Starting phenix.real_space_refine on Sat Mar 16 06:56:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a08_11601/03_2024/7a08_11601.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a08_11601/03_2024/7a08_11601.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a08_11601/03_2024/7a08_11601.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a08_11601/03_2024/7a08_11601.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a08_11601/03_2024/7a08_11601.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a08_11601/03_2024/7a08_11601.pdb" } resolution = 3.11 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= 0.007 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 262 5.49 5 S 23 5.16 5 C 7994 2.51 5 N 2569 2.21 5 O 3120 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a ASP 155": "OD1" <-> "OD2" Residue "a GLU 166": "OE1" <-> "OE2" Residue "a GLU 176": "OE1" <-> "OE2" Residue "a GLU 193": "OE1" <-> "OE2" Residue "a GLU 211": "OE1" <-> "OE2" Residue "a GLU 219": "OE1" <-> "OE2" Residue "a GLU 230": "OE1" <-> "OE2" Residue "a ARG 241": "NH1" <-> "NH2" Residue "a ARG 244": "NH1" <-> "NH2" Residue "a GLU 253": "OE1" <-> "OE2" Residue "a GLU 273": "OE1" <-> "OE2" Residue "a GLU 285": "OE1" <-> "OE2" Residue "a GLU 303": "OE1" <-> "OE2" Residue "a GLU 324": "OE1" <-> "OE2" Residue "a GLU 343": "OE1" <-> "OE2" Residue "a GLU 381": "OE1" <-> "OE2" Residue "a ARG 394": "NH1" <-> "NH2" Residue "a GLU 406": "OE1" <-> "OE2" Residue "a ARG 443": "NH1" <-> "NH2" Residue "a PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 463": "OE1" <-> "OE2" Residue "a PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 496": "OE1" <-> "OE2" Residue "c ARG 92": "NH1" <-> "NH2" Residue "c GLU 113": "OE1" <-> "OE2" Residue "d ARG 40": "NH1" <-> "NH2" Residue "d ARG 42": "NH1" <-> "NH2" Residue "d ARG 53": "NH1" <-> "NH2" Residue "d PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 73": "OE1" <-> "OE2" Residue "d GLU 94": "OE1" <-> "OE2" Residue "f GLU 56": "OE1" <-> "OE2" Residue "f GLU 92": "OE1" <-> "OE2" Residue "g GLU 71": "OE1" <-> "OE2" Residue "g GLU 105": "OE1" <-> "OE2" Residue "g GLU 113": "OE1" <-> "OE2" Residue "h ASP 106": "OD1" <-> "OD2" Residue "h ASP 123": "OD1" <-> "OD2" Residue "i GLU 52": "OE1" <-> "OE2" Residue "i GLU 53": "OE1" <-> "OE2" Residue "i GLU 63": "OE1" <-> "OE2" Residue "i GLU 74": "OE1" <-> "OE2" Residue "i ARG 95": "NH1" <-> "NH2" Residue "i PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13969 Number of models: 1 Model: "" Number of chains: 12 Chain: "a" Number of atoms: 2977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2977 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 15, 'TRANS': 344} Chain: "I" Number of atoms: 2691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2691 Classifications: {'DNA': 132} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 131} Chain: "J" Number of atoms: 2698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2698 Classifications: {'DNA': 131} Link IDs: {'rna3p': 130} Chain: "b" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 808 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "c" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "d" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 780 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "e" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 618 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "f" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 717 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "g" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "h" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 628 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 2, 'TRANS': 75} Chain: "i" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1987 SG CYS a 392 76.301 40.287 17.746 1.00 76.33 S Time building chain proxies: 7.82, per 1000 atoms: 0.56 Number of scatterers: 13969 At special positions: 0 Unit cell: (113.313, 120.726, 122.844, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 23 16.00 P 262 15.00 O 3120 8.00 N 2569 7.00 C 7994 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS a 397 " - pdb=" SG CYS a 448 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.82 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN a 601 " pdb="ZN ZN a 601 " - pdb=" SG CYS a 392 " 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2008 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 12 sheets defined 62.2% alpha, 6.6% beta 93 base pairs and 224 stacking pairs defined. Time for finding SS restraints: 6.15 Creating SS restraints... Processing helix chain 'a' and resid 148 through 185 removed outlier: 4.207A pdb=" N THR a 170 " --> pdb=" O GLU a 166 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS a 173 " --> pdb=" O GLU a 169 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG a 177 " --> pdb=" O LYS a 173 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ARG a 180 " --> pdb=" O GLU a 176 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ARG a 181 " --> pdb=" O ARG a 177 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N MET a 182 " --> pdb=" O