2 HIS B 89 " pdb="FE HEC B 502 " model vdw 2.029 3.080 nonbonded pdb=" NE2 HIS A 89 " pdb="FE HEC A 502 " model vdw 2.030 3.080 nonbonded pdb=" NE2 HIS D 89 " pdb="FE HEC D 502 " model vdw 2.030 3.080 nonbonded pdb=" NE2 HIS E 89 " pdb="FE HEC E 502 " model vdw 2.030 3.080 ... (remaining 95285 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: 2.210 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: 7.150 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 33.920 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 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 : 0.017 0.249 12370 Z= 1.061 Angle : 1.167 16.575 17190 Z= 0.561 Chirality : 0.057 0.397 1685 Planarity : 0.006 0.097 2145 Dihedral : 16.511 89.819 4050 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 22.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.71 % Favored : 87.29 % Rotamer: Outliers : 0.00 % Allowed : 15.74 % Favored : 84.26 % 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: -2.96 (0.21), residues: 1455 helix: -0.28 (0.37), residues: 210 sheet: -1.73 (0.47), residues: 150 loop : -2.56 (0.17), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 93 HIS 0.004 0.001 HIS E 38 PHE 0.015 0.001 PHE C 309 TYR 0.010 0.001 TYR C 123 ARG 0.006 0.001 ARG C 234 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.240 Fit side-chains REVERT: A 102 ASN cc_start: 0.8307 (t160) cc_final: 0.7910 (t0) REVERT: A 267 MET cc_start: 0.8940 (tpp) cc_final: 0.8359 (tpt) REVERT: B 102 ASN cc_start: 0.8395 (t160) cc_final: 0.8056 (t0) REVERT: C 102 ASN cc_start: 0.8318 (t160) cc_final: 0.8010 (t0) REVERT: D 102 ASN cc_start: 0.8348 (t160) cc_final: 0.7961 (t0) REVERT: D 156 ASP cc_start: 0.7953 (p0) cc_final: 0.7123 (p0) REVERT: E 260 PRO cc_start: 0.8134 (Cg_endo) cc_final: 0.7874 (Cg_endo) REVERT: E 264 THR cc_start: 0.9126 (p) cc_final: 0.8906 (t) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.2269 time to fit residues: 49.2890 Evaluate side-chains 130 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 84 optimal weight: 0.3980 chunk 131 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 GLN C 229 GLN D 229 GLN ** D 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 12370 Z= 0.291 Angle : 0.833 12.035 17190 Z= 0.367 Chirality : 0.050 0.205 1685 Planarity : 0.005 0.040 2145 Dihedral : 12.972 84.397 1735 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.54 % Favored : 86.46 % Rotamer: Outliers : 4.85 % Allowed : 12.68 % 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: -3.10 (0.20), residues: 1455 helix: -0.19 (0.36), residues: 200 sheet: -1.93 (0.47), residues: 150 loop : -2.67 (0.17), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 82 HIS 0.006 0.001 HIS D 273 PHE 0.014 0.002 PHE D 224 TYR 0.013 0.002 TYR D 123 ARG 0.005 0.001 ARG E 288 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 172 time to evaluate : 0.987 Fit side-chains REVERT: A 102 ASN cc_start: 0.8098 (t160) cc_final: 0.7683 (t0) REVERT: A 130 TYR cc_start: 0.8514 (OUTLIER) cc_final: 0.7943 (m-80) REVERT: A 234 ARG cc_start: 0.8247 (ttp80) cc_final: 0.7969 (ttp-170) REVERT: A 267 MET cc_start: 0.8838 (tpp) cc_final: 0.8244 (tpt) REVERT: B 51 SER cc_start: 0.9135 (t) cc_final: 0.8917 (m) REVERT: B 102 ASN cc_start: 0.8227 (t160) cc_final: 0.7855 (t0) REVERT: B 130 TYR cc_start: 0.8605 (OUTLIER) cc_final: 0.7661 (m-80) REVERT: B 149 PHE cc_start: 0.9136 (p90) cc_final: 0.8930 (p90) REVERT: B 229 GLN cc_start: 0.8523 (pt0) cc_final: 0.8279 (pt0) REVERT: B 260 PRO cc_start: 0.8194 (Cg_endo) cc_final: 0.7899 (Cg_endo) REVERT: C 102 ASN cc_start: 0.8213 (t160) cc_final: 0.7848 (t0) REVERT: C 130 TYR cc_start: 0.8379 (OUTLIER) cc_final: 0.7882 (m-80) REVERT: D 51 SER cc_start: 0.9330 (t) cc_final: 0.9051 (m) REVERT: D 102 ASN cc_start: 