Starting phenix.real_space_refine on Sat Dec 9 18:13:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5f_27911/12_2023/8e5f_27911_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5f_27911/12_2023/8e5f_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_27911/12_2023/8e5f_27911.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5f_27911/12_2023/8e5f_27911.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5f_27911/12_2023/8e5f_27911_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5f_27911/12_2023/8e5f_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-1.21rc1-5172/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: 6.98, per 1000 atoms: 0.59 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: 4.93 Conformation dependent library (CDL) restraints added in 2.3 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: 2.26 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: 3.22 Time building geometry restraints manager: 5.30 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: 1.630 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: 7.030 Check model and map are aligned: 0.200 Set scattering table: 0.110 Process input model: 35.540 Find NCS groups from input model: 0.730 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.000 ------------------------------------------------------------------------------- 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 : 1.306 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.2612 time to fit residues: 57.3937 Evaluate side-chains 127 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.597 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4761 ------------------------------------------------------------------------------- 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 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: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 12370 Z= 0.293 Angle : 0.840 12.127 17190 Z= 0.368 Chirality : 0.050 0.205 1685 Planarity : 0.005 0.041 2145 Dihedral : 12.946 84.826 1735 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.54 % Favored : 86.46 % Rotamer: Outliers : 4.77 % Allowed : 12.51 % Favored : 82.72 % 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: -0.20 (0.37), 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 0.005 0.001 HIS D 273 PHE 0.015 0.002 PHE D 224 TYR 0.012 0.001 TYR C 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 221 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 165 time to evaluate : 1.258 Fit side-chains outliers start: 56 outliers final: 24 residues processed: 208 average time/residue: 0.2316 time to fit residues: 70.6246 Evaluate side-chains 173 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 149 time to evaluate : 1.249 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1057 time to fit residues: 6.4326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 73 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 229 GLN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 GLN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 GLN ** C 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 GLN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 GLN ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 GLN ** E 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 GLN ** E 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.088 12370 Z= 0.501 Angle : 0.998 19.135 17190 Z= 0.433 Chirality : 0.057 0.229 1685 Planarity : 0.005 0.049 2145 Dihedral : 13.354 89.997 1735 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.91 % Favored : 83.09 % Rotamer: Outliers : 2.89 % Allowed : 15.57 % Favored : 81.53 % 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: -3.29 (0.20), residues: 1455 helix: 0.15 (0.39), residues: 170 sheet: -2.50 (0.44), residues: 140 loop : -2.77 (0.17), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 82 HIS 0.006 0.001 HIS A 89 PHE 0.021 0.002 PHE B 224 TYR 0.023 0.002 TYR A 123 ARG 0.006 0.001 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 164 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 130 time to evaluate : 1.257 Fit side-chains outliers start: 34 outliers final: 19 residues processed: 152 average time/residue: 0.2139 time to fit residues: 49.3013 Evaluate side-chains 138 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 119 time to evaluate : 1.182 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1102 time to fit residues: 5.5629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0070 chunk 68 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 140 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 125 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 HIS ** 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 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 HIS E 229 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12370 Z= 0.239 Angle : 0.819 13.218 17190 Z= 0.359 Chirality : 0.050 0.205 1685 Planarity : 0.004 0.041 2145 Dihedral : 12.632 86.975 1735 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.02 % Favored : 85.98 % Rotamer: Outliers : 1.62 % Allowed : 17.96 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.20), residues: 1455 helix: -0.37 (0.36), residues: 205 sheet: -1.96 (0.46), residues: 150 loop : -2.80 (0.17), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 93 HIS 0.005 0.001 HIS C 89 PHE 0.012 0.001 PHE B 224 TYR 0.016 0.001 TYR C 123 ARG 0.005 0.000 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 180 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 161 time to evaluate : 1.225 Fit side-chains outliers start: 19 outliers final: 6 residues processed: 179 average time/residue: 0.2154 time to fit residues: 59.0037 Evaluate side-chains 141 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 135 time to evaluate : 1.181 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1172 time to fit residues: 2.9120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 116 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** 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 229 GLN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.095 12370 Z= 0.582 Angle : 1.027 18.154 17190 Z= 0.451 Chirality : 0.057 0.252 1685 Planarity : 0.005 0.051 2145 Dihedral : 13.317 89.538 1735 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.94 % Favored : 82.06 % Rotamer: Outliers : 2.98 % Allowed : 20.34 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.20), residues: 1455 helix: 0.08 (0.40), residues: 170 sheet: -2.47 (0.43), residues: 140 loop : -2.91 (0.17), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 71 HIS 0.007 0.002 HIS A 89 PHE 0.025 0.002 PHE A 224 TYR 0.028 0.002 TYR D 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 161 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 126 time to evaluate : 1.204 Fit side-chains outliers start: 35 outliers final: 22 residues processed: 149 average time/residue: 0.1913 time to fit residues: 44.9973 Evaluate side-chains 137 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 115 time to evaluate : 1.209 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1124 time to fit residues: 6.1698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 27 optimal weight: 0.5980 chunk 82 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 116 optimal weight: 0.5980 chunk 64 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 48 GLN ** C 89 HIS ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12370 Z= 0.244 Angle : 0.829 13.083 17190 Z= 0.364 Chirality : 0.050 0.201 1685 Planarity : 0.004 0.043 2145 Dihedral : 13.097 89.412 1735 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.30 % Favored : 85.70 % Rotamer: Outliers : 1.70 % Allowed : 20.17 % Favored : 78.13 % 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: -3.36 (0.20), residues: 1455 helix: -0.47 (0.36), residues: 205 sheet: -1.91 (0.46), residues: 150 loop : -2.89 (0.17), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 93 HIS 0.005 0.001 HIS C 89 PHE 0.016 0.001 PHE A 224 TYR 0.016 0.001 TYR C 130 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 167 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 147 time to evaluate : 1.145 Fit side-chains outliers start: 20 outliers final: 12 residues processed: 163 average time/residue: 0.2036 time to fit residues: 51.8687 Evaluate side-chains 147 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 135 time to evaluate : 1.223 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1040 time to fit residues: 3.8618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 135 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 85 optimal weight: 0.0870 chunk 64 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 overall best weight: 1.