Starting phenix.real_space_refine on Sat Mar 16 11:01:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wb9_21587/03_2024/6wb9_21587_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wb9_21587/03_2024/6wb9_21587.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wb9_21587/03_2024/6wb9_21587.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wb9_21587/03_2024/6wb9_21587.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wb9_21587/03_2024/6wb9_21587_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wb9_21587/03_2024/6wb9_21587_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 P 2 5.49 5 S 62 5.16 5 C 9399 2.51 5 N 2319 2.21 5 O 2725 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 ARG 85": "NH1" <-> "NH2" Residue "0 ARG 121": "NH1" <-> "NH2" Residue "1 PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 181": "NH1" <-> "NH2" Residue "1 TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 384": "NH1" <-> "NH2" Residue "1 ARG 466": "NH1" <-> "NH2" Residue "1 TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 530": "NH1" <-> "NH2" Residue "1 PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 571": "NH1" <-> "NH2" Residue "1 PHE 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 641": "NH1" <-> "NH2" Residue "1 PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 64": "NH1" <-> "NH2" Residue "2 ARG 78": "NH1" <-> "NH2" Residue "2 ARG 202": "NH1" <-> "NH2" Residue "2 TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 177": "NH1" <-> "NH2" Residue "5 PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 28": "NH1" <-> "NH2" Residue "7 PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 163": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14507 Number of models: 1 Model: "" Number of chains: 12 Chain: "0" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 902 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 6, 'TRANS': 110} Chain: "1" Number of atoms: 5275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5275 Classifications: {'peptide': 649} Link IDs: {'PTRANS': 28, 'TRANS': 620} Chain breaks: 4 Chain: "2" Number of atoms: 2377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2377 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 3, 'TRANS': 288} Chain: "3" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1591 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 6, 'TRANS': 190} Chain breaks: 2 Chain: "4" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1197 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 10, 'TRANS': 137} Chain breaks: 2 Chain: "5" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1025 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain breaks: 1 Chain: "6" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 804 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "7" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1160 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain breaks: 2 Chain: "1" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "4" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 4 Chain: "5" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 4 Chain: "7" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 7.72, per 1000 atoms: 0.53 Number of scatterers: 14507 At special positions: 0 Unit cell: (158.466, 142.002, 119.364, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 62 16.00 P 2 15.00 O 2725 8.00 N 2319 7.00 C 9399 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS 0 65 " - pdb=" SG CYS 0 78 " distance=1.71 Simple disulfide: pdb=" SG CYS 1 701 " - pdb=" SG CYS 1 709 " 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=0, symmetry=0 Links applied NAG-ASN " NAG 1 801 " - " ASN 1 73 " " NAG 1 802 " - " ASN 1 106 " " NAG 1 803 " - " ASN 1 192 " " NAG 7 301 " - " ASN 7 53 " " NAG 7 302 " - " ASN 7 85 " " NAG 7 303 " - " ASN 7 115 " Time building additional restraints: 5.96 Conformation dependent library (CDL) restraints added in 2.5 seconds 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3388 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 16 sheets defined 36.1% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.63 Creating SS restraints... Processing helix chain '1' and resid 248 through 269 Processing helix chain '1' and resid 292 through 295 No H-bonds generated for 'chain '1' and resid 292 through 295' Processing helix chain '1' and resid 645 through 650 removed outlier: 4.022A pdb=" N ALA 1 649 " --> pdb=" O ALA 1 645 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS 1 650 " --> pdb=" O GLU 1 646 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 645 through 650' Processing helix chain '1' and resid 727 through 757 Proline residue: 1 746 - end of helix removed outlier: 3.677A pdb=" N LEU 1 753 " --> pdb=" O SER 1 749 " (cutoff:3.500A) Processing helix chain '2' and resid 2 through 15 Processing helix chain '2' and resid 18 through 21 Processing helix chain '2' and resid 24 through 38 Processing helix chain '2' and resid 47 through 63 Processing helix chain '2' and resid 67 through 80 Processing helix chain '2' and resid 86 through 98 Processing helix chain '2' and resid 102 through 115 Processing helix chain '2' and resid 123 through 140 Processing helix chain '2' and resid 145 through 157 Processing helix chain '2' and resid 163 through 175 Processing helix chain '2' and resid 179 through 192 Processing helix chain '2' and resid 197 through 214 Processing helix chain '2' and resid 218 through 235 removed outlier: 3.740A pdb=" N LYS 2 225 " --> pdb=" O GLU 2 221 " (cutoff:3.500A) Processing helix chain '2' and resid 241 through 254 Processing helix chain '2' and resid 263 through 276 Processing helix chain '2' and resid 279 through 289 Processing helix chain '3' and resid 5 through 33 removed outlier: 4.859A pdb=" N LEU 3 13 " --> pdb=" O TYR 3 9 " (cutoff:3.500A) Proline residue: 3 14 - end of helix Processing helix chain '3' and resid 44 through 65 removed outlier: 5.757A pdb=" N GLY 3 64 " --> pdb=" O ILE 3 60 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASN 3 65 " --> pdb=" O GLY 3 61 " (cutoff:3.500A) Processing helix chain '3' and resid 68 through 83 removed outlier: 4.164A pdb=" N ALA 3 73 " --> pdb=" O ASP 3 69 " (cutoff:3.500A) Processing helix chain '3' and resid 126 through 139 Processing helix chain '3' and resid 154 through 160 removed outlier: 4.205A pdb=" N LEU 3 160 " --> pdb=" O LYS 3 157 " (cutoff:3.500A) Processing helix chain '3' and resid 176 through 193 removed outlier: 3.594A pdb=" N LEU 3 185 " --> pdb=" O PHE 3 181 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ASN 3 188 " --> pdb=" O VAL 3 184 " (cutoff:3.500A) Proline residue: 3 189 - end of helix Processing helix chain '3' and resid 222 through 233 Processing helix chain '3' and resid 244 through 251 Processing helix chain '4' and resid 8 through 11 No H-bonds generated for 'chain '4' and resid 8 through 11' Processing helix chain '4' and resid 16 through 21 removed outlier: 3.796A pdb=" N GLU 4 20 " --> pdb=" O THR 4 16 " (cutoff:3.500A) Processing helix chain '4' and resid 63 through 75 Processing helix chain '4' and resid 84 through 91 Processing helix chain '4' and resid 100 through 115 Proline residue: 4 113 - end of helix Processing helix chain '4' and resid 137 through 162 removed outlier: 3.627A pdb=" N ILE 4 145 " --> pdb=" O MET 4 141 " (cutoff:3.500A) Processing helix chain '5' and resid 3 through 30 Processing helix chain '5' and resid 47 through 65 Processing helix chain '5' and resid 95 through 98 No H-bonds generated for 'chain '5' and resid 95 through 98' Processing helix chain '5' and resid 100 through 105 Processing helix chain '5' and resid 111 through 114 No H-bonds generated for 'chain '5' and resid 111 through 114' Processing helix chain '5' and resid 122 through 134 Processing helix chain '6' and resid 14 through 41 Processing helix chain '6' and resid 46 through 67 Processing helix chain '6' and resid 80 through 84 Processing helix chain '6' and resid 89 through 106 Processing helix chain '7' and resid 32 through 34 No H-bonds generated for 'chain '7' and resid 32 through 34' Processing helix chain '7' and resid 41 through 43 No H-bonds generated for 'chain '7' and resid 41 through 43' Processing sheet with id= A, first strand: chain '0' and resid 80 through 84 removed outlier: 3.698A pdb=" N SER 0 80 " --> pdb=" O LEU 0 66 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N