0.8171 (t160) cc_final: 0.7716 (t0) REVERT: D 130 TYR cc_start: 0.8575 (OUTLIER) cc_final: 0.7900 (m-10) REVERT: D 156 ASP cc_start: 0.7928 (p0) cc_final: 0.7253 (p0) REVERT: D 260 PRO cc_start: 0.8092 (Cg_endo) cc_final: 0.7819 (Cg_endo) REVERT: E 51 SER cc_start: 0.9264 (t) cc_final: 0.8983 (m) REVERT: E 66 GLN cc_start: 0.8858 (mm-40) cc_final: 0.8315 (mm-40) REVERT: E 102 ASN cc_start: 0.8184 (t160) cc_final: 0.7628 (t0) REVERT: E 130 TYR cc_start: 0.8478 (OUTLIER) cc_final: 0.7780 (m-10) REVERT: E 264 THR cc_start: 0.9022 (OUTLIER) cc_final: 0.8803 (t) outliers start: 57 outliers final: 22 residues processed: 215 average time/residue: 0.2161 time to fit residues: 67.8884 Evaluate side-chains 180 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 152 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 130 TYR Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 304 CYS Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 130 TYR Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 304 CYS Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 304 CYS Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 304 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 73 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 chunk 89 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 142 optimal weight: 0.9980 chunk 117 optimal weight: 6.9990 chunk 130 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 GLN ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 GLN ** D 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12370 Z= 0.252 Angle : 0.805 13.383 17190 Z= 0.351 Chirality : 0.050 0.215 1685 Planarity : 0.004 0.041 2145 Dihedral : 12.683 85.903 1735 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.09 % Favored : 85.91 % Rotamer: Outliers : 2.72 % Allowed : 16.17 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.20), residues: 1455 helix: -0.24 (0.36), residues: 200 sheet: -2.00 (0.46), residues: 150 loop : -2.73 (0.17), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 82 HIS 0.006 0.001 HIS D 89 PHE 0.011 0.001 PHE A 309 TYR 0.011 0.001 TYR A 123 ARG 0.005 0.000 ARG E 288 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 171 time to evaluate : 1.221 Fit side-chains REVERT: A 102 ASN cc_start: 0.8137 (t160) cc_final: 0.7712 (t0) REVERT: A 130 TYR cc_start: 0.8469 (OUTLIER) cc_final: 0.7851 (m-80) REVERT: A 229 GLN cc_start: 0.8344 (pt0) cc_final: 0.8133 (pt0) REVERT: B 102 ASN cc_start: 0.8144 (t160) cc_final: 0.7781 (t0) REVERT: B 130 TYR cc_start: 0.8545 (OUTLIER) cc_final: 0.7711 (m-10) REVERT: B 260 PRO cc_start: 0.8198 (Cg_endo) cc_final: 0.7933 (Cg_endo) REVERT: C 51 SER cc_start: 0.9240 (m) cc_final: 0.8890 (t) REVERT: C 102 ASN cc_start: 0.8158 (t160) cc_final: 0.7761 (t0) REVERT: C 130 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.7917 (m-80) REVERT: C 229 GLN cc_start: 0.8342 (pt0) cc_final: 0.8130 (pt0) REVERT: D 51 SER cc_start: 0.9302 (t) cc_final: 0.9057 (m) REVERT: D 102 ASN cc_start: 0.8145 (t160) cc_final: 0.7695 (t0) REVERT: D 130 TYR cc_start: 0.8556 (OUTLIER) cc_final: 0.8064 (m-10) REVERT: D 156 ASP cc_start: 0.7899 (p0) cc_final: 0.7199 (p0) REVERT: D 187 GLU cc_start: 0.8735 (tp30) cc_final: 0.8387 (mm-30) REVERT: E 66 GLN cc_start: 0.8866 (mm-40) cc_final: 0.8312 (mm-40) REVERT: E 102 ASN cc_start: 0.8169 (t160) cc_final: 0.7618 (t0) REVERT: E 130 TYR cc_start: 0.8421 (OUTLIER) cc_final: 0.7705 (m-10) REVERT: E 187 GLU cc_start: 0.8883 (tp30) cc_final: 0.8336 (mm-30) REVERT: E 264 THR cc_start: 0.8974 (OUTLIER) cc_final: 0.8757 (t) outliers start: 32 outliers final: 20 residues processed: 194 average time/residue: 0.2197 time to fit residues: 62.4719 Evaluate side-chains 181 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 155 