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 229 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: 0.8412 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 12370 Z= 0.420 Angle : 0.904 15.141 17190 Z= 0.399 Chirality : 0.053 0.258 1685 Planarity : 0.005 0.047 2145 Dihedral : 13.464 89.969 1735 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.66 % Favored : 82.34 % Rotamer: Outliers : 2.04 % Allowed : 21.79 % Favored : 76.17 % 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: -3.36 (0.20), residues: 1455 helix: 0.17 (0.40), residues: 170 sheet: -1.96 (0.46), residues: 150 loop : -2.93 (0.17), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 82 HIS 0.005 0.001 HIS B 89 PHE 0.021 0.002 PHE A 224 TYR 0.025 0.002 TYR D 123 ARG 0.005 0.000 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 157 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 133 time to evaluate : 1.324 Fit side-chains outliers start: 24 outliers final: 15 residues processed: 144 average time/residue: 0.2041 time to fit residues: 45.4148 Evaluate side-chains 136 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 1.257 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1129 time to fit residues: 4.7357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 55 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 109 optimal weight: 0.4980 chunk 127 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 ASN ** 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 ** D 229 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: 0.8338 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 : 0.004 0.064 12370 Z= 0.266 Angle : 0.824 13.045 17190 Z= 0.363 Chirality : 0.051 0.254 1685 Planarity : 0.004 0.043 2145 Dihedral : 13.319 89.917 1735 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.05 % Favored : 84.95 % Rotamer: Outliers : 0.77 % Allowed : 21.70 % Favored : 77.53 % 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: 0.20 (0.40), residues: 170 sheet: -1.91 (0.45), residues: 150 loop : -2.92 (0.17), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 93 HIS 0.005 0.001 HIS C 273 PHE 0.019 0.001 PHE D 224 TYR 0.018 0.001 TYR C 130 ARG 0.005 0.000 ARG E 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 156 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 147 time to evaluate : 1.242 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 153 average time/residue: 0.2210 time to fit residues: 52.1870 Evaluate side-chains 141 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 137 time to evaluate : 1.238 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1269 time to fit residues: 2.6059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 78 optimal weight: 0.1980 chunk 56 optimal weight: 0.0670 chunk 102 optimal weight: 0.0670 chunk 39 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 HIS C 102 ASN ** 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 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12370 Z= 0.221 Angle : 0.781 10.795 17190 Z= 0.336 Chirality : 0.047 0.177 1685 Planarity : 0.004 0.041 2145 Dihedral : 13.092 89.218 1735 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 14.71 % Favored : 85.22 % Rotamer: Outliers : 0.60 % Allowed : 23.32 % Favored : 76.09 % 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: -3.38 (0.20), residues: 1455 helix: 0.11 (0.38), residues: 175 sheet: -1.39 (0.40), residues: 195 loop : -3.10 (0.17), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 82 HIS 0.005 0.001 HIS C 89 PHE 0.025 0.001 PHE E 224 TYR 0.014 0.001 TYR A 123 ARG 0.005 0.000 ARG E 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 177 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 170 time to evaluate : 1.304 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 174 average time/residue: 0.2188 time to fit residues: 57.4686 Evaluate side-chains 154 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 150 time to evaluate : 1.264 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1102 time to fit residues: 2.4203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 137 optimal weight: 0.3980 chunk 84 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 70 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** 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 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 12370 Z= 0.268 Angle : 0.812 17.432 17190 Z= 0.361 Chirality : 0.049 0.293 1685 Planarity : 0.004 0.041 2145 Dihedral : 13.133 89.283 1735 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 0.43 % Allowed : 24.17 % Favored : 75.40 % 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: -3.54 (0.20), residues: 1455 helix: -0.55 (0.35), residues: 205 sheet: -1.82 (0.45), residues: 150 loop : -3.06 (0.16), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 82 HIS 0.006 0.001 HIS A 89 PHE 0.011 0.001 PHE A 309 TYR 0.014 0.001 TYR A 123 ARG 0.007 0.001 ARG B 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 158 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 153 time to evaluate : 1.281 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 157 average time/residue: 0.2036 time to fit residues: 48.8418 Evaluate side-chains 150 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 147 time to evaluate : 1.189 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1056 time to fit residues: 2.1623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 118 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 GLN ** 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 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.099525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.086771 restraints weight = 22342.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.089552 restraints weight = 11164.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.091365 restraints weight = 6881.911| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 12370 Z= 0.421 Angle : 0.918 16.195 17190 Z= 0.407 Chirality : 0.053 0.305 1685 Planarity : 0.005 0.046 2145 Dihedral : 13.353 89.739 1735 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 17.32 % Favored : 82.61 % Rotamer: Outliers : 0.43 % Allowed : 23.91 % Favored : 75.66 % 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: -3.44 (0.20), residues: 1455 helix: -0.06 (0.39), 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 0.007 0.001 TRP E 82 HIS 0.006 0.001 HIS C 273 PHE 0.024 0.002 PHE B 224 TYR 0.029 0.002 TYR E 123 ARG 0.007 0.001 ARG A 288 =============================================================================== Job complete usr+sys time: 2208.88 seconds wall clock time: 41 minutes 28.34 seconds (2488.34 seconds total)