TYR 0 25 " --> pdb=" O PRO 0 34 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLU 0 39 " --> pdb=" O THR 0 52 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N THR 0 52 " --> pdb=" O GLU 0 39 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '0' and resid 117 through 122 removed outlier: 3.726A pdb=" N THR 0 117 " --> pdb=" O TYR 0 90 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '1' and resid 35 through 37 removed outlier: 3.763A pdb=" N VAL 1 707 " --> pdb=" O LEU 1 37 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE 1 708 " --> pdb=" O ASP 1 702 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '1' and resid 43 through 48 removed outlier: 6.745A pdb=" N LEU 1 59 " --> pdb=" O GLU 1 44 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N VAL 1 46 " --> pdb=" O LEU 1 57 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU 1 57 " --> pdb=" O VAL 1 46 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N ARG 1 55 " --> pdb=" O PRO 1 48 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ASN 1 73 " --> pdb=" O ILE 1 79 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ILE 1 79 " --> pdb=" O ASN 1 73 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '1' and resid 92 through 94 Processing sheet with id= F, first strand: chain '1' and resid 177 through 179 removed outlier: 6.492A pdb=" N SER 1 200 " --> pdb=" O PRO 1 208 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '1' and resid 224 through 226 Processing sheet with id= H, first strand: chain '1' and resid 336 through 338 removed outlier: 6.227A pdb=" N GLU 1 359 " --> pdb=" O ILE 1 367 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ILE 1 367 " --> pdb=" O GLU 1 359 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '1' and resid 391 through 395 Processing sheet with id= J, first strand: chain '1' and resid 426 through 432 removed outlier: 3.817A pdb=" N ILE 1 426 " --> pdb=" O ILE 1 441 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLY 1 435 " --> pdb=" O ASP 1 432 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TRP 1 450 " --> pdb=" O GLY 1 438 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ILE 1 440 " --> pdb=" O GLN 1 448 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N GLN 1 448 " --> pdb=" O ILE 1 440 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '1' and resid 475 through 477 Processing sheet with id= L, first strand: chain '1' and resid 458 through 465 removed outlier: 6.466A pdb=" N LEU 1 496 " --> pdb=" O VAL 1 461 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N TYR 1 463 " --> pdb=" O ALA 1 494 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ALA 1 494 " --> pdb=" O TYR 1 463 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE 1 519 " --> pdb=" O LEU 1 509 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '1' and resid 534 through 537 Processing sheet with id= N, first strand: chain '1' and resid 630 through 634 Processing sheet with id= O, first strand: chain '5' and resid 72 through 74 Processing sheet with id= P, first strand: chain '7' and resid 61 through 64 600 hydrogen bonds defined for protein. 1746 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: 4.34 Time building geometry restraints manager: 6.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2382 1.31 - 1.43: 3903 1.43 - 1.56: 8407 1.56 - 1.69: 14 1.69 - 1.81: 112 Bond restraints: 14818 Sorted by residual: bond pdb=" C31 POV 5 201 " pdb=" O31 POV 5 201 " ideal model delta sigma weight residual 1.327 1.426 -0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" C21 POV 5 201 " pdb=" O21 POV 5 201 " ideal model delta sigma weight residual 1.330 1.429 -0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" C31 POV 4 201 " pdb=" O31 POV 4 201 " ideal model delta sigma weight residual 1.327 1.425 -0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" C21 POV 4 201 " pdb=" O21 POV 4 201 " ideal model delta sigma weight residual 1.330 1.428 -0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" O11 POV 5 201 " pdb=" P POV 5 201 " ideal model delta sigma weight residual 1.626 1.693 -0.067 2.00e-02 2.50e+03 1.13e+01 ... (remaining 14813 not shown) Histogram of bond angle deviations from ideal: 98.37 - 105.52: 258 105.52 - 112.67: 7847 112.67 - 119.82: 5020 119.82 - 126.96: 6764 126.96 - 134.11: 181 Bond angle restraints: 20070 Sorted by residual: angle pdb=" N ALA 4 81 " pdb=" CA ALA 4 81 " pdb=" C ALA 4 81 " ideal model delta sigma weight residual 111.28 105.61 5.67 1.09e+00 8.42e-01 2.71e+01 angle pdb=" C LEU 4 78 " pdb=" N GLN 4 79 " pdb=" CA GLN 4 79 " ideal model delta sigma weight residual 120.09 126.08 -5.99 1.25e+00 6.40e-01 2.30e+01 angle pdb=" C ASP 1 52 " pdb=" N ARG 1 53 " pdb=" CA ARG 1 53 " ideal model delta sigma weight residual 121.54 130.47 -8.93 1.91e+00 2.74e-01 2.19e+01 angle pdb=" C ASN 3 197 " pdb=" N ASP 3 198 " pdb=" CA ASP 3 198 " ideal model delta sigma weight residual 121.56 128.85 -7.29 1.56e+00 4.11e-01 2.18e+01 angle pdb=" N LEU 4 78 " pdb=" CA LEU 4 78 " pdb=" C LEU 4 78 " ideal model delta sigma weight residual 113.23 107.84 5.39 1.24e+00 6.50e-01 1.89e+01 ... (remaining 20065 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 8205 17.89 - 35.78: 580 35.78 - 53.67: 131 53.67 - 71.56: 31 71.56 - 89.46: 11 Dihedral angle restraints: 8958 sinusoidal: 3740 harmonic: 5218 Sorted by residual: dihedral pdb=" CB CYS 0 65 " pdb=" SG CYS 0 65 " pdb=" SG CYS 0 78 " pdb=" CB CYS 0 78 " ideal model delta sinusoidal sigma weight residual -86.00 -175.46 89.46 1 1.00e+01 1.00e-02 9.51e+01 dihedral pdb=" CA THR 1 692 " pdb=" C THR 1 692 " pdb=" N ASN 1 693 " pdb=" CA ASN 1 693 " ideal model delta harmonic sigma weight residual 180.00 155.01 24.99 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA VAL 3 171 " pdb=" C VAL 3 171 " pdb=" N ARG 3 172 " pdb=" CA ARG 3 172 " ideal model delta harmonic sigma weight residual 180.00 155.31 24.69 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 8955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 2062 0.080 - 0.160: 225 0.160 - 0.240: 3 0.240 - 0.319: 2 0.319 - 0.399: 3 Chirality restraints: 2295 Sorted by residual: chirality pdb=" C1 NAG 7 301 " pdb=" ND2 ASN 7 53 " pdb=" C2 NAG 7 301 " pdb=" O5 NAG 7 301 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.98e+00 chirality pdb=" C1 NAG 7 302 " pdb=" ND2 ASN 7 85 " pdb=" C2 NAG 7 302 " pdb=" O5 NAG 7 302 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" C1 NAG 7 303 " pdb=" ND2 ASN 7 115 " pdb=" C2 NAG 7 303 " pdb=" O5 NAG 7 303 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.93e+00 ... (remaining 2292 not shown) Planarity restraints: 2510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE 4 84 " -0.055 5.00e-02 4.00e+02 8.23e-02 1.08e+01 pdb=" N PRO 4 85 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO 4 85 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO 4 85 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL 1 552 " -0.051 5.00e-02 4.00e+02 7.79e-02 9.71e+00 pdb=" N PRO 1 553 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO 1 553 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO 1 553 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE 1 303 " 0.013 2.00e-02 2.50e+03 2.67e-02 7.12e+00 pdb=" C ILE 1 303 " -0.046 2.00e-02 2.50e+03 pdb=" O ILE 1 303 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL 1 304 " 0.015 2.00e-02 2.50e+03 ... (remaining 2507 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 139 2.57 - 3.15: 10907 3.15 - 3.73: 22750 3.73 - 4.32: 33055 4.32 - 4.90: 55279 Nonbonded interactions: 122130 Sorted by model distance: nonbonded pdb=" O ASN 1 434 " pdb=" OD1 ASN 1 434 " model vdw 1.983 3.040 nonbonded pdb=" O LEU 3 66 " pdb=" OG1 THR 3 239 " model vdw 2.250 2.440 nonbonded pdb=" O LEU 1 94 " pdb=" OG1 THR 1 133 " model vdw 2.275 2.440 nonbonded pdb=" O ASP 4 15 " pdb=" OD1 ASP 4 15 " model vdw 2.284 3.040 nonbonded pdb=" OE2 GLU 2 120 " pdb=" CB TYR 2 126 " model vdw 2.293 3.440 ... (remaining 122125 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 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: 3.610 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 40.350 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 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 : 0.006 0.099 14818 Z= 0.361 Angle : 0.833 12.779 20070 Z= 0.431 Chirality : 0.050 0.399 2295 Planarity : 0.006 0.082 2504 Dihedral : 13.616 86.801 