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain B residue 130 TYR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 304 CYS Chi-restraints excluded: chain C residue 130 TYR Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 304 CYS Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 304 CYS Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 304 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 130 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 68 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 GLN ** B 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 GLN ** D 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 12370 Z= 0.266 Angle : 0.802 12.948 17190 Z= 0.351 Chirality : 0.051 0.223 1685 Planarity : 0.004 0.039 2145 Dihedral : 12.683 87.500 1735 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.64 % Favored : 85.36 % Rotamer: Outliers : 3.57 % Allowed : 16.94 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.20), residues: 1455 helix: -0.36 (0.35), residues: 205 sheet: -1.87 (0.46), residues: 150 loop : -2.77 (0.17), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 82 HIS 0.007 0.001 HIS C 89 PHE 0.015 0.001 PHE A 224 TYR 0.013 0.001 TYR A 123 ARG 0.006 0.001 ARG E 288 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 157 time to evaluate : 1.310 Fit side-chains REVERT: A 102 ASN cc_start: 0.8115 (t160) cc_final: 0.7695 (t0) REVERT: A 130 TYR cc_start: 0.8517 (OUTLIER) cc_final: 0.7974 (m-80) REVERT: B 68 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.6529 (tp30) REVERT: B 102 ASN cc_start: 0.8179 (t160) cc_final: 0.7732 (t0) REVERT: B 130 TYR cc_start: 0.8538 (OUTLIER) cc_final: 0.7782 (m-10) REVERT: B 187 GLU cc_start: 0.8763 (tp30) cc_final: 0.8484 (mm-30) REVERT: B 229 GLN cc_start: 0.8474 (pt0) cc_final: 0.8188 (pt0) REVERT: B 260 PRO cc_start: 0.8300 (Cg_exo) cc_final: 0.8036 (Cg_endo) REVERT: C 102 ASN cc_start: 0.8189 (t160) cc_final: 0.7758 (t0) REVERT: C 130 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.7832 (m-80) REVERT: D 102 ASN cc_start: 0.8182 (t160) cc_final: 0.7751 (t0) REVERT: D 130 TYR cc_start: 0.8587 (OUTLIER) cc_final: 0.8188 (m-10) REVERT: D 156 ASP cc_start: 0.7946 (p0) cc_final: 0.7239 (p0) REVERT: D 187 GLU cc_start: 0.8711 (tp30) cc_final: 0.8196 (mm-30) REVERT: E 66 GLN cc_start: 0.8853 (mm-40) cc_final: 0.8302 (mm-40) REVERT: E 102 ASN cc_start: 0.8232 (t160) cc_final: 0.7680 (t0) REVERT: E 130 TYR cc_start: 0.8493 (OUTLIER) cc_final: 0.7820 (m-10) REVERT: E 187 GLU cc_start: 0.8896 (tp30) cc_final: 0.8235 (mm-30) REVERT: E 264 THR cc_start: 0.8968 (OUTLIER) cc_final: 0.8736 (t) outliers start: 42 outliers final: 25 residues processed: 190 average time/residue: 0.2157 time to fit residues: 60.6913 Evaluate side-chains 178 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 146 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 130 TYR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 304 CYS Chi-restraints excluded: chain C residue 130 TYR Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 304 CYS Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 304 CYS Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 304 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 116 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 57 optimal weight: 0.0570 chunk 119 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN ** A 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 12370 Z= 0.424 Angle : 0.939 17.234 17190 Z= 0.406 Chirality : 0.054 0.256 1685 Planarity : 0.005 0.046 2145 Dihedral : 13.035 89.331 1735 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.04 % Favored : 82.96 % Rotamer: Outliers : 5.11 % Allowed : 17.28 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.20), residues: 1455 helix: -0.60 (0.36), residues: 205 sheet: -2.33 (0.45), residues: 140 loop : -2.77 (0.17), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 82 HIS 0.006 0.001 HIS C 89 PHE 0.023 0.002 PHE D 224 TYR 0.021 0.002 TYR A 123 ARG 0.006 0.001 ARG E 288 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 136 time to evaluate : 1.178 Fit side-chains REVERT: A 70 VAL cc_start: 0.9112 (t) cc_final: 0.8750 (m) REVERT: A 130 TYR cc_start: 0.8551 (OUTLIER) cc_final: 0.8088 (m-80) REVERT: A 267 MET cc_start: 0.8680 (ttm) cc_final: 0.8217 (tpt) REVERT: A 280 VAL cc_start: 0.8057 (OUTLIER) cc_final: 0.7807 (m) REVERT: B 68 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.6587 (tp30) REVERT: B 130 TYR cc_start: 0.8552 (OUTLIER) cc_final: 0.7934 (m-10) REVERT: B 156 ASP cc_start: 0.8035 (p0) cc_final: 0.7259 (p0) REVERT: C 130 TYR cc_start: 0.8621 (OUTLIER) cc_final: 0.8052 (m-80) REVERT: C 280 VAL cc_start: 0.7940 (OUTLIER) cc_final: 0.7665 (m) REVERT: D 66 GLN cc_start: 0.8849 (mm-40) cc_final: 0.8280 (mm-40) REVERT: D 130 TYR cc_start: 0.8484 (OUTLIER) cc_final: 0.8085 (m-10) REVERT: D 156 ASP cc_start: 0.8122 (p0) cc_final: 0.7331 (p0) REVERT: D 280 VAL cc_start: 0.8132 (OUTLIER) cc_final: 0.7848 (m) REVERT: E 66 GLN cc_start: 0.8904 (mm-40) cc_final: 0.8359 (mm-40) REVERT: E 130 TYR cc_start: 0.8475 (OUTLIER) cc_final: 0.7919 (m-10) REVERT: E 280 VAL cc_start: 0.7987 (OUTLIER) cc_final: 0.7747 (m) outliers start: 60 outliers final: 37 residues processed: 179 average time/residue: 0.1762 time to fit residues: 50.2839 Evaluate side-chains 169 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 122 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 130 TYR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 304 CYS Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 130 TYR Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 304 CYS Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 304 CYS Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 115 CYS Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 304 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 47 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 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 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 12370 Z= 0.289 Angle : 0.859 14.310 17190 Z= 0.370 Chirality : 0.051 0.237 1685 Planarity : 0.004 0.041 2145 Dihedral : 12.727 89.008 1735 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.40 % Favored : 84.60 % Rotamer: Outliers : 4.68 % Allowed : 18.98 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.20), residues: 1455 helix: -0.54 (0.36), residues: 205 sheet: -1.90 (0.46), residues: 150 loop : -2.84 (0.17), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 71 HIS 0.006 0.001 HIS C 89 PHE 0.015 0.001 PHE D 224 TYR 0.015 0.001 TYR B 123 ARG 0.005 0.001 ARG E 288 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 135 time to evaluate : 1.220 Fit side-chains REVERT: A 70 VAL cc_start: 0.9059 (t) cc_final: 0.8695 (m) REVERT: A 130 TYR cc_start: 0.8516 (OUTLIER) cc_final: 0.8041 (m-80) REVERT: A 267 MET cc_start: 0.8668 (ttm) cc_final: 0.8261 (tpt) REVERT: A 280 VAL cc_start: 0.7836 (OUTLIER) cc_final: 0.7557 (m) REVERT: B 68 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.6541 (tp30) REVERT: B 130 TYR cc_start: 0.8524 (OUTLIER) cc_final: 0.7922 (m-10) REVERT: B 187 GLU cc_start: 0.8808 (tp30) cc_final: 0.8445 (mm-30) REVERT: B 244 VAL cc_start: 0.8562 (t) cc_final: 0.8345 (t) REVERT: B 280 VAL cc_start: 0.7965 (OUTLIER) cc_final: 0.7635 (m) REVERT: B 299 PRO cc_start: 0.9373 (Cg_endo) cc_final: 0.9024 (Cg_exo) REVERT: C 130 TYR cc_start: 0.8548 (OUTLIER) cc_final: 0.7947 (m-80) REVERT: C 280 VAL cc_start: 0.7747 (OUTLIER) cc_final: 0.7473 (m) REVERT: D 66 GLN cc_start: 0.8877 (mm-40) cc_final: 0.8423 (mm-40) REVERT: D 130 TYR cc_start: 0.8606 (OUTLIER) cc_final: 0.8261 (m-10) REVERT: D 156 ASP cc_start: 0.7997 (p0) cc_final: 0.7253 (p0) REVERT: D 187 GLU cc_start: 0.8751 (tp30) cc_final: 0.8168 (mm-30) REVERT: D 280 VAL cc_start: 0.8021 (OUTLIER) cc_final: 0.7693 (m) REVERT: E 66 GLN cc_start: 0.8878 (mm-40) cc_final: 0.8376 (mm-40) REVERT: E 130 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.7746 (m-10) REVERT: E 187 GLU cc_start: 0.8871 (tp30) cc_final: 0.8432 (mm-30) REVERT: E 280 VAL cc_start: 0.7748 (OUTLIER) cc_final: 0.7458 (m) outliers start: 55 outliers final: 41 residues processed: 180 average time/residue: 0.1756 time to fit residues: 49.6862 Evaluate side-chains 180 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 128 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 130 TYR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 304 CYS Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 130 TYR Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 304 CYS Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 304 CYS Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 115 CYS Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 304 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 135 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 chunk 118 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 64 optimal weight: 0.1980 chunk 86 optimal weight: 3.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN C 48 GLN ** C 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 GLN ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 12370 Z= 0.453 Angle : 0.951 16.465 17190 Z= 0.413 Chirality : 0.055 0.272 1685 Planarity : 0.005 0.046 2145 Dihedral : 13.151 89.264 1735 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.73 % Favored : 82.27 % Rotamer: Outliers : 5.45 % Allowed : 19.40 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.20), residues: 1455 helix: 0.06 (0.40), residues: 170 sheet: -2.32 (0.44), residues: 140 loop : -2.91 (0.17), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 71 HIS 0.005 0.001 HIS E 38 PHE 0.017 0.002 PHE D 224 TYR 0.022 0.002 TYR D 123 ARG 0.005 0.001 ARG E 288 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 128 time to evaluate : 1.243 Fit side-chains REVERT: A 70 VAL cc_start: 0.9116 (t) cc_final: 0.8820 (m) REVERT: A 130 TYR cc_start: 0.8568 (OUTLIER) cc_final: 0.8060 (m-80) REVERT: A 244 VAL cc_start: 0.8608 (t) cc_final: 0.8405 (t) REVERT: A 280 VAL cc_start: 0.8092 (OUTLIER) cc_final: 0.7841 (m) REVERT: B 68 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.6605 (tp30) REVERT: B 130 TYR cc_start: 0.8537 (OUTLIER) cc_final: 0.7999 (m-10) REVERT: B 156 ASP cc_start: 0.8171 (p0) cc_final: 0.7432 (p0) REVERT: B 280 VAL cc_start: 0.8143 (OUTLIER) cc_final: 0.7856 (m) REVERT: C 130 TYR cc_start: 0.8611 (OUTLIER) cc_final: 0.8116 (m-80) REVERT: C 280 VAL cc_start: 0.7969 (OUTLIER) cc_final: 0.7759 (m) REVERT: D 66 GLN cc_start: 0.8910 (mm-40) cc_final: 0.8610 (mm-40) REVERT: D 130 TYR cc_start: 0.8485 (OUTLIER) cc_final: 0.8119 (m-10) REVERT: D 156 ASP cc_start: 0.8168 (p0) cc_final: 0.7396 (p0) REVERT: D 280 VAL cc_start: 0.8260 (OUTLIER) cc_final: 0.7994 (m) REVERT: E 66 GLN cc_start: 0.8920 (mm-40) cc_final: 0.8383 (mm-40) REVERT: E 130 TYR cc_start: 0.8518 (OUTLIER) cc_final: 0.7932 (m-10) REVERT: E 280 VAL cc_start: 0.8036 (OUTLIER) cc_final: 0.7786 (m) outliers start: 64 outliers final: 44 residues processed: 176 average time/residue: 0.1779 time to fit residues: 48.6198 Evaluate side-chains 173 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 118 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 130 TYR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 304 