LEU a 178 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN a 183 " --> pdb=" O LEU a 179 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS a 184 " --> pdb=" O ARG a 180 " (cutoff:3.500A) Processing helix chain 'a' and resid 258 through 277 removed outlier: 3.696A pdb=" N MET a 262 " --> pdb=" O SER a 258 " (cutoff:3.500A) Processing helix chain 'a' and resid 319 through 323 removed outlier: 3.814A pdb=" N LYS a 323 " --> pdb=" O ILE a 320 " (cutoff:3.500A) Processing helix chain 'a' and resid 328 through 333 Processing helix chain 'a' and resid 333 through 339 Processing helix chain 'a' and resid 367 through 377 Processing helix chain 'a' and resid 394 through 412 Processing helix chain 'a' and resid 413 through 418 removed outlier: 3.668A pdb=" N ALA a 417 " --> pdb=" O GLU a 414 " (cutoff:3.500A) Processing helix chain 'a' and resid 420 through 432 removed outlier: 3.978A pdb=" N LYS a 424 " --> pdb=" O SER a 420 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR a 432 " --> pdb=" O PHE a 428 " (cutoff:3.500A) Processing helix chain 'a' and resid 444 through 463 Processing helix chain 'a' and resid 482 through 498 removed outlier: 4.135A pdb=" N LYS a 486 " --> pdb=" O ASP a 482 " (cutoff:3.500A) Processing helix chain 'a' and resid 501 through 505 Processing helix chain 'b' and resid 16 through 21 removed outlier: 3.582A pdb=" N ARG b 20 " --> pdb=" O SER b 16 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA b 21 " --> pdb=" O ARG b 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 16 through 21' Processing helix chain 'b' and resid 26 through 37 Processing helix chain 'b' and resid 46 through 73 removed outlier: 3.676A pdb=" N LEU b 65 " --> pdb=" O GLU b 61 " (cutoff:3.500A) Processing helix chain 'b' and resid 90 through 97 Processing helix chain 'c' and resid 37 through 48 removed outlier: 3.588A pdb=" N GLN c 47 " --> pdb=" O LYS c 43 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL c 48 " --> pdb=" O VAL c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 57 through 84 removed outlier: 3.559A pdb=" N GLU c 71 " --> pdb=" O ASN c 67 " (cutoff:3.500A) Processing helix chain 'c' and resid 90 through 102 removed outlier: 3.620A pdb=" N THR c 96 " --> pdb=" O ARG c 92 " (cutoff:3.500A) Processing helix chain 'c' and resid 104 through 115 removed outlier: 3.750A pdb=" N LYS c 108 " --> pdb=" O GLY c 104 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL c 111 " --> pdb=" O ALA c 107 " (cutoff:3.500A) Processing helix chain 'c' and resid 115 through 123 removed outlier: 3.712A pdb=" N LYS c 120 " --> pdb=" O LYS c 116 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR c 122 " --> pdb=" O VAL c 118 " (cutoff:3.500A) Processing helix chain 'd' and resid 44 through 50 removed outlier: 3.917A pdb=" N GLU d 50 " --> pdb=" O VAL d 46 " (cutoff:3.500A) Processing helix chain 'd' and resid 50 through 55 removed outlier: 3.641A pdb=" N TYR d 54 " --> pdb=" O GLU d 50 " (cutoff:3.500A) Processing helix chain 'd' and resid 63 through 76 Processing helix chain 'd' and resid 85 through 114 removed outlier: 3.551A pdb=" N ALA d 98 " --> pdb=" O GLU d 94 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR d 99 " --> pdb=" O ALA d 95 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU d 109 " --> pdb=" O GLU d 105 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA d 114 " --> pdb=" O CYS d 110 " (cutoff:3.500A) Processing helix chain 'd' and resid 120 through 131 removed outlier: 3.680A pdb=" N ARG d 131 " --> pdb=" O ALA d 127 " (cutoff:3.500A) Processing helix chain 'e' and resid 25 through 29 Processing helix chain 'e' and resid 30 through 42 Processing helix chain 'e' and resid 50 through 76 removed outlier: 3.626A pdb=" N GLY e 56 " --> pdb=" O GLU e 52 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP e 68 " --> pdb=" O ASN e 64 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA e 76 " --> pdb=" O TYR e 72 " (cutoff:3.500A) Processing helix chain 'e' and resid 82 through 93 removed outlier: 3.587A pdb=" N GLN e 93 " --> pdb=" O ALA e 89 " (cutoff:3.500A) Processing helix chain 'f' and resid 16 through 22 Processing helix chain 'f' and resid 26 through 36 Processing helix chain 'f' and resid 46 through 74 removed outlier: 3.654A pdb=" N ASN f 68 " --> pdb=" O GLU f 64 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP f 72 " --> pdb=" O ASN f 68 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN f 73 " --> pdb=" O ALA f 69 " (cutoff:3.500A) Processing helix chain 'f' and resid 79 through 90 Processing helix chain 'f' and resid 92 through 97 Processing helix chain 'g' and resid 39 through 49 removed outlier: 3.636A pdb=" N GLN g 47 " --> pdb=" O LYS g 43 " (cutoff:3.500A) Processing helix chain 'g' and resid 55 through 84 removed outlier: 3.819A pdb=" N ARG g 79 " --> pdb=" O GLY g 75 " (cutoff:3.500A) Processing helix chain 'g' and resid 90 through 102 removed outlier: 3.692A pdb=" N THR g 96 " --> pdb=" O ARG g 92 " (cutoff:3.500A) Processing helix chain 'g' and resid 104 through 122 removed outlier: 3.822A pdb=" N SER g 112 " --> pdb=" O LYS g 108 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA g 117 " --> pdb=" O GLU g 113 " (cutoff:3.500A) Processing helix chain 'h' and resid 63 through 76 Processing helix chain 'h' and resid 86 through 113 removed outlier: 3.615A pdb=" N GLY h 90 " --> pdb=" O SER h 86 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU h 92 " --> pdb=" O ALA h 88 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA h 98 " --> pdb=" O GLU h 94 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU h 109 " --> pdb=" O GLU h 105 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N CYS h 110 " --> pdb=" O ASP h 106 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA h 111 " --> pdb=" O THR h 107 " (cutoff:3.500A) Processing helix chain 'h' and resid 124 through 130 removed outlier: 3.514A pdb=" N ARG h 128 " --> pdb=" O ILE h 124 " (cutoff:3.500A) Processing helix chain 'i' and resid 25 through 29 Processing helix chain 'i' and resid 30 through 41 Processing helix chain 'i' and resid 49 through 77 removed outlier: 3.804A pdb=" N GLY i 56 " --> pdb=" O GLU i 52 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL i 60 " --> pdb=" O GLY i 56 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN i 64 " --> pdb=" O VAL i 60 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP i 68 " --> pdb=" O ASN i 64 " (cutoff:3.500A) Processing helix chain 'i' and resid 82 through 93 removed outlier: 3.566A pdb=" N VAL i 86 " --> pdb=" O THR i 82 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN i 93 " --> pdb=" O ALA i 89 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 193 through 194 removed outlier: 3.505A pdb=" N GLU a 193 " --> pdb=" O LYS a 217 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL a 214 " --> pdb=" O ILE a 309 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ALA a 311 " --> pdb=" O VAL a 214 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N PHE a 216 " --> pdb=" O ALA a 311 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLU a 313 " --> pdb=" O PHE a 216 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU a 218 " --> pdb=" O GLU a 313 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE a 308 " --> pdb=" O VAL a 294 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL a 294 " --> pdb=" O ILE a 308 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 193 through 194 removed outlier: 3.505A pdb=" N GLU a 193 " --> pdb=" O LYS a 217 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL a 214 " --> pdb=" O ILE a 309 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ALA a 311 " --> pdb=" O VAL a 214 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N PHE a 216 " --> pdb=" O ALA a 311 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLU a 313 " --> pdb=" O PHE a 216 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU a 218 " --> pdb=" O GLU a 313 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N LEU a 310 " --> pdb=" O PRO a 349 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 223 through 226 Processing sheet with id=AA4, first strand: chain 'b' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'b' and resid 100 through 102 Processing sheet with id=AA6, first strand: chain 'd' and resid 83 through 84 removed outlier: 7.177A pdb=" N ARG d 83 " --> pdb=" O VAL i 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'd' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'e' and resid 45 through 46 removed outlier: 7.588A pdb=" N ARG e 45 " --> pdb=" O ILE h 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'e' and resid 80 through 81 Processing sheet with id=AB1, first strand: chain 'e' and resid 96 through 98 removed outlier: 6.706A pdb=" N THR e 96 " --> pdb=" O THR f 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'f' and resid 42 through 43 removed outlier: 7.148A pdb=" N ARG f 42 " --> pdb=" O ILE g 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'f' and resid 77 through 78 454 hydrogen bonds defined for protein. 1326 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 235 hydrogen bonds 470 hydrogen bond angles 0 basepair planarities 93 basepair parallelities 224 stacking parallelities Total time for adding SS restraints: 6.08 Time building geometry restraints manager: 7.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3726 1.34 - 1.46: 4721 1.46 - 1.59: 5759 1.59 - 1.71: 517 1.71 - 1.84: 36 Bond restraints: 14759 Sorted by residual: bond pdb=" C1' DG I -70 " pdb=" N9 DG I -70 " ideal model delta sigma weight residual 1.460 1.397 0.063 2.00e-02 2.50e+03 9.98e+00 bond pdb=" C1' DA J 72 " pdb=" N9 DA J 72 " ideal model delta sigma weight residual 1.460 1.398 0.062 2.00e-02 2.50e+03 9.72e+00 bond pdb=" N GLU a 313 " pdb=" CA GLU a 313 " ideal model delta sigma weight residual 1.456 1.421 0.036 1.21e-02 6.83e+03 8.66e+00 bond pdb=" C1' DG J 33 " pdb=" N9 DG J 33 " ideal model delta sigma weight residual 1.460 1.405 0.055 2.00e-02 2.50e+03 7.59e+00 bond pdb=" C1' DG I -71 " pdb=" N9 DG I -71 " ideal model delta sigma weight residual 1.460 1.407 0.053 2.00e-02 2.50e+03 6.92e+00 ... (remaining 14754 not shown) Histogram of bond angle deviations from ideal: 98.92 - 105.94: 1588 105.94 - 112.96: 7942 112.96 - 