5564 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 0.87 % Allowed : 8.39 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.16), residues: 1733 helix: -2.06 (0.14), residues: 676 sheet: -1.36 (0.27), residues: 310 loop : -2.88 (0.19), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP 6 52 HIS 0.006 0.001 HIS 1 675 PHE 0.022 0.002 PHE 1 81 TYR 0.025 0.002 TYR 1 544 ARG 0.003 0.001 ARG 7 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 322 time to evaluate : 1.446 Fit side-chains revert: symmetry clash REVERT: 0 89 LYS cc_start: 0.8563 (mttm) cc_final: 0.8156 (mtpp) REVERT: 0 99 ASP cc_start: 0.7484 (p0) cc_final: 0.7077 (p0) REVERT: 1 78 GLN cc_start: 0.7510 (mt0) cc_final: 0.7265 (pt0) REVERT: 1 93 GLN cc_start: 0.7256 (mt0) cc_final: 0.7002 (mt0) REVERT: 1 359 GLU cc_start: 0.7457 (tm-30) cc_final: 0.7204 (tp30) REVERT: 1 457 LYS cc_start: 0.8094 (mmtm) cc_final: 0.7870 (mptp) REVERT: 1 500 GLU cc_start: 0.6890 (mt-10) cc_final: 0.6684 (mt-10) REVERT: 1 602 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7417 (mm-30) REVERT: 1 643 LYS cc_start: 0.7682 (mmtt) cc_final: 0.7270 (mppt) REVERT: 1 678 ASN cc_start: 0.7223 (m110) cc_final: 0.6883 (m-40) REVERT: 2 1 MET cc_start: 0.6586 (mmt) cc_final: 0.5651 (ptt) REVERT: 2 39 LYS cc_start: 0.7232 (mttt) cc_final: 0.7022 (tmmt) REVERT: 2 92 LYS cc_start: 0.8154 (tttp) cc_final: 0.7834 (tmtt) REVERT: 2 123 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7917 (p90) REVERT: 2 150 LYS cc_start: 0.8016 (ttmm) cc_final: 0.7782 (mttp) REVERT: 2 153 VAL cc_start: 0.7472 (t) cc_final: 0.7106 (t) REVERT: 2 157 ASP cc_start: 0.6768 (m-30) cc_final: 0.6480 (m-30) REVERT: 3 228 MET cc_start: 0.6480 (tpp) cc_final: 0.6224 (mmt) REVERT: 3 246 GLN cc_start: 0.7864 (pt0) cc_final: 0.6935 (mp-120) REVERT: 4 104 MET cc_start: 0.6528 (tpt) cc_final: 0.4451 (ttm) REVERT: 4 162 MET cc_start: 0.8109 (mtt) cc_final: 0.7819 (mtm) REVERT: 5 124 MET cc_start: 0.7472 (tpt) cc_final: 0.7161 (tpt) outliers start: 14 outliers final: 3 residues processed: 334 average time/residue: 1.1123 time to fit residues: 413.8447 Evaluate side-chains 237 residues out of total 1609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 233 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 17 LYS Chi-restraints excluded: chain 2 residue 123 PHE Chi-restraints excluded: chain 7 residue 99 PHE Chi-restraints excluded: chain 7 residue 169 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 72 optimal weight: 0.0970 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 100 optimal weight: 8.9990 chunk 156 optimal weight: 3.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 GLN 0 104 GLN 1 39 ASN 1 265 ASN ** 1 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 629 GLN 1 678 ASN 2 257 ASN 3 138 HIS 3 199 GLN 3 246 GLN 4 4 GLN 4 71 GLN 4 79 GLN 4 167 ASN 6 43 GLN 6 70 GLN 7 119 GLN 7 121 ASN 7 158 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 14818 Z= 0.339 Angle : 0.618 13.871 20070 Z= 0.316 Chirality : 0.046 0.382 2295 Planarity : 0.005 0.066 2504 Dihedral : 9.196 85.217 2092 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 3.54 % Allowed : 14.67 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.18), residues: 1733 helix: -0.12 (0.18), residues: 681 sheet: -1.04 (0.27), residues: 312 loop : -2.49 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 4 175 HIS 0.007 0.001 HIS 1 675 PHE 0.018 0.002 PHE 1 81 TYR 0.025 0.002 TYR 1 544 ARG 0.005 0.001 ARG 7 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 242 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 69 GLN cc_start: 0.7445 (tt0) cc_final: 0.6581 (mt0) REVERT: 0 89 LYS cc_start: 0.8582 (mttm) cc_final: 0.8342 (mtpp) REVERT: 1 78 GLN cc_start: 0.7592 (mt0) cc_final: 0.7319 (pt0) REVERT: 1 93 GLN cc_start: 0.7346 (mt0) cc_final: 0.7109 (mt0) REVERT: 1 321 GLN cc_start: 0.7981 (tp40) cc_final: 0.7378 (tm-30) REVERT: 1 432 ASP cc_start: 0.7924 (t0) cc_final: 0.7614 (t0) REVERT: 1 457 LYS cc_start: 0.8134 (mmtm) cc_final: 0.7907 (mptp) REVERT: 1 500 GLU cc_start: 0.6831 (mt-10) cc_final: 0.6613 (mt-10) REVERT: 1 602 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7285 (mm-30) REVERT: 1 643 LYS cc_start: 0.7687 (mmtt) cc_final: 0.7111 (mttp) REVERT: 1 703 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8539 (mt) REVERT: 2 1 MET cc_start: 0.6826 (mmt) cc_final: 0.5756 (ptt) REVERT: 2 29 GLN cc_start: 0.7679 (tp-100) cc_final: 0.7361 (tp40) REVERT: 2 39 LYS cc_start: 0.7295 (mttt) cc_final: 0.7040 (tmmt) REVERT: 2 91 MET cc_start: 0.8775 (mtm) cc_final: 0.8550 (mtm) REVERT: 2 92 LYS cc_start: 0.8177 (tttp) cc_final: 0.7850 (tptt) REVERT: 2 103 LYS cc_start: 0.7670 (mppt) cc_final: 0.6616 (mttt) REVERT: 2 150 LYS cc_start: 0.7999 (ttmm) cc_final: 0.7776 (mttp) REVERT: 3 30 MET cc_start: 0.7439 (mmt) cc_final: 0.7236 (mmp) REVERT: 3 79 VAL cc_start: 0.7028 (t) cc_final: 0.6799 (m) REVERT: 3 228 MET cc_start: 0.6352 (tpp) cc_final: 0.6132 (mmt) REVERT: 3 246 GLN cc_start: 0.7981 (pt0) cc_final: 0.7053 (mp-120) REVERT: 4 69 GLN cc_start: 0.4199 (mm110) cc_final: 0.3102 (pt0) REVERT: 4 75 GLN cc_start: 0.6149 (mt0) cc_final: 0.5841 (mt0) REVERT: 4 104 MET cc_start: 0.6375 (tpt) cc_final: 0.4612 (ttm) REVERT: 5 91 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8296 (mttp) REVERT: 5 97 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8482 (mmtm) REVERT: 5 124 MET cc_start: 0.7606 (tpt) cc_final: 0.7388 (tpt) REVERT: 6 63 ILE cc_start: 0.9020 (mt) cc_final: 0.8765 (mt) REVERT: 7 22 ARG cc_start: 0.7644 (mtp85) cc_final: 0.7372 (mtp180) outliers start: 57 outliers final: 24 residues processed: 280 average time/residue: 1.0666 time to fit residues: 333.7006 Evaluate side-chains 247 residues out of total 1609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 220 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 22 GLN Chi-restraints excluded: chain 0 residue 67 ASN Chi-restraints excluded: chain 0 residue 74 LEU Chi-restraints excluded: chain 1 residue 26 PHE Chi-restraints excluded: chain 1 residue 56 VAL Chi-restraints excluded: chain 1 residue 67 CYS Chi-restraints excluded: chain 1 residue 104 CYS Chi-restraints excluded: chain 1 residue 209 VAL Chi-restraints excluded: chain 1 residue 317 VAL Chi-restraints excluded: chain 1 residue 371 SER Chi-restraints excluded: chain 1 residue 526 SER Chi-restraints excluded: chain 1 residue 703 LEU Chi-restraints excluded: chain 1 residue 706 ASP Chi-restraints excluded: chain 2 residue 123 PHE Chi-restraints excluded: chain 2 residue 175 GLU Chi-restraints excluded: chain 3 residue 21 LEU Chi-restraints excluded: chain 3 residue 53 LEU Chi-restraints excluded: chain 4 residue 86 MET Chi-restraints excluded: chain 4 residue 146 VAL Chi-restraints excluded: chain 5 residue 76 ILE Chi-restraints excluded: chain 5 residue 91 LYS Chi-restraints excluded: chain 5 residue 96 ASN Chi-restraints excluded: chain 5 residue 97 LYS Chi-restraints excluded: chain 6 residue 11 ILE Chi-restraints excluded: chain 7 residue 99 PHE Chi-restraints excluded: chain 7 residue 149 HIS Chi-restraints excluded: chain 7 residue 169 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 129 optimal weight: 10.0000 chunk 106 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 156 optimal weight: 0.7980 chunk 169 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 125 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 GLN 1 354 HIS ** 1 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 678 ASN 4 4 GLN 7 100 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14818 Z= 0.177 Angle : 0.531 12.073 20070 Z= 0.272 Chirality : 0.042 0.367 2295 Planarity : 0.004 0.061 2504 Dihedral : 8.440 79.485 2088 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 3.36 % Allowed : 16.66 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.20), residues: 1733 helix: 0.96 (0.19), residues: 679 sheet: -0.73 (0.28), residues: 314 loop : -2.29 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 6 52 HIS 0.005 0.001 HIS 7 149 PHE 0.018 0.001 PHE 1 81 TYR 0.022 0.001 TYR 1 544 ARG 0.004 0.000 ARG 7 22 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 228 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 69 GLN cc_start: 0.7681 (tt0) cc_final: 0.6895 (mt0) REVERT: 0 85 ARG cc_start: 0.7768 (mmt180) cc_final: 0.7493 (mpt180) REVERT: 0 89 LYS cc_start: 0.8482 (mttm) cc_final: 0.7885 (mtpt) REVERT: 0 133 LYS cc_start: 