CYS Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 130 TYR Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 304 CYS Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 304 CYS Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 115 CYS Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 304 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 55 optimal weight: 0.4980 chunk 83 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 27 optimal weight: 0.1980 chunk 88 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 HIS C 89 HIS ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12370 Z= 0.242 Angle : 0.821 11.770 17190 Z= 0.358 Chirality : 0.050 0.222 1685 Planarity : 0.004 0.041 2145 Dihedral : 12.828 88.791 1735 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.30 % Favored : 85.70 % Rotamer: Outliers : 4.43 % Allowed : 20.09 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.20), residues: 1455 helix: 0.22 (0.40), residues: 170 sheet: -1.89 (0.45), residues: 150 loop : -2.93 (0.17), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 93 HIS 0.005 0.001 HIS D 89 PHE 0.014 0.001 PHE D 224 TYR 0.011 0.001 TYR C 123 ARG 0.006 0.001 ARG D 288 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 142 time to evaluate : 1.221 Fit side-chains REVERT: A 66 GLN cc_start: 0.8649 (mm-40) cc_final: 0.8102 (mm-40) REVERT: A 70 VAL cc_start: 0.8932 (t) cc_final: 0.8608 (m) REVERT: A 130 TYR cc_start: 0.8443 (OUTLIER) cc_final: 0.8035 (m-80) REVERT: A 131 THR cc_start: 0.8429 (m) cc_final: 0.8205 (m) REVERT: A 228 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8496 (mm-30) REVERT: A 267 MET cc_start: 0.8665 (ttm) cc_final: 0.8321 (tpt) REVERT: A 280 VAL cc_start: 0.7793 (OUTLIER) cc_final: 0.7496 (m) REVERT: B 68 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.6507 (tp30) REVERT: B 130 TYR cc_start: 0.8398 (OUTLIER) cc_final: 0.7906 (m-10) REVERT: B 156 ASP cc_start: 0.7985 (p0) cc_final: 0.6961 (p0) REVERT: B 187 GLU cc_start: 0.8638 (tp30) cc_final: 0.8425 (mm-30) REVERT: B 280 VAL cc_start: 0.7921 (OUTLIER) cc_final: 0.7566 (m) REVERT: B 299 PRO cc_start: 0.9318 (Cg_endo) cc_final: 0.8971 (Cg_exo) REVERT: C 66 GLN cc_start: 0.8824 (mm-40) cc_final: 0.8239 (mm-40) REVERT: C 130 TYR cc_start: 0.8530 (OUTLIER) cc_final: 0.7962 (m-80) REVERT: C 184 GLN cc_start: 0.8449 (mm-40) cc_final: 0.8247 (mm-40) REVERT: C 280 VAL cc_start: 0.7911 (OUTLIER) cc_final: 0.7626 (m) REVERT: D 66 GLN cc_start: 0.8893 (mm-40) cc_final: 0.8600 (mm-40) REVERT: D 130 TYR cc_start: 0.8556 (OUTLIER) cc_final: 0.8070 (m-10) REVERT: D 156 ASP cc_start: 0.7983 (p0) cc_final: 0.7350 (p0) REVERT: D 187 GLU cc_start: 0.8725 (tp30) cc_final: 0.8318 (mm-30) REVERT: D 229 GLN cc_start: 0.9160 (pp30) cc_final: 0.8072 (pp30) REVERT: D 267 MET cc_start: 0.8674 (ttm) cc_final: 0.8363 (tpt) REVERT: D 280 VAL cc_start: 0.8071 (OUTLIER) cc_final: 0.7727 (m) REVERT: E 130 TYR cc_start: 0.8373 (OUTLIER) cc_final: 0.7727 (m-10) REVERT: E 187 GLU cc_start: 0.8878 (tp30) cc_final: 0.8466 (mm-30) REVERT: E 280 VAL cc_start: 0.7702 (OUTLIER) cc_final: 0.7403 (m) outliers start: 52 outliers final: 37 residues processed: 184 average time/residue: 0.1898 time to fit residues: 53.6955 Evaluate side-chains 174 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 126 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 130 TYR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 304 CYS Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 130 TYR Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 304 CYS Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 304 CYS Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 115 CYS Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 280 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 56 optimal weight: 