119.98: 5353 119.98 - 127.00: 5480 127.00 - 134.02: 670 Bond angle restraints: 21033 Sorted by residual: angle pdb=" N LYS c 57 " pdb=" CA LYS c 57 " pdb=" C LYS c 57 " ideal model delta sigma weight residual 113.88 109.71 4.17 1.23e+00 6.61e-01 1.15e+01 angle pdb=" N LEU a 445 " pdb=" CA LEU a 445 " pdb=" CB LEU a 445 " ideal model delta sigma weight residual 110.22 105.54 4.68 1.54e+00 4.22e-01 9.24e+00 angle pdb=" N ASN a 300 " pdb=" CA ASN a 300 " pdb=" C ASN a 300 " ideal model delta sigma weight residual 109.81 103.18 6.63 2.21e+00 2.05e-01 9.00e+00 angle pdb=" CA VAL a 220 " pdb=" C VAL a 220 " pdb=" N PRO a 221 " ideal model delta sigma weight residual 116.57 119.40 -2.83 9.80e-01 1.04e+00 8.36e+00 angle pdb=" N ARG a 394 " pdb=" CA ARG a 394 " pdb=" C ARG a 394 " ideal model delta sigma weight residual 113.18 109.39 3.79 1.33e+00 5.65e-01 8.13e+00 ... (remaining 21028 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.74: 6957 34.74 - 69.47: 1218 69.47 - 104.21: 43 104.21 - 138.94: 0 138.94 - 173.68: 4 Dihedral angle restraints: 8222 sinusoidal: 5114 harmonic: 3108 Sorted by residual: dihedral pdb=" CB CYS a 397 " pdb=" SG CYS a 397 " pdb=" SG CYS a 448 " pdb=" CB CYS a 448 " ideal model delta sinusoidal sigma weight residual 93.00 139.31 -46.31 1 1.00e+01 1.00e-02 2.97e+01 dihedral pdb=" CA ASP h 123 " pdb=" C ASP h 123 " pdb=" N ILE h 124 " pdb=" CA ILE h 124 " ideal model delta harmonic sigma weight residual 180.00 159.53 20.47 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" C4' DG I -53 " pdb=" C3' DG I -53 " pdb=" O3' DG I -53 " pdb=" P DG I -52 " ideal model delta sinusoidal sigma weight residual 220.00 46.32 173.68 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 8219 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1352 0.033 - 0.065: 688 0.065 - 0.098: 250 0.098 - 0.130: 70 0.130 - 0.163: 8 Chirality restraints: 2368 Sorted by residual: chirality pdb=" CA ASN a 300 " pdb=" N ASN a 300 " pdb=" C ASN a 300 " pdb=" CB ASN a 300 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.65e-01 chirality pdb=" C1' DG I -70 " pdb=" O4' DG I -70 " pdb=" C2' DG I -70 " pdb=" N9 DG I -70 " both_signs ideal model delta sigma weight residual False 2.42 2.26 0.16 2.00e-01 2.50e+01 6.64e-01 chirality pdb=" C1' DA I -32 " pdb=" O4' DA I -32 " pdb=" C2' DA I -32 " pdb=" N9 DA I -32 " both_signs ideal model delta sigma weight residual False 2.42 2.26 0.16 2.00e-01 2.50e+01 6.27e-01 ... (remaining 2365 not shown) Planarity restraints: 1755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE a 449 " -0.020 2.00e-02 2.50e+03 1.51e-02 3.98e+00 pdb=" CG PHE a 449 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE a 449 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE a 449 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE a 449 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE a 449 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE a 449 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT J 32 " 0.022 2.00e-02 2.50e+03 1.13e-02 3.21e+00 pdb=" N1 DT J 32 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DT J 32 " -0.005 2.00e-02 2.50e+03 pdb=" O2 DT J 32 " -0.013 2.00e-02 2.50e+03 pdb=" N3 DT J 32 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DT J 32 " 0.003 2.00e-02 2.50e+03 pdb=" O4 DT J 32 " 0.018 2.00e-02 2.50e+03 pdb=" C5 DT J 32 " -0.007 2.00e-02 2.50e+03 pdb=" C7 DT J 32 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DT J 32 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER a 291 " 0.027 5.00e-02 4.00e+02 4.03e-02 2.59e+00 pdb=" N PRO a 292 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO a 292 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO a 292 " 0.022 5.00e-02 4.00e+02 ... (remaining 1752 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 72 2.53 - 3.12: 10230 3.12 - 3.72: 22504 3.72 - 4.31: 35011 4.31 - 4.90: 51127 Nonbonded interactions: 118944 Sorted by model distance: nonbonded pdb=" OG1 THR h 107 " pdb=" O ASP h 123 " model vdw 1.939 2.440 nonbonded pdb=" OG1 THR i 73 " pdb=" OD2 ASP i 85 " model vdw 1.982 2.440 nonbonded pdb=" OP1 DG I 48 " pdb=" OH TYR g 40 " model vdw 2.055 2.440 nonbonded pdb=" O LYS a 205 " pdb=" CG1 ILE a 206 " model vdw 2.090 3.440 nonbonded pdb=" NZ LYS a 409 " pdb=" O PHE a 418 " model vdw 2.100 2.520 ... (remaining 118939 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'b' and resid 14 through 106) selection = chain 'f' } ncs_group { reference = (chain 'c' and resid 35 through 124) selection = chain 'g' } ncs_group { reference = chain 'e' selection = (chain 'i' and resid 24 through 100) } 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: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.410 Check model and map are aligned: 0.220 Set scattering table: 0.160 Process input model: 47.990 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 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 0.063 14759 Z= 0.339 Angle : 0.670 9.263 21033 Z= 0.409 Chirality : 0.044 0.163 2368 Planarity : 0.004 0.040 1755 Dihedral : 26.055 173.677 6211 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.22 % Allowed : 0.11 