0.8778 (mmtm) cc_final: 0.8531 (mmtm) REVERT: 1 78 GLN cc_start: 0.7543 (mt0) cc_final: 0.7332 (pt0) REVERT: 1 93 GLN cc_start: 0.7287 (mt0) cc_final: 0.7081 (mt0) REVERT: 1 117 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7658 (mp) REVERT: 1 321 GLN cc_start: 0.7919 (tp40) cc_final: 0.7355 (tm-30) REVERT: 1 432 ASP cc_start: 0.7868 (t0) cc_final: 0.7541 (t0) REVERT: 1 457 LYS cc_start: 0.8112 (mmtm) cc_final: 0.7617 (mptp) REVERT: 1 588 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8248 (pp) REVERT: 1 602 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7456 (mm-30) REVERT: 1 643 LYS cc_start: 0.7585 (mmtt) cc_final: 0.7103 (mttp) REVERT: 1 703 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8435 (mt) REVERT: 2 1 MET cc_start: 0.6767 (mmt) cc_final: 0.5721 (ptt) REVERT: 2 29 GLN cc_start: 0.7673 (tp-100) cc_final: 0.7369 (tp40) REVERT: 2 39 LYS cc_start: 0.7330 (mttt) cc_final: 0.7008 (tmmt) REVERT: 2 92 LYS cc_start: 0.8056 (tttp) cc_final: 0.7807 (tptt) REVERT: 2 103 LYS cc_start: 0.7673 (mppt) cc_final: 0.6723 (mttt) REVERT: 2 150 LYS cc_start: 0.7924 (ttmm) cc_final: 0.7702 (mtmm) REVERT: 2 157 ASP cc_start: 0.6892 (OUTLIER) cc_final: 0.6302 (m-30) REVERT: 2 287 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8676 (tp) REVERT: 3 30 MET cc_start: 0.7443 (mmt) cc_final: 0.7231 (mmp) REVERT: 3 246 GLN cc_start: 0.7950 (pt0) cc_final: 0.7007 (mp-120) REVERT: 4 71 GLN cc_start: 0.4079 (mt0) cc_final: 0.3186 (mm110) REVERT: 4 75 GLN cc_start: 0.6192 (mt0) cc_final: 0.5663 (mp10) REVERT: 4 104 MET cc_start: 0.6282 (tpt) cc_final: 0.4447 (ttm) REVERT: 4 108 MET cc_start: 0.5475 (OUTLIER) cc_final: 0.5211 (mpm) REVERT: 4 141 MET cc_start: 0.4859 (ttm) cc_final: 0.3624 (mmp) REVERT: 4 143 MET cc_start: 0.6260 (ttm) cc_final: 0.6039 (ttm) REVERT: 5 91 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8305 (mttp) REVERT: 5 124 MET cc_start: 0.7565 (tpt) cc_final: 0.7276 (tpt) REVERT: 7 22 ARG cc_start: 0.7695 (mtp85) cc_final: 0.7377 (mtp180) REVERT: 7 57 GLU cc_start: 0.7984 (tt0) cc_final: 0.7492 (tt0) REVERT: 7 111 LYS cc_start: 0.8366 (ttpp) cc_final: 0.8035 (ttpp) outliers start: 54 outliers final: 20 residues processed: 260 average time/residue: 1.0608 time to fit residues: 308.0760 Evaluate side-chains 227 residues out of total 1609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 200 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 ASP Chi-restraints excluded: chain 0 residue 65 CYS Chi-restraints excluded: chain 0 residue 67 ASN Chi-restraints excluded: chain 0 residue 74 LEU Chi-restraints excluded: chain 1 residue 26 PHE Chi-restraints excluded: chain 1 residue 56 VAL Chi-restraints excluded: chain 1 residue 67 CYS Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 1 residue 134 THR Chi-restraints excluded: chain 1 residue 193 ASP Chi-restraints excluded: chain 1 residue 317 VAL Chi-restraints excluded: chain 1 residue 371 SER Chi-restraints excluded: chain 1 residue 588 ILE Chi-restraints excluded: chain 1 residue 703 LEU Chi-restraints excluded: chain 2 residue 69 ASP Chi-restraints excluded: chain 2 residue 123 PHE Chi-restraints excluded: chain 2 residue 156 THR Chi-restraints excluded: chain 2 residue 157 ASP Chi-restraints excluded: chain 2 residue 212 LEU Chi-restraints excluded: chain 2 residue 287 LEU Chi-restraints excluded: chain 4 residue 108 MET Chi-restraints excluded: chain 5 residue 91 LYS Chi-restraints excluded: chain 5 residue 96 ASN Chi-restraints excluded: chain 7 residue 69 ASP Chi-restraints excluded: chain 7 residue 99 PHE Chi-restraints excluded: chain 7 residue 149 HIS Chi-restraints excluded: chain 7 residue 169 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 74 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 166 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 148 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 GLN ** 1 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 4 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14818 Z= 0.167 Angle : 0.509 11.669 20070 Z= 0.260 Chirality : 0.042 0.357 2295 Planarity : 0.004 0.056 2504 Dihedral : 7.840 79.221 2088 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 3.60 % Allowed : 17.46 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.20), residues: 1733 helix: 1.56 (0.20), residues: 673 sheet: -0.48 (0.29), residues: 314 loop : -2.09 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 6 52 HIS 0.005 0.001 HIS 1 675 PHE 0.016 0.001 PHE 1 81 TYR 0.022 0.001 TYR 1 544 ARG 0.003 0.000 ARG 7 22 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 222 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 69 GLN cc_start: 0.7496 (tt0) cc_final: 0.6633 (mt0) REVERT: 0 89 LYS cc_start: 0.8447 (mttm) cc_final: 0.8141 (mtpp) REVERT: 0 133 LYS cc_start: 0.8661 (mmtm) cc_final: 0.8383 (mmtm) REVERT: 1 321 GLN cc_start: 0.7913 (tp40) cc_final: 0.7367 (tm-30) REVERT: 1 432 ASP cc_start: 0.7856 (t0) cc_final: 0.7524 (t0) REVERT: 1 457 LYS cc_start: 0.7764 (mmtm) cc_final: 0.7361 (mptp) REVERT: 1 588 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8282 (pp) REVERT: 1 602 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7470 (mm-30) REVERT: 1 643 LYS cc_start: 0.7550 (mmtt) cc_final: 0.7095 (mttp) REVERT: 1 703 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8396 (mt) REVERT: 2 1 MET cc_start: 0.6875 (mmt) cc_final: 0.5888 (ptt) REVERT: 2 29 GLN cc_start: 0.7660 (tp-100) cc_final: 0.7379 (tp40) REVERT: 2 39 LYS cc_start: 0.7272 (mttt) cc_final: 0.6958 (tmmt) REVERT: 2 92 LYS cc_start: 0.8173 (tttp) cc_final: 0.7842 (tptt) REVERT: 2 150 LYS cc_start: 0.7915 (ttmm) cc_final: 0.7698 (mtmm) REVERT: 2 287 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8541 (tp) REVERT: 3 30 MET cc_start: 0.7473 (mmt) cc_final: 0.7251 (mmp) REVERT: 3 246 GLN cc_start: 0.7927 (pt0) cc_final: 0.7013 (mp-120) REVERT: 4 71 GLN cc_start: 0.3600 (mt0) cc_final: 0.2796 (mm110) REVERT: 4 75 GLN cc_start: 0.6224 (mt0) cc_final: 0.5660 (mp10) REVERT: 4 104 MET cc_start: 0.6148 (tpt) cc_final: 0.4342 (ttm) REVERT: 4 141 MET cc_start: 0.4979 (ttm) cc_final: 0.3630 (mmp) REVERT: 5 91 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8364 (mttp) REVERT: 5 124 MET cc_start: 0.7544 (tpt) cc_final: 0.7307 (tpt) REVERT: 7 22 ARG cc_start: 0.7725 (mtp85) cc_final: 0.7406 (mtp180) REVERT: 7 111 LYS cc_start: 0.8355 (ttpp) cc_final: 0.8026 (ttpp) outliers start: 58 outliers final: 31 residues processed: 255 average time/residue: 1.0422 time to fit residues: 297.3611 Evaluate side-chains 240 residues out of total 1609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 205 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 22 GLN Chi-restraints excluded: chain 0 residue 28 ASP Chi-restraints excluded: chain 0 residue 65 CYS Chi-restraints excluded: chain 0 residue 67 ASN Chi-restraints excluded: chain 0 residue 120 VAL Chi-restraints excluded: chain 1 residue 26 PHE Chi-restraints excluded: chain 1 residue 56 VAL Chi-restraints excluded: chain 1 residue 67 CYS Chi-restraints excluded: chain 1 residue 95 ASP Chi-restraints excluded: chain 1 residue 104 CYS Chi-restraints excluded: chain 1 residue 134 THR Chi-restraints excluded: chain 1 residue 193 ASP Chi-restraints excluded: chain 1 residue 317 VAL Chi-restraints excluded: chain 1 residue 378 THR Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 406 LEU Chi-restraints excluded: chain 1 residue 526 SER Chi-restraints excluded: chain 1 residue 588 ILE Chi-restraints excluded: chain 1 residue 703 LEU Chi-restraints excluded: chain 1 residue 747 SER Chi-restraints excluded: chain 2 residue 123 PHE Chi-restraints excluded: chain 2 residue 156 THR Chi-restraints excluded: chain 2 residue 212 LEU Chi-restraints excluded: chain 2 residue 287 LEU Chi-restraints excluded: chain 3 residue 21 LEU Chi-restraints excluded: chain 3 residue 45 VAL Chi-restraints excluded: chain 3 residue 85 GLU Chi-restraints excluded: chain 5 residue 76 ILE Chi-restraints excluded: chain 5 residue 91 LYS Chi-restraints excluded: chain 5 residue 96 ASN Chi-restraints excluded: chain 7 residue 30 ASP Chi-restraints excluded: chain 7 residue 69 ASP Chi-restraints excluded: chain 7 residue 99 PHE Chi-restraints excluded: chain 7 residue 149 HIS Chi-restraints excluded: chain 7 residue 169 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 7.9990 chunk 94 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 