0.0870 chunk 102 optimal weight: 0.0870 chunk 39 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 123 optimal weight: 0.3980 chunk 129 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 ASN ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 12370 Z= 0.252 Angle : 0.807 11.654 17190 Z= 0.354 Chirality : 0.050 0.263 1685 Planarity : 0.004 0.040 2145 Dihedral : 12.939 88.716 1735 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.40 % Favored : 84.60 % Rotamer: Outliers : 4.34 % Allowed : 21.02 % Favored : 74.64 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.20), residues: 1455 helix: 0.14 (0.39), residues: 175 sheet: -1.81 (0.45), residues: 150 loop : -3.03 (0.16), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 82 HIS 0.005 0.001 HIS D 89 PHE 0.015 0.001 PHE D 309 TYR 0.016 0.001 TYR D 123 ARG 0.007 0.000 ARG D 288 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 143 time to evaluate : 1.234 Fit side-chains REVERT: A 70 VAL cc_start: 0.8910 (t) cc_final: 0.8591 (m) REVERT: A 102 ASN cc_start: 0.8243 (t160) cc_final: 0.7731 (t0) REVERT: A 130 TYR cc_start: 0.8475 (OUTLIER) cc_final: 0.8110 (m-80) REVERT: A 267 MET cc_start: 0.8649 (ttm) cc_final: 0.8256 (tpt) REVERT: A 280 VAL cc_start: 0.7782 (OUTLIER) cc_final: 0.7478 (m) REVERT: A 288 ARG cc_start: 0.8502 (mtm-85) cc_final: 0.8267 (mtm-85) REVERT: B 68 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.6455 (tp30) REVERT: B 102 ASN cc_start: 0.8312 (t160) cc_final: 0.7827 (t0) REVERT: B 130 TYR cc_start: 0.8460 (OUTLIER) cc_final: 0.7876 (m-10) REVERT: B 280 VAL cc_start: 0.7889 (OUTLIER) cc_final: 0.7460 (m) REVERT: B 299 PRO cc_start: 0.9369 (Cg_endo) cc_final: 0.9032 (Cg_exo) REVERT: C 130 TYR cc_start: 0.8573 (OUTLIER) cc_final: 0.7994 (m-80) REVERT: C 280 VAL cc_start: 0.7786 (OUTLIER) cc_final: 0.7427 (m) REVERT: D 66 GLN cc_start: 0.8914 (mm-40) cc_final: 0.8506 (mm-40) REVERT: D 102 ASN cc_start: 0.8307 (t160) cc_final: 0.7862 (t0) REVERT: D 130 TYR cc_start: 0.8519 (OUTLIER) cc_final: 0.8230 (m-10) REVERT: D 187 GLU cc_start: 0.8756 (tp30) cc_final: 0.8433 (mm-30) REVERT: D 229 GLN cc_start: 0.9136 (pp30) cc_final: 0.8044 (pp30) REVERT: D 280 VAL cc_start: 0.7896 (OUTLIER) cc_final: 0.7506 (m) REVERT: E 130 TYR cc_start: 0.8379 (OUTLIER) cc_final: 0.7720 (m-10) REVERT: E 187 GLU cc_start: 0.8911 (tp30) cc_final: 0.8257 (mm-30) outliers start: 51 outliers final: 37 residues processed: 184 average time/residue: 0.1974 time to fit residues: 55.7102 Evaluate side-chains 186 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 139 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 130 TYR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 304 CYS Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 130 TYR Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 304 CYS Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 304 CYS Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 115 CYS Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 304 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 137 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 65 optimal weight: 0.3980 chunk 95 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 12370 Z= 0.270 Angle : 0.797 12.204 17190 Z= 0.344 Chirality : 0.049 0.166 1685 Planarity : 0.004 0.040 2145 Dihedral : 12.921 89.188 1735 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.50 % Favored : 85.50 % Rotamer: Outliers : 4.17 % Allowed : 21.36 % Favored : 74.47 % 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: -3.45 (0.20), residues: 1455 helix: 0.08 (0.39), residues: 175 sheet: -1.76 (0.45), residues: 150 loop : -3.05 (0.16), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 82 HIS 0.005 0.001 HIS D 89 PHE 0.020 0.001 PHE D 224 TYR 0.015 0.001 TYR