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.24), residues: 1052 helix: -1.02 (0.20), residues: 659 sheet: -0.92 (0.76), residues: 47 loop : -2.61 (0.29), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP a 363 HIS 0.005 0.001 HIS c 82 PHE 0.033 0.002 PHE a 449 TYR 0.013 0.002 TYR b 57 ARG 0.014 0.001 ARG c 86 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 160 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 401 MET cc_start: 0.5012 (tpt) cc_final: 0.4803 (tpp) REVERT: b 64 GLU cc_start: 0.7542 (tt0) cc_final: 0.7219 (tt0) REVERT: b 71 ARG cc_start: 0.8074 (mtp-110) cc_final: 0.7674 (ttm-80) REVERT: i 78 ARG cc_start: 0.7952 (mtm-85) cc_final: 0.7696 (mtm-85) outliers start: 2 outliers final: 1 residues processed: 161 average time/residue: 0.3718 time to fit residues: 78.9732 Evaluate side-chains 134 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 133 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 313 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.6980 chunk 97 optimal weight: 0.0270 chunk 54 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 101 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 203 HIS ** a 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 407 GLN a 422 HIS c 84 ASN e 27 GLN ** i 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14759 Z= 0.189 Angle : 0.598 9.978 21033 Z= 0.347 Chirality : 0.038 0.163 2368 Planarity : 0.004 0.036 1755 Dihedral : 29.428 178.388 4039 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.53 % Allowed : 5.99 % Favored : 92.48 % 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: -0.95 (0.25), residues: 1052 helix: 0.11 (0.20), residues: 659 sheet: -0.61 (0.76), residues: 52 loop : -1.98 (0.30), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP a 363 HIS 0.003 0.001 HIS e 75 PHE 0.016 0.001 PHE h 67 TYR 0.014 0.001 TYR a 346 ARG 0.004 0.000 ARG e 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 143 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 449 PHE cc_start: 0.5186 (OUTLIER) cc_final: 0.4671 (m-80) REVERT: a 462 THR cc_start: 0.7803 (p) cc_final: 0.7513 (p) REVERT: b 71 ARG cc_start: 0.7807 (mtp-110) cc_final: 0.7492 (ttm-80) REVERT: d 56 LYS cc_start: 0.8133 (ttpp) cc_final: 0.7749 (ttpp) REVERT: d 123 ASP cc_start: 0.6902 (t0) cc_final: 0.6649 (t0) outliers start: 14 outliers final: 6 residues processed: 149 average time/residue: 0.3771 time to fit residues: 76.5417 Evaluate side-chains 129 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 122 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 297 LEU Chi-restraints excluded: chain a residue 449 PHE Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain g residue 87 SER Chi-restraints excluded: chain h residue 118 THR Chi-restraints excluded: chain h residue 134 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 116 optimal weight: 0.5980 chunk 40 optimal weight: 5.9990 chunk 94 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 27 GLN g 47 GLN i 27 GLN i 75 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14759 Z= 0.190 Angle : 0.555 9.872 21033 Z= 0.323 Chirality : 0.036 0.142 2368 Planarity : 0.004 0.041 1755 Dihedral : 29.339 179.070 4036 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.63 % Allowed : 8.93 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.26), residues: 1052 helix: 0.76 (0.21), residues: 656 sheet: -0.90 (0.80), residues: 47 loop : -1.82 (0.29), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP a 363 HIS 0.003 0.001 HIS a 369 PHE 0.013 0.001 PHE h 67 TYR 0.014 0.001 TYR e 72 ARG 0.003 0.000 ARG e 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 131 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 449 PHE cc_start: 0.5012 (OUTLIER) cc_final: 0.4598 (m-80) REVERT: b 71 ARG cc_start: 0.7869 (mtp-110) cc_final: 0.7511 (ttm-80) REVERT: d 123 ASP cc_start: 0.6771 (t0) cc_final: 0.6535 (t0) outliers start: 15 outliers final: 10 residues processed: 141 average time/residue: 0.3398 time to fit residues: 64.6509 Evaluate side-chains 128 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 117 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 214 VAL Chi-restraints excluded: chain a residue 297 LEU Chi-restraints excluded: chain a residue 445 LEU Chi-restraints excluded: chain a residue 449 PHE Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 112 SER Chi-restraints excluded: chain g residue 64 SER Chi-restraints excluded: chain g residue 87 SER Chi-restraints excluded: chain h residue 118 THR Chi-restraints excluded: chain h residue 134 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 78 optimal weight: 0.5980 chunk 117 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 111 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 27 GLN i 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14759 Z= 0.262 Angle : 0.586 9.503 21033 Z= 0.338 Chirality : 0.038 0.161 2368 Planarity : 0.004 0.042 1755 Dihedral : 29.459 178.204 4036 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.40 % Allowed : 10.57 % Favored : 87.04 % 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: -0.31 (0.25), residues: 1052 helix: 