141 optimal weight: 0.4980 chunk 114 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 84 optimal weight: 0.8980 chunk 149 optimal weight: 0.0030 chunk 41 optimal weight: 2.9990 overall best weight: 0.8392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 GLN 1 78 GLN ** 1 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 97 GLN 4 4 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14818 Z= 0.192 Angle : 0.516 12.206 20070 Z= 0.263 Chirality : 0.042 0.354 2295 Planarity : 0.004 0.056 2504 Dihedral : 7.641 79.421 2088 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 4.41 % Allowed : 17.53 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.21), residues: 1733 helix: 1.75 (0.20), residues: 679 sheet: -0.37 (0.29), residues: 313 loop : -2.04 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 6 52 HIS 0.005 0.001 HIS 1 675 PHE 0.016 0.001 PHE 1 81 TYR 0.022 0.001 TYR 1 544 ARG 0.002 0.000 ARG 7 22 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 212 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 69 GLN cc_start: 0.7423 (tt0) cc_final: 0.6579 (mt0) REVERT: 0 89 LYS cc_start: 0.8435 (mttm) cc_final: 0.8127 (mtpp) REVERT: 1 321 GLN cc_start: 0.7938 (tp40) cc_final: 0.7394 (tm-30) REVERT: 1 432 ASP cc_start: 0.7870 (t0) cc_final: 0.7525 (t0) REVERT: 1 500 GLU cc_start: 0.6792 (mp0) cc_final: 0.6418 (mt-10) REVERT: 1 588 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8295 (pp) REVERT: 1 602 GLU cc_start: 0.7739 (mm-30) cc_final: 0.6980 (mm-30) REVERT: 1 643 LYS cc_start: 0.7528 (mmtt) cc_final: 0.7086 (mttp) REVERT: 1 647 GLU cc_start: 0.7114 (mt-10) cc_final: 0.6722 (mt-10) REVERT: 1 703 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8348 (mt) REVERT: 2 1 MET cc_start: 0.6875 (mmt) cc_final: 0.5881 (ptt) REVERT: 2 29 GLN cc_start: 0.7621 (tp-100) cc_final: 0.7364 (tp40) REVERT: 2 39 LYS cc_start: 0.7265 (mttt) cc_final: 0.6951 (tmmt) REVERT: 2 92 LYS cc_start: 0.8256 (tttp) cc_final: 0.7916 (tptt) REVERT: 2 103 LYS cc_start: 0.7787 (mppt) cc_final: 0.6787 (mttt) REVERT: 2 150 LYS cc_start: 0.7884 (ttmm) cc_final: 0.7681 (mtmm) REVERT: 2 287 LEU cc_start: 0.8909 (tp) cc_final: 0.8548 (tp) REVERT: 3 246 GLN cc_start: 0.7951 (pt0) cc_final: 0.7015 (mp-120) REVERT: 3 249 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7813 (mm) REVERT: 4 71 GLN cc_start: 0.3498 (mt0) cc_final: 0.2702 (mm110) REVERT: 4 75 GLN cc_start: 0.6274 (mt0) cc_final: 0.5719 (mp10) REVERT: 4 104 MET cc_start: 0.6023 (tpt) cc_final: 0.4580 (ttm) REVERT: 4 141 MET cc_start: 0.4947 (ttm) cc_final: 0.3605 (mmp) REVERT: 5 91 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8366 (mttp) REVERT: 5 124 MET cc_start: 0.7514 (tpt) cc_final: 0.7294 (tpt) REVERT: 7 22 ARG cc_start: 0.7743 (mtp85) cc_final: 0.7451 (mtp180) REVERT: 7 111 LYS cc_start: 0.8347 (ttpp) cc_final: 0.8130 (ttpp) outliers start: 71 outliers final: 40 residues processed: 257 average time/residue: 1.0192 time to fit residues: 294.6618 Evaluate side-chains 246 residues out of total 1609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 202 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 ASP Chi-restraints excluded: chain 0 residue 50 VAL Chi-restraints excluded: chain 0 residue 65 CYS Chi-restraints excluded: chain 0 residue 67 ASN Chi-restraints excluded: chain 0 residue 74 LEU Chi-restraints excluded: chain 0 residue 120 VAL Chi-restraints excluded: chain 1 residue 26 PHE Chi-restraints excluded: chain 1 residue 56 VAL Chi-restraints excluded: chain 1 residue 67 CYS Chi-restraints excluded: chain 1 residue 95 ASP Chi-restraints excluded: chain 1 residue 104 CYS Chi-restraints excluded: chain 1 residue 134 THR Chi-restraints excluded: chain 1 residue 193 ASP Chi-restraints excluded: chain 1 residue 317 VAL Chi-restraints excluded: chain 1 residue 340 ASP Chi-restraints excluded: chain 1 residue 378 THR Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 406 LEU Chi-restraints excluded: chain 1 residue 480 ASP Chi-restraints excluded: chain 1 residue 526 SER Chi-restraints excluded: chain 1 residue 588 ILE Chi-restraints excluded: chain 1 residue 595 THR Chi-restraints excluded: chain 1 residue 703 LEU Chi-restraints excluded: chain 1 residue 739 VAL Chi-restraints excluded: chain 2 residue 69 ASP Chi-restraints excluded: chain 2 residue 123 PHE Chi-restraints excluded: chain 2 residue 156 THR Chi-restraints excluded: chain 2 residue 161 LEU Chi-restraints excluded: chain 2 residue 212 LEU Chi-restraints excluded: chain 3 residue 21 LEU Chi-restraints excluded: chain 3 residue 45 VAL Chi-restraints excluded: chain 3 residue 222 ASP Chi-restraints excluded: chain 3 residue 249 LEU Chi-restraints excluded: chain 4 residue 86 MET Chi-restraints excluded: chain 5 residue 76 ILE Chi-restraints excluded: chain 5 residue 78 SER Chi-restraints excluded: chain 5 residue 91 LYS Chi-restraints excluded: chain 5 residue 96 ASN Chi-restraints excluded: chain 6 residue 106 LEU Chi-restraints excluded: chain 7 residue 42 THR Chi-restraints excluded: chain 7 residue 69 ASP Chi-restraints excluded: chain 7 residue 99 PHE Chi-restraints excluded: chain 7 residue 149 HIS Chi-restraints excluded: chain 7 residue 169 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 166 optimal weight: 0.9990 chunk 138 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 160 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 GLN 1 78 GLN 1 211 GLN ** 1 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 97 GLN 4 4 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14818 Z= 0.197 Angle : 0.520 12.385 20070 Z= 0.265 Chirality : 0.042 0.352 2295 Planarity : 0.004 0.056 2504 Dihedral : 7.487 79.494 2088 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 4.10 % Allowed : 17.96 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.21), residues: 1733 helix: 1.91 (0.20), residues: 678 sheet: -0.33 (0.29), residues: 315 loop : -2.00 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 6 52 HIS 0.005 0.001 HIS 1 675 PHE 0.016 0.001 PHE 1 81 TYR 0.023 0.001 TYR 1 544 ARG 0.002 0.000 ARG 7 22 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 213 time to evaluate : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 69 GLN cc_start: 0.7463 (tt0) cc_final: 0.6603 (mt0) REVERT: 0 85 ARG cc_start: 0.7796 (mmt180) cc_final: 0.7547 (mpt180) REVERT: 0 89 LYS cc_start: 0.8469 (mttm) cc_final: 0.7935 (mtpt) REVERT: 1 117 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7653 (mp) REVERT: 1 189 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7494 (mm) REVERT: 1 321 GLN cc_start: 0.7917 (tp40) cc_final: 0.7377 (tm-30) REVERT: 1 380 ASP cc_start: 0.8053 (t70) cc_final: 0.7698 (t0) REVERT: 1 432 ASP cc_start: 0.7880 (t0) cc_final: 0.7543 (t0) REVERT: 1 522 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6596 (tt0) REVERT: 1 588 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8284 (pp) REVERT: 1 602 GLU cc_start: 0.7713 (mm-30) cc_final: 0.6955 (mm-30) REVERT: 1 643 LYS cc_start: 0.7485 (mmtt) cc_final: 0.7077 (mttp) REVERT: 1 647 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6793 (mt-10) REVERT: 1 703 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8358 (mt) REVERT: 2 1 MET cc_start: 0.6896 (mmt) cc_final: 0.5878 (ptt) REVERT: 2 29 GLN cc_start: 0.7620 (tp-100) cc_final: 0.7373 (tp40) REVERT: 2 39 LYS cc_start: 0.7221 (mttt) cc_final: 0.6925 (tmmt) REVERT: 2 92 LYS cc_start: 0.8241 (tttp) cc_final: 0.7932 (tptt) REVERT: 2 103 LYS cc_start: 0.7736 (mppt) cc_final: 0.6835 (mttt) REVERT: 2 150 LYS cc_start: 0.7899 (ttmm) cc_final: 0.7682 (mtmm) REVERT: 2 287 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8554 (tp) REVERT: 3 159 MET cc_start: 0.8085 (ttp) cc_final: 0.7851 (ttp) REVERT: 3 246 GLN cc_start: 0.7895 (pt0) cc_final: 0.6995 (mp-120) REVERT: 3 249 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7802 (mm) REVERT: 4 71 GLN cc_start: 0.3483 (mt0) cc_final: 0.2704 (mm110) REVERT: 4 75 GLN cc_start: 0.6200 (mt0) cc_final: 0.5636 (mp10) REVERT: 4 104 MET cc_start: 0.6022 (tpt) cc_final: 0.4599 (ttm) REVERT: 4 141 MET cc_start: 0.4920 (ttm) cc_final: 0.3579 (mmp) REVERT: 5 91 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8380 (mttp) REVERT: 5 124 MET cc_start: 0.7488 (tpt) cc_final: 0.7258 (tpt) REVERT: 7 22 ARG cc_start: 0.7759 (mtp85) cc_final: 0.7483 (mtp180) REVERT: 7 111 LYS cc_start: 0.8311 (ttpp) cc_final: 0.8007 (ttpp) outliers start: 66 outliers