B 123 ARG 0.007 0.000 ARG D 288 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 143 time to evaluate : 1.264 Fit side-chains REVERT: A 66 GLN cc_start: 0.8718 (mm-40) cc_final: 0.8180 (mm-40) REVERT: A 70 VAL cc_start: 0.8928 (t) cc_final: 0.8608 (m) REVERT: A 102 ASN cc_start: 0.8255 (t160) cc_final: 0.7739 (t0) REVERT: A 130 TYR cc_start: 0.8437 (OUTLIER) cc_final: 0.8099 (m-80) REVERT: A 267 MET cc_start: 0.8661 (ttm) cc_final: 0.8242 (tpt) REVERT: A 280 VAL cc_start: 0.7815 (OUTLIER) cc_final: 0.7512 (m) REVERT: B 68 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.6458 (tp30) REVERT: B 102 ASN cc_start: 0.8328 (t160) cc_final: 0.7843 (t0) REVERT: B 130 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.7930 (m-10) REVERT: B 280 VAL cc_start: 0.7857 (OUTLIER) cc_final: 0.7470 (m) REVERT: B 299 PRO cc_start: 0.9384 (Cg_endo) cc_final: 0.9042 (Cg_exo) REVERT: C 130 TYR cc_start: 0.8553 (OUTLIER) cc_final: 0.8027 (m-80) REVERT: C 280 VAL cc_start: 0.7802 (OUTLIER) cc_final: 0.7499 (m) REVERT: D 66 GLN cc_start: 0.8894 (mm-40) cc_final: 0.8612 (mm-40) REVERT: D 102 ASN cc_start: 0.8294 (t160) cc_final: 0.7843 (t0) REVERT: D 130 TYR cc_start: 0.8544 (OUTLIER) cc_final: 0.8295 (m-80) REVERT: D 156 ASP cc_start: 0.7957 (p0) cc_final: 0.7185 (p0) REVERT: D 187 GLU cc_start: 0.8769 (tp30) cc_final: 0.8432 (mm-30) REVERT: D 229 GLN cc_start: 0.9123 (pp30) cc_final: 0.8050 (pp30) REVERT: D 280 VAL cc_start: 0.8038 (OUTLIER) cc_final: 0.7702 (m) REVERT: E 130 TYR cc_start: 0.8329 (OUTLIER) cc_final: 0.7721 (m-10) REVERT: E 187 GLU cc_start: 0.8867 (tp30) cc_final: 0.8454 (mm-30) REVERT: E 264 THR cc_start: 0.9028 (p) cc_final: 0.8751 (t) outliers start: 49 outliers final: 38 residues processed: 185 average time/residue: 0.2030 time to fit residues: 57.2695 Evaluate side-chains 187 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 139 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 130 TYR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 304 CYS Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 130 TYR Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 304 CYS Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 304 CYS Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 115 CYS Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 304 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 48 optimal weight: 0.0970 chunk 118 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 overall best weight: 1.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN C 74 GLN ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 GLN ** E 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.099519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.086812 restraints weight = 22343.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.089665 restraints weight = 11111.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.091494 restraints weight = 6769.768| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 12370 Z= 0.418 Angle : 0.907 17.686 17190 Z= 0.397 Chirality : 0.053 0.281 1685 Planarity : 0.005 0.044 2145 Dihedral : 13.299 89.943 1735 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.80 % Favored : 82.20 % Rotamer: Outliers : 4.34 % Allowed : 21.11 % Favored : 74.55 % 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: -3.41 (0.20), residues: 1455 helix: 0.13 (0.40), residues: 170 sheet: -1.74 (0.46), residues: 150 loop : -3.00 (0.17), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 71 HIS 0.005 0.001 HIS B 89 PHE 0.020 0.002 PHE D 224 TYR 0.023 0.002 TYR D 123 ARG 0.006 0.001 ARG D 288 =============================================================================== Job complete usr+sys time: 2193.73 seconds wall clock time: 40 minutes 44.55 seconds (2444.55 seconds total)