0.67 (0.21), residues: 661 sheet: -0.87 (0.79), residues: 47 loop : -1.78 (0.29), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 363 HIS 0.004 0.001 HIS h 113 PHE 0.017 0.002 PHE a 476 TYR 0.013 0.001 TYR b 57 ARG 0.004 0.000 ARG e 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 125 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 449 PHE cc_start: 0.5064 (OUTLIER) cc_final: 0.4669 (m-80) REVERT: b 71 ARG cc_start: 0.7989 (mtp-110) cc_final: 0.7786 (mtp85) REVERT: d 123 ASP cc_start: 0.6868 (t0) cc_final: 0.6619 (t0) outliers start: 22 outliers final: 15 residues processed: 139 average time/residue: 0.3205 time to fit residues: 60.8516 Evaluate side-chains 138 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 122 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 214 VAL Chi-restraints excluded: chain a residue 297 LEU Chi-restraints excluded: chain a residue 322 THR Chi-restraints excluded: chain a residue 445 LEU Chi-restraints excluded: chain a residue 449 PHE Chi-restraints excluded: chain b residue 18 SER Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 112 SER Chi-restraints excluded: chain f residue 62 ILE Chi-restraints excluded: chain g residue 64 SER Chi-restraints excluded: chain g residue 87 SER Chi-restraints excluded: chain h residue 76 GLN Chi-restraints excluded: chain h residue 117 VAL Chi-restraints excluded: chain h residue 118 THR Chi-restraints excluded: chain h residue 134 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 51 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 407 GLN e 27 GLN i 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14759 Z= 0.264 Angle : 0.583 9.605 21033 Z= 0.336 Chirality : 0.038 0.187 2368 Planarity : 0.004 0.043 1755 Dihedral : 29.493 178.008 4036 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.29 % Allowed : 11.55 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.25), residues: 1052 helix: 0.69 (0.20), residues: 659 sheet: -0.81 (0.80), residues: 47 loop : -1.70 (0.29), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 363 HIS 0.004 0.001 HIS h 113 PHE 0.017 0.002 PHE a 501 TYR 0.012 0.001 TYR b 57 ARG 0.005 0.000 ARG e 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 126 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 449 PHE cc_start: 0.4993 (OUTLIER) cc_final: 0.4678 (m-80) REVERT: b 71 ARG cc_start: 0.8011 (mtp-110) cc_final: 0.7580 (ttm-80) REVERT: d 123 ASP cc_start: 0.6740 (t0) cc_final: 0.6458 (t0) outliers start: 21 outliers final: 17 residues processed: 138 average time/residue: 0.3375 time to fit residues: 63.4941 Evaluate side-chains 138 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 120 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 204 VAL Chi-restraints excluded: chain a residue 214 VAL Chi-restraints excluded: chain a residue 223 ILE Chi-restraints excluded: chain a residue 297 LEU Chi-restraints excluded: chain a residue 322 THR Chi-restraints excluded: chain a residue 445 LEU Chi-restraints excluded: chain a residue 449 PHE Chi-restraints excluded: chain b residue 18 SER Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 112 SER Chi-restraints excluded: chain g residue 64 SER Chi-restraints excluded: chain g residue 87 SER Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 76 GLN Chi-restraints excluded: chain h residue 117 VAL Chi-restraints excluded: chain h residue 118 THR Chi-restraints excluded: chain h residue 134 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 6.9990 chunk 112 optimal weight: 0.7980 chunk 24 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 359 GLN a 407 GLN e 27 GLN i 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14759 Z= 0.219 Angle : 0.571 10.039 21033 Z= 0.332 Chirality : 0.037 0.163 2368 Planarity : 0.004 0.043 1755 Dihedral : 29.475 178.212 4036 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.51 % Allowed : 12.85 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.26), residues: 1052 helix: 0.82 (0.21), residues: 659 sheet: -0.76 (0.80), residues: 47 loop : -1.64 (0.29), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 363 HIS 0.003 0.001 HIS h 113 PHE 0.015 0.001 PHE a 476 TYR 0.012 0.001 TYR b 57 ARG 0.007 0.000 ARG c 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 124 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 359 GLN cc_start: 0.6781 (OUTLIER) cc_final: 0.6506 (tp-100) REVERT: a 449 PHE cc_start: 0.4964 (OUTLIER) cc_final: 0.4662 (m-80) REVERT: b 71 ARG cc_start: 0.8004 (mtp-110) cc_final: 0.7575 (ttm-80) REVERT: d 123 ASP cc_start: 0.6679 (t0) cc_final: 0.6418 (t0) outliers start: 23 outliers final: 16 residues processed: 137 average time/residue: 0.3528 time to fit residues: 65.2213 Evaluate side-chains 139 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 121 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 204 VAL Chi-restraints excluded: chain a residue 214 VAL Chi-restraints excluded: chain a residue 297 LEU Chi-restraints excluded: chain a residue 322 THR Chi-restraints excluded: chain a residue 359 GLN Chi-restraints excluded: chain a residue 445 LEU Chi-restraints excluded: chain a residue 449 PHE