final: 37 residues processed: 257 average time/residue: 1.0605 time to fit residues: 305.1188 Evaluate side-chains 247 residues out of total 1609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 202 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 22 GLN Chi-restraints excluded: chain 0 residue 50 VAL Chi-restraints excluded: chain 0 residue 65 CYS Chi-restraints excluded: chain 0 residue 67 ASN Chi-restraints excluded: chain 0 residue 74 LEU Chi-restraints excluded: chain 0 residue 120 VAL Chi-restraints excluded: chain 1 residue 26 PHE Chi-restraints excluded: chain 1 residue 56 VAL Chi-restraints excluded: chain 1 residue 67 CYS Chi-restraints excluded: chain 1 residue 95 ASP Chi-restraints excluded: chain 1 residue 104 CYS Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 1 residue 134 THR Chi-restraints excluded: chain 1 residue 189 LEU Chi-restraints excluded: chain 1 residue 193 ASP Chi-restraints excluded: chain 1 residue 317 VAL Chi-restraints excluded: chain 1 residue 340 ASP Chi-restraints excluded: chain 1 residue 378 THR Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 406 LEU Chi-restraints excluded: chain 1 residue 522 GLU Chi-restraints excluded: chain 1 residue 526 SER Chi-restraints excluded: chain 1 residue 588 ILE Chi-restraints excluded: chain 1 residue 595 THR Chi-restraints excluded: chain 1 residue 703 LEU Chi-restraints excluded: chain 1 residue 739 VAL Chi-restraints excluded: chain 2 residue 69 ASP Chi-restraints excluded: chain 2 residue 123 PHE Chi-restraints excluded: chain 2 residue 212 LEU Chi-restraints excluded: chain 2 residue 287 LEU Chi-restraints excluded: chain 3 residue 21 LEU Chi-restraints excluded: chain 3 residue 45 VAL Chi-restraints excluded: chain 3 residue 222 ASP Chi-restraints excluded: chain 3 residue 249 LEU Chi-restraints excluded: chain 4 residue 86 MET Chi-restraints excluded: chain 5 residue 76 ILE Chi-restraints excluded: chain 5 residue 78 SER Chi-restraints excluded: chain 5 residue 91 LYS Chi-restraints excluded: chain 5 residue 96 ASN Chi-restraints excluded: chain 6 residue 106 LEU Chi-restraints excluded: chain 7 residue 42 THR Chi-restraints excluded: chain 7 residue 69 ASP Chi-restraints excluded: chain 7 residue 99 PHE Chi-restraints excluded: chain 7 residue 149 HIS Chi-restraints excluded: chain 7 residue 169 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 0.0470 chunk 94 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 165 optimal weight: 0.0970 chunk 103 optimal weight: 9.9990 chunk 101 optimal weight: 7.9990 chunk 76 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 GLN 1 78 GLN ** 1 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 97 GLN 4 4 GLN ** 4 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14818 Z= 0.186 Angle : 0.525 12.054 20070 Z= 0.267 Chirality : 0.042 0.350 2295 Planarity : 0.004 0.055 2504 Dihedral : 7.399 79.355 2088 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 3.85 % Allowed : 18.96 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.21), residues: 1733 helix: 1.97 (0.20), residues: 683 sheet: -0.27 (0.29), residues: 315 loop : -1.94 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 6 52 HIS 0.005 0.001 HIS 1 675 PHE 0.025 0.001 PHE 1 404 TYR 0.022 0.001 TYR 1 544 ARG 0.002 0.000 ARG 7 22 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 209 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 69 GLN cc_start: 0.7587 (tt0) cc_final: 0.6682 (mt0) REVERT: 0 89 LYS cc_start: 0.8434 (mttm) cc_final: 0.7880 (mtpt) REVERT: 1 189 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7458 (mm) REVERT: 1 321 GLN cc_start: 0.7922 (tp40) cc_final: 0.7385 (tm-30) REVERT: 1 380 ASP cc_start: 0.8030 (t70) cc_final: 0.7712 (t0) REVERT: 1 432 ASP cc_start: 0.7876 (t0) cc_final: 0.7539 (t0) REVERT: 1 588 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8281 (pp) REVERT: 1 602 GLU cc_start: 0.7748 (mm-30) cc_final: 0.6968 (mm-30) REVERT: 1 643 LYS cc_start: 0.7497 (mmtt) cc_final: 0.7075 (mttp) REVERT: 1 647 GLU cc_start: 0.7105 (mt-10) cc_final: 0.6866 (mt-10) REVERT: 1 703 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8351 (mt) REVERT: 2 1 MET cc_start: 0.6910 (mmt) cc_final: 0.5885 (ptt) REVERT: 2 29 GLN cc_start: 0.7617 (tp-100) cc_final: 0.7376 (tp40) REVERT: 2 39 LYS cc_start: 0.7199 (mttt) cc_final: 0.6936 (tmmt) REVERT: 2 92 LYS cc_start: 0.8248 (tttp) cc_final: 0.7963 (tptt) REVERT: 2 103 LYS cc_start: 0.7690 (mppt) cc_final: 0.6810 (mttt) REVERT: 2 150 LYS cc_start: 0.7952 (ttmm) cc_final: 0.7718 (mtmm) REVERT: 2 221 GLU cc_start: 0.6815 (tm-30) cc_final: 0.6393 (tp30) REVERT: 2 287 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8541 (tp) REVERT: 3 159 MET cc_start: 0.8150 (ttp) cc_final: 0.7901 (ttp) REVERT: 3 246 GLN cc_start: 0.7888 (pt0) cc_final: 0.6997 (mp-120) REVERT: 3 249 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7800 (mm) REVERT: 4 71 GLN cc_start: 0.3526 (mt0) cc_final: 0.2622 (mm110) REVERT: 4 75 GLN cc_start: 0.6239 (mt0) cc_final: 0.5727 (mp10) REVERT: 4 104 MET cc_start: 0.5994 (tpt) cc_final: 0.4658 (ttm) REVERT: 4 141 MET cc_start: 0.4913 (ttm) cc_final: 0.3561 (mmp) REVERT: 5 91 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8402 (mttp) REVERT: 5 97 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8408 (mmtm) REVERT: 5 124 MET cc_start: 0.7467 (tpt) cc_final: 0.7235 (tpt) REVERT: 7 22 ARG cc_start: 0.7760 (mtp85) cc_final: 0.7489 (mtp180) REVERT: 7 111 LYS cc_start: 0.8097 (ttpp) cc_final: 0.7833 (ttpp) outliers start: 62 outliers final: 39 residues processed: 251 average time/residue: 1.0824 time to fit residues: 303.5883 Evaluate side-chains 254 residues out of total 1609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 208 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 22 GLN Chi-restraints excluded: chain 0 residue 50 VAL Chi-restraints excluded: chain 0 residue 65 CYS Chi-restraints excluded: chain 0 residue 67 ASN Chi-restraints excluded: chain 0 residue 74 LEU Chi-restraints excluded: chain 0 residue 120 VAL Chi-restraints excluded: chain 1 residue 26 PHE Chi-restraints excluded: chain 1 residue 56 VAL Chi-restraints excluded: chain 1 residue 67 CYS Chi-restraints excluded: chain 1 residue 95 ASP Chi-restraints excluded: chain 1 residue 104 CYS Chi-restraints excluded: chain 1 residue 134 THR Chi-restraints excluded: chain 1 residue 189 LEU Chi-restraints excluded: chain 1 residue 193 ASP Chi-restraints excluded: chain 1 residue 317 VAL Chi-restraints excluded: chain 1 residue 340 ASP Chi-restraints excluded: chain 1 residue 371 SER Chi-restraints excluded: chain 1 residue 378 THR Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 406 LEU Chi-restraints excluded: chain 1 residue 526 SER Chi-restraints excluded: chain 1 residue 588 ILE Chi-restraints excluded: chain 1 residue 595 THR Chi-restraints excluded: chain 1 residue 703 LEU Chi-restraints excluded: chain 1 residue 739 VAL Chi-restraints excluded: chain 2 residue 69 ASP Chi-restraints excluded: chain 2 residue 123 PHE Chi-restraints excluded: chain 2 residue 212 LEU Chi-restraints excluded: chain 2 residue 287 LEU Chi-restraints excluded: chain 3 residue 21 LEU Chi-restraints excluded: chain 3 residue 45 VAL Chi-restraints excluded: chain 3 residue 222 ASP Chi-restraints excluded: chain 3 residue 249 LEU Chi-restraints excluded: chain 4 residue 86 MET Chi-restraints excluded: chain 4 residue 143 MET Chi-restraints excluded: chain 5 residue 76 ILE Chi-restraints excluded: chain 5 residue 78 SER Chi-restraints excluded: chain 5 residue 91 LYS Chi-restraints excluded: chain 5 residue 96 ASN Chi-restraints excluded: chain 5 residue 97 LYS Chi-restraints excluded: chain 6 residue 106 LEU Chi-restraints excluded: chain 7 residue 42 THR Chi-restraints excluded: chain 7 residue 69 ASP Chi-restraints excluded: chain 7 residue 99 PHE Chi-restraints excluded: chain 7 residue 149 HIS Chi-restraints excluded: chain 7 residue 169 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 chunk 112 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 130 optimal weight: 0.2980 chunk 150 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 GLN 1 78 GLN 1 401 HIS ** 1 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 97 GLN 4 4 GLN ** 4 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14818 Z= 0.230 Angle : 0.542 12.145 20070 Z= 0.275 Chirality : 0.042 0.350 2295 Planarity : 0.004 0.056 2504 