Chi-restraints excluded: chain b residue 18 SER Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 112 SER Chi-restraints excluded: chain g residue 87 SER Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 76 GLN Chi-restraints excluded: chain h residue 117 VAL Chi-restraints excluded: chain h residue 118 THR Chi-restraints excluded: chain h residue 120 MET Chi-restraints excluded: chain h residue 134 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 77 optimal weight: 0.0980 chunk 75 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 27 GLN i 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14759 Z= 0.196 Angle : 0.555 10.147 21033 Z= 0.324 Chirality : 0.036 0.157 2368 Planarity : 0.004 0.044 1755 Dihedral : 29.414 178.046 4036 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.51 % Allowed : 13.18 % Favored : 84.31 % 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: 0.15 (0.26), residues: 1052 helix: 0.99 (0.21), residues: 660 sheet: -0.50 (0.75), residues: 54 loop : -1.56 (0.30), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP a 363 HIS 0.003 0.001 HIS h 113 PHE 0.014 0.001 PHE h 67 TYR 0.011 0.001 TYR a 346 ARG 0.005 0.000 ARG c 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 120 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 449 PHE cc_start: 0.4902 (OUTLIER) cc_final: 0.4639 (m-80) REVERT: b 71 ARG cc_start: 0.7997 (mtp-110) cc_final: 0.7577 (ttm-80) REVERT: d 123 ASP cc_start: 0.6611 (t0) cc_final: 0.6341 (t0) REVERT: e 92 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7691 (ttp80) outliers start: 23 outliers final: 18 residues processed: 135 average time/residue: 0.3563 time to fit residues: 64.4525 Evaluate side-chains 137 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 204 VAL Chi-restraints excluded: chain a residue 214 VAL Chi-restraints excluded: chain a residue 223 ILE Chi-restraints excluded: chain a residue 297 LEU Chi-restraints excluded: chain a residue 322 THR Chi-restraints excluded: chain a residue 445 LEU Chi-restraints excluded: chain a residue 449 PHE Chi-restraints excluded: chain b residue 18 SER Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 112 SER Chi-restraints excluded: chain e residue 92 ARG Chi-restraints excluded: chain g residue 64 SER Chi-restraints excluded: chain g residue 87 SER Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 76 GLN Chi-restraints excluded: chain h residue 117 VAL Chi-restraints excluded: chain h residue 118 THR Chi-restraints excluded: chain h residue 120 MET Chi-restraints excluded: chain h residue 134 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 27 GLN i 25 ASN i 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14759 Z= 0.308 Angle : 0.612 10.164 21033 Z= 0.349 Chirality : 0.039 0.193 2368 Planarity : 0.005 0.048 1755 Dihedral : 29.568 179.042 4036 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.61 % Allowed : 13.18 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.25), residues: 1052 helix: 0.77 (0.20), residues: 659 sheet: -0.83 (0.79), residues: 47 loop : -1.65 (0.29), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP a 331 HIS 0.004 0.001 HIS h 113 PHE 0.019 0.002 PHE a 476 TYR 0.012 0.002 TYR b 57 ARG 0.007 0.000 ARG e 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 126 time to evaluate : 1.212 Fit side-chains revert: symmetry clash REVERT: a 449 PHE cc_start: 0.4908 (OUTLIER) cc_final: 0.4607 (m-80) REVERT: b 71 ARG cc_start: 0.8052 (mtp-110) cc_final: 0.7594 (ttm-80) REVERT: d 123 ASP cc_start: 0.6738 (t0) cc_final: 0.6484 (t0) outliers start: 24 outliers final: 18 residues processed: 140 average time/residue: 0.3479 time to fit residues: 65.1976 Evaluate side-chains 141 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 122 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 204 VAL Chi-restraints excluded: chain a residue 214 VAL Chi-restraints excluded: chain a residue 223 ILE Chi-restraints excluded: chain a residue 297 LEU Chi-restraints excluded: chain a residue 322 THR Chi-restraints excluded: chain a residue 445 LEU Chi-restraints excluded: chain a residue 449 PHE Chi-restraints excluded: chain b residue 18 SER Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 112 SER Chi-restraints excluded: chain g residue 64 SER Chi-restraints excluded: chain g residue 87 SER Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 76 GLN Chi-restraints excluded: chain h residue 117 VAL Chi-restraints excluded: chain h residue 118 THR Chi-restraints excluded: chain h residue 134 ARG Chi-restraints excluded: chain i residue 82 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.8980 chunk 115 optimal weight: 5.9990 chunk 119 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 122 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 27 GLN i 25 ASN i 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14759 Z= 0.189 Angle : 0.572 10.530 21033 Z= 0.331 Chirality : 0.036 0.165 2368 Planarity : 0.004 0.043 1755 Dihedral : 29.517 178.993 4036 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.29 % Allowed : 13.62 % Favored : 84.10 % 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: 