Dihedral : 7.403 80.238 2088 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 3.79 % Allowed : 19.08 % Favored : 77.13 % 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: -0.06 (0.21), residues: 1733 helix: 1.96 (0.20), residues: 684 sheet: -0.27 (0.29), residues: 315 loop : -1.96 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 6 52 HIS 0.006 0.001 HIS 1 675 PHE 0.015 0.001 PHE 1 81 TYR 0.024 0.001 TYR 1 544 ARG 0.002 0.000 ARG 1 370 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 205 time to evaluate : 1.822 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 27 ASP cc_start: 0.6657 (t0) cc_final: 0.6319 (m-30) REVERT: 0 69 GLN cc_start: 0.7574 (tt0) cc_final: 0.6638 (mt0) REVERT: 0 89 LYS cc_start: 0.8489 (mttm) cc_final: 0.7953 (mtpt) REVERT: 1 189 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7487 (mm) REVERT: 1 321 GLN cc_start: 0.7916 (tp40) cc_final: 0.7387 (tm-30) REVERT: 1 380 ASP cc_start: 0.8022 (t70) cc_final: 0.7701 (t0) REVERT: 1 588 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8170 (pp) REVERT: 1 602 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7258 (mm-30) REVERT: 1 643 LYS cc_start: 0.7504 (mmtt) cc_final: 0.7086 (mttp) REVERT: 1 703 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8395 (mt) REVERT: 2 1 MET cc_start: 0.6921 (mmt) cc_final: 0.5891 (ptt) REVERT: 2 29 GLN cc_start: 0.7616 (tp-100) cc_final: 0.7374 (tp40) REVERT: 2 39 LYS cc_start: 0.7210 (mttt) cc_final: 0.6941 (tmmt) REVERT: 2 92 LYS cc_start: 0.8309 (tttp) cc_final: 0.7998 (tptt) REVERT: 2 150 LYS cc_start: 0.7963 (ttmm) cc_final: 0.7724 (mtmm) REVERT: 2 221 GLU cc_start: 0.6800 (tm-30) cc_final: 0.6383 (tp30) REVERT: 2 287 LEU cc_start: 0.8878 (tp) cc_final: 0.8549 (tp) REVERT: 3 159 MET cc_start: 0.8222 (ttp) cc_final: 0.7998 (ttp) REVERT: 3 246 GLN cc_start: 0.7866 (pt0) cc_final: 0.7025 (mp-120) REVERT: 3 249 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7877 (mm) REVERT: 4 71 GLN cc_start: 0.3507 (mt0) cc_final: 0.2622 (mm110) REVERT: 4 75 GLN cc_start: 0.6254 (mt0) cc_final: 0.5753 (mp10) REVERT: 4 104 MET cc_start: 0.6040 (tpt) cc_final: 0.4646 (ttm) REVERT: 4 141 MET cc_start: 0.4909 (ttm) cc_final: 0.3550 (mmp) REVERT: 5 91 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8428 (mttm) REVERT: 5 97 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8546 (mmtm) REVERT: 7 111 LYS cc_start: 0.8301 (ttpp) cc_final: 0.8012 (ttpp) outliers start: 61 outliers final: 40 residues processed: 247 average time/residue: 1.0574 time to fit residues: 292.4437 Evaluate side-chains 255 residues out of total 1609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 209 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 22 GLN Chi-restraints excluded: chain 0 residue 50 VAL Chi-restraints excluded: chain 0 residue 65 CYS Chi-restraints excluded: chain 0 residue 67 ASN Chi-restraints excluded: chain 0 residue 74 LEU Chi-restraints excluded: chain 0 residue 120 VAL Chi-restraints excluded: chain 1 residue 26 PHE Chi-restraints excluded: chain 1 residue 56 VAL Chi-restraints excluded: chain 1 residue 67 CYS Chi-restraints excluded: chain 1 residue 95 ASP Chi-restraints excluded: chain 1 residue 104 CYS Chi-restraints excluded: chain 1 residue 134 THR Chi-restraints excluded: chain 1 residue 189 LEU Chi-restraints excluded: chain 1 residue 193 ASP Chi-restraints excluded: chain 1 residue 317 VAL Chi-restraints excluded: chain 1 residue 340 ASP Chi-restraints excluded: chain 1 residue 371 SER Chi-restraints excluded: chain 1 residue 378 THR Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 526 SER Chi-restraints excluded: chain 1 residue 588 ILE Chi-restraints excluded: chain 1 residue 595 THR Chi-restraints excluded: chain 1 residue 703 LEU Chi-restraints excluded: chain 1 residue 739 VAL Chi-restraints excluded: chain 2 residue 69 ASP Chi-restraints excluded: chain 2 residue 123 PHE Chi-restraints excluded: chain 2 residue 175 GLU Chi-restraints excluded: chain 2 residue 212 LEU Chi-restraints excluded: chain 3 residue 21 LEU Chi-restraints excluded: chain 3 residue 45 VAL Chi-restraints excluded: chain 3 residue 222 ASP Chi-restraints excluded: chain 3 residue 249 LEU Chi-restraints excluded: chain 4 residue 86 MET Chi-restraints excluded: chain 4 residue 143 MET Chi-restraints excluded: chain 5 residue 76 ILE Chi-restraints excluded: chain 5 residue 78 SER Chi-restraints excluded: chain 5 residue 91 LYS Chi-restraints excluded: chain 5 residue 96 ASN Chi-restraints excluded: chain 5 residue 97 LYS Chi-restraints excluded: chain 6 residue 106 LEU Chi-restraints excluded: chain 7 residue 42 THR Chi-restraints excluded: chain 7 residue 69 ASP Chi-restraints excluded: chain 7 residue 99 PHE Chi-restraints excluded: chain 7 residue 143 LEU Chi-restraints excluded: chain 7 residue 149 HIS Chi-restraints excluded: chain 7 residue 169 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 1.9990 chunk 158 optimal weight: 0.0980 chunk 92 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 163 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 GLN 1 78 GLN ** 1 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 97 GLN 4 4 GLN ** 4 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14818 Z= 0.275 Angle : 0.568 12.706 20070 Z= 0.288 Chirality : 0.043 0.350 2295 Planarity : 0.004 0.056 2504 Dihedral : 7.481 81.167 2088 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 3.29 % Allowed : 19.95 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.21), residues: 1733 helix: 1.92 (0.20), residues: 684 sheet: -0.30 (0.29), residues: 315 loop : -1.94 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 6 52 HIS 0.007 0.001 HIS 1 675 PHE 0.028 0.001 PHE 1 404 TYR 0.025 0.002 TYR 1 544 ARG 0.006 0.000 ARG 7 22 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 208 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 69 GLN cc_start: 0.7570 (tt0) cc_final: 0.6607 (mt0) REVERT: 1 189 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7487 (mm) REVERT: 1 321 GLN cc_start: 0.7932 (tp40) cc_final: 0.7372 (tm-30) REVERT: 1 380 ASP cc_start: 0.8034 (t70) cc_final: 0.7701 (t0) REVERT: 1 588 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8198 (pp) REVERT: 1 602 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7282 (mm-30) REVERT: 1 643 LYS cc_start: 0.7515 (mmtt) cc_final: 0.7088 (mttp) REVERT: 1 703 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8424 (mt) REVERT: 2 1 MET cc_start: 0.6944 (mmt) cc_final: 0.5934 (ptt) REVERT: 2 29 GLN cc_start: 0.7619 (tp-100) cc_final: 0.7385 (tp40) REVERT: 2 39 LYS cc_start: 0.7216 (mttt) cc_final: 0.6947 (tmmt) REVERT: 2 92 LYS cc_start: 0.8328 (tttp) cc_final: 0.7992 (tptt) REVERT: 2 103 LYS cc_start: 0.7770 (mppt) cc_final: 0.6796 (mttt) REVERT: 2 150 LYS cc_start: 0.7969 (ttmm) cc_final: 0.7706 (mtmm) REVERT: 2 157 ASP cc_start: 0.6938 (m-30) cc_final: 0.6468 (m-30) REVERT: 2 221 GLU cc_start: 0.6817 (tm-30) cc_final: 0.6379 (tp30) REVERT: 2 287 LEU cc_start: 0.8913 (tp) cc_final: 0.8573 (tp) REVERT: 3 159 MET cc_start: 0.8306 (ttp) cc_final: 0.8080 (ttp) REVERT: 3 246 GLN cc_start: 0.7868 (pt0) cc_final: 0.7076 (mp-120) REVERT: 3 249 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7880 (mm) REVERT: 4 71 GLN cc_start: 0.3370 (mt0) cc_final: 0.2537 (mm110) REVERT: 4 75 GLN cc_start: 0.6204 (mt0) cc_final: 0.5682 (mp10) REVERT: 4 104 MET cc_start: 0.6047 (tpt) cc_final: 0.4756 (ttm) REVERT: 4 141 MET cc_start: 0.4882 (ttm) cc_final: 0.3563 (mmp) REVERT: 5 91 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8434 (mttm) REVERT: 5 97 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8432 (mmtm) REVERT: 6 22 LYS cc_start: 0.7766 (ttmm) cc_final: 0.7422 (tttm) REVERT: 6 63 ILE cc_start: 0.8979 (mt) cc_final: 0.8705 (mt) outliers start: 53 outliers final: 39 residues processed: 244 average time/residue: 1.0757 time to fit residues: 293.3321 Evaluate side-chains 250 residues out of total 1609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 205 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 50 VAL Chi-restraints excluded: chain 0 residue 65 CYS Chi-restraints excluded: chain 0 residue 67 ASN Chi-restraints excluded: chain 0 residue 74 LEU Chi-restraints excluded: chain 0 residue 112 THR Chi-restraints excluded: chain 0 residue 120 VAL Chi-restraints excluded: chain 1 residue 26 PHE Chi-restraints excluded: chain 1 residue 56 VAL Chi-restraints excluded: chain 1 residue 67 CYS Chi-restraints excluded: chain 1 residue 95 ASP Chi-restraints excluded: chain 1 residue 104 CYS Chi-restraints excluded: chain 1 residue 134 THR Chi-restraints excluded: chain 1 residue 189 LEU Chi-restraints excluded: chain 1 residue 193 ASP Chi-restraints excluded: chain 1 residue 317 VAL Chi-restraints excluded: chain 1 residue 340 ASP Chi-restraints excluded: chain 1 residue 371 SER Chi-restraints excluded: chain 1 residue 378 THR Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 526 SER Chi-restraints excluded: chain 1 residue 588 ILE Chi-restraints excluded: chain 1 residue 595 THR Chi-restraints excluded: chain 1 residue 703 LEU Chi-restraints excluded: chain 1 residue 739 VAL Chi-restraints excluded: chain 2 residue 69 ASP Chi-restraints excluded: chain 2 residue 123 PHE Chi-restraints excluded: chain 2 residue 175 GLU Chi-restraints excluded: chain 2 residue 212 LEU Chi-restraints excluded: chain 3 residue 21 LEU Chi-restraints excluded: chain 3 residue 45 VAL Chi-restraints excluded: chain 3 residue 222 ASP Chi-restraints excluded: chain 3 residue 249 LEU Chi-restraints excluded: chain 4 residue 86 MET Chi-restraints excluded: chain 5 residue 76 ILE Chi-restraints excluded: chain 5 residue 78 SER Chi-restraints excluded: chain 5 residue 91 LYS Chi-restraints excluded: chain 5 residue 96 ASN Chi-restraints excluded: chain 5 residue 97 LYS Chi-restraints excluded: chain 6 residue 106 LEU Chi-restraints excluded: chain 7 residue 30 ASP Chi-restraints excluded: chain 7 residue 42 THR Chi-restraints excluded: chain 7 residue 69 ASP Chi-restraints excluded: chain 7 residue 99 PHE Chi-restraints excluded: chain 7 residue 149 HIS Chi-restraints excluded: chain 7 residue 169 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 171 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 105 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 chunk 145 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 GLN 1 78 GLN ** 1 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 491 ASN ** 1 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 97 GLN 4 4 GLN ** 4 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 14818 Z= 0.290 Angle : 0.580 12.744 20070 Z= 0.294 Chirality : 0.043 0.352 2295 Planarity : 0.004 0.056 2504 Dihedral : 7.580 81.924 2088 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 3.11 % Allowed : 20.39 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.21), residues: 1733 helix: 1.89 (0.20), residues: 683 sheet: -0.31 (0.29), residues: 314 loop : -1.93 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 6 52 HIS 0.007 0.001 HIS 1 675 PHE 0.026 0.001 PHE 1 404 TYR 0.025 0.002 TYR 1 544 ARG 0.006 0.000 ARG 7 22 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3466 Ramachandran restraints generated. 1733 Oldfield, 0 Emsley, 1733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 201 time to evaluate : 1.605 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 27 ASP cc_start: 0.6720 (t0) cc_final: 0.6361 (m-30) REVERT: 0 69 GLN cc_start: 0.7492 (tt0) cc_final: 0.6602 (mt0) REVERT: 0 89 LYS cc_start: 0.8553 (mtpp) cc_final: 0.7942 (mtpt) REVERT: 1 189 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7517 (mm) REVERT: 1 321 GLN cc_start: 0.7912 (tp40) cc_final: 0.7362 (tm-30) REVERT: 1 380 ASP cc_start: 0.8046 (t70) cc_final: 0.7722 (t0) REVERT: 1 602 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7260 (mm-30) REVERT: 1 643 LYS cc_start: 0.7447 (mmtt) cc_final: 0.7079 (mttp) REVERT: 1 703 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8484 (mt) REVERT: 2 1 MET cc_start: 0.6945 (mmt) cc_final: 0.5941 (ptt) REVERT: 2 29 GLN cc_start: 0.7618 (tp-100) cc_final: 0.7368 (tp40) REVERT: 2 39 LYS cc_start: 0.7235 (mttt) cc_final: 0.6959 (tmmt) REVERT: 2 92 LYS cc_start: 0.8341 (tttp) cc_final: 0.8032 (tptt) REVERT: 2 103 LYS cc_start: 0.7764 (mppt) cc_final: 0.6805 (mttt) REVERT: 2 150 LYS cc_start: 0.7971 (ttmm) cc_final: 0.7708 (mtmm) REVERT: 2 157 ASP cc_start: 0.6915 (m-30) cc_final: 0.6427 (m-30) REVERT: 2 221 GLU cc_start: 0.6832 (tm-30) cc_final: 0.6389 (tp30) REVERT: 2 287 LEU cc_start: 0.8922 (tp) cc_final: 0.8549 (tp) REVERT: 3 159 MET cc_start: 0.8310 (ttp) cc_final: 0.8081 (ttp) REVERT: 3 246 GLN cc_start: 0.7917 (pt0) cc_final: 0.7140 (mp-120) REVERT: 3 249 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7891 (mm) REVERT: 4 71 GLN cc_start: 0.3224 (mt0) cc_final: 0.2425 (mm110) REVERT: 4 75 GLN cc_start: 0.6218 (mt0) cc_final: 0.5705 (mp10) REVERT: 4 104 MET cc_start: 0.5960 (tpt) cc_final: 0.4682 (ttm) REVERT: 4 141 MET cc_start: 0.4933 (ttm) cc_final: 0.3593 (mmp) REVERT: 5 91 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8429 (mttm) REVERT: 5 97 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8600 (mmtm) REVERT: 6 22 LYS cc_start: 0.7786 (ttmm) cc_final: 0.7430 (tttm) REVERT: 6 63 ILE cc_start: 0.8986 (mt) cc_final: 0.8705 (mt) outliers start: 50 outliers final: 36 residues processed: 237 average time/residue: 1.0906 time to fit residues: 288.8519 Evaluate side-chains 240 residues out of total 1609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 199 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 22 GLN Chi-restraints excluded: chain 0 residue 50 VAL Chi-restraints excluded: chain 0 residue 65 CYS Chi-restraints excluded: chain 0 residue 67 ASN Chi-restraints excluded: chain 0 residue 74 LEU Chi-restraints excluded: chain 0 residue 120 VAL Chi-restraints excluded: chain 1 residue 26 PHE Chi-restraints excluded: chain 1 residue 56 VAL Chi-restraints excluded: chain 1 residue 67 CYS Chi-restraints excluded: chain 1 residue 104 CYS Chi-restraints excluded: chain 1 residue 134 THR Chi-restraints excluded: chain 1 residue 189 LEU Chi-restraints excluded: chain 1 residue 193 ASP Chi-restraints excluded: chain 1 residue 317 VAL Chi-restraints excluded: chain 1 residue 340 ASP Chi-restraints excluded: chain 1 residue 371 SER Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 526 SER Chi-restraints excluded: chain 1 residue 595 THR Chi-restraints excluded: chain 1 residue 703 LEU Chi-restraints excluded: chain 1 residue 739 VAL Chi-restraints excluded: chain 2 residue 69 ASP Chi-restraints excluded: chain 2 residue 123 PHE Chi-restraints excluded: chain 2 residue 212 LEU Chi-restraints excluded: chain 3 residue 21 LEU Chi-restraints excluded: chain 3 residue 45 VAL Chi-restraints excluded: chain 3 residue 222 ASP Chi-restraints excluded: chain 3 residue 249 LEU Chi-restraints excluded: chain 4 residue 86 MET Chi-restraints excluded: chain 4 residue 143 MET Chi-restraints excluded: chain 5 residue 76 ILE Chi-restraints excluded: chain 5 residue 78 SER Chi-restraints excluded: chain 5 residue 91 LYS Chi-restraints excluded: chain 5 residue 96 ASN Chi-restraints excluded: chain 5 residue 97 LYS Chi-restraints excluded: chain 6 residue 106 LEU Chi-restraints excluded: chain 7 residue 42 THR Chi-restraints excluded: chain 7 residue 69 ASP Chi-restraints excluded: chain 7 residue 99 PHE Chi-restraints excluded: chain 7 residue 149 HIS Chi-restraints excluded: chain 7 residue 169 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 0.9980 chunk 125 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 140 optimal weight: 0.2980 chunk 17 optimal weight: 0.0000 chunk 25 optimal weight: 5.9990 chunk 119 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 78 GLN ** 1 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 97 GLN ** 4 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.159375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.120603 restraints weight = 16234.428| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.84 r_work: 0.2993 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 14818 Z= 0.266 Angle : 0.810 59.196 20070 Z= 0.453 Chirality : 0.043 0.352 2295 Planarity : 0.004 0.056 2504 Dihedral : 7.582 81.850 2088 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 2.92 % Allowed : 20.63 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.21), residues: 1733 helix: 1.91 (0.20), residues: 683 sheet: -0.34 (0.29), residues: 314 loop : -1.93 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 6 52 HIS 0.007 0.001 HIS 1 675 PHE 0.024 0.001 PHE 1 404 TYR 0.025 0.001 TYR 1 544 ARG 0.005 0.000 ARG 7 22 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5376.53 seconds wall clock time: 95 minutes 50.74 seconds (5750.74 seconds total)