0.12 (0.26), residues: 1052 helix: 1.00 (0.21), residues: 659 sheet: -0.74 (0.79), residues: 47 loop : -1.57 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 363 HIS 0.003 0.001 HIS h 113 PHE 0.017 0.001 PHE h 67 TYR 0.013 0.001 TYR a 346 ARG 0.008 0.000 ARG c 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 125 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 449 PHE cc_start: 0.4846 (OUTLIER) cc_final: 0.4588 (m-80) REVERT: b 71 ARG cc_start: 0.8023 (mtp-110) cc_final: 0.7572 (ttm-80) REVERT: d 123 ASP cc_start: 0.6585 (t0) cc_final: 0.6336 (t0) REVERT: e 92 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7656 (ttp80) REVERT: i 95 ARG cc_start: 0.8307 (mtt90) cc_final: 0.7975 (mtp85) outliers start: 21 outliers final: 16 residues processed: 138 average time/residue: 0.3704 time to fit residues: 68.4419 Evaluate side-chains 142 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 124 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 204 VAL Chi-restraints excluded: chain a residue 214 VAL Chi-restraints excluded: chain a residue 297 LEU Chi-restraints excluded: chain a residue 445 LEU Chi-restraints excluded: chain a residue 449 PHE Chi-restraints excluded: chain b residue 18 SER Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 112 SER Chi-restraints excluded: chain e residue 92 ARG Chi-restraints excluded: chain g residue 87 SER Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 76 GLN Chi-restraints excluded: chain h residue 117 VAL Chi-restraints excluded: chain h residue 118 THR Chi-restraints excluded: chain h residue 123 ASP Chi-restraints excluded: chain h residue 134 ARG Chi-restraints excluded: chain i residue 82 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 10 optimal weight: 0.0570 chunk 79 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 81 optimal weight: 0.0060 chunk 109 optimal weight: 0.5980 overall best weight: 0.4714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 27 GLN i 25 ASN i 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14759 Z= 0.169 Angle : 0.565 10.639 21033 Z= 0.327 Chirality : 0.036 0.153 2368 Planarity : 0.004 0.044 1755 Dihedral : 29.445 178.028 4036 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.95 % Favored : 96.96 % Rotamer: Outliers : 2.18 % Allowed : 14.05 % Favored : 83.77 % 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: 0.29 (0.26), residues: 1052 helix: 1.12 (0.21), residues: 666 sheet: -0.71 (0.77), residues: 47 loop : -1.51 (0.30), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 363 HIS 0.003 0.001 HIS e 75 PHE 0.047 0.002 PHE a 358 TYR 0.012 0.001 TYR a 346 ARG 0.007 0.000 ARG c 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 123 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 449 PHE cc_start: 0.5022 (OUTLIER) cc_final: 0.4802 (m-80) REVERT: b 71 ARG cc_start: 0.7994 (mtp-110) cc_final: 0.7542 (ttm-80) REVERT: e 92 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7668 (ttp80) REVERT: i 78 ARG cc_start: 0.7851 (mtm-85) cc_final: 0.7354 (mtm180) REVERT: i 95 ARG cc_start: 0.8255 (mtt90) cc_final: 0.7936 (mtp85) outliers start: 20 outliers final: 16 residues processed: 136 average time/residue: 0.3599 time to fit residues: 65.7226 Evaluate side-chains 138 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 120 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 204 VAL Chi-restraints excluded: chain a residue 214 VAL Chi-restraints excluded: chain a residue 297 LEU Chi-restraints excluded: chain a residue 322 THR Chi-restraints excluded: chain a residue 445 LEU Chi-restraints excluded: chain a residue 449 PHE Chi-restraints excluded: chain b residue 18 SER Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 112 SER Chi-restraints excluded: chain e residue 92 ARG Chi-restraints excluded: chain g residue 87 SER Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 76 GLN Chi-restraints excluded: chain h residue 118 THR Chi-restraints excluded: chain h residue 123 ASP Chi-restraints excluded: chain h residue 134 ARG Chi-restraints excluded: chain i residue 82 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 27 GLN i 25 ASN i 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.188149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.150914 restraints weight = 14867.007| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 0.98 r_work: 0.3304 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14759 Z= 0.306 Angle : 0.609 10.308 21033 Z= 0.348 Chirality : 0.039 0.156 2368 Planarity : 0.005 0.049 1755 Dihedral : 29.549 179.143 4036 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.71 % Favored : 96.20 % Rotamer: Outliers : 2.29 % Allowed : 13.94 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.25), residues: 1052 helix: 0.84 (0.20), residues: 664 sheet: -0.82 (0.77), residues: 47 loop : -1.60 (0.30), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 363 HIS 0.004 0.001 HIS h 113 PHE 0.020 0.002 PHE a 476 TYR 0.018 0.002 TYR a 373 ARG 0.006 0.000 ARG c 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2636.57 seconds wall clock time: 48 minutes 14.73 seconds (2894.73 seconds total)