Starting phenix.real_space_refine on Fri Mar 15 05:32:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6a_31740/03_2024/7v6a_31740_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6a_31740/03_2024/7v6a_31740.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6a_31740/03_2024/7v6a_31740.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6a_31740/03_2024/7v6a_31740.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6a_31740/03_2024/7v6a_31740_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v6a_31740/03_2024/7v6a_31740_updated.pdb" } resolution = 3.6 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= 0.001 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2132 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 65 5.16 5 C 5497 2.51 5 N 1460 2.21 5 O 1562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 395": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8584 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1646 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 72 Chain: "B" Number of atoms: 2562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2562 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 435 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 1746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1746 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "R" Number of atoms: 2195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2195 Unusual residues: {'5XI': 1} Classifications: {'peptide': 277, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 266, None: 1} Not linked: pdbres="GLN R 471 " pdbres="5XI R 601 " Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 5.47, per 1000 atoms: 0.64 Number of scatterers: 8584 At special positions: 0 Unit cell: (94.2936, 123.414, 123.414, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 65 16.00 O 1562 8.00 N 1460 7.00 C 5497 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 185 " distance=2.03 Simple disulfide: pdb=" SG CYS R 426 " - pdb=" SG CYS R 429 " 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 Time building additional restraints: 3.78 Conformation dependent library (CDL) restraints added in 1.8 seconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2104 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 14 sheets defined 32.4% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 7 through 31 Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 271 through 280 Processing helix chain 'A' and resid 296 through 307 Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'C' and resid 11 through 23 Processing helix chain 'C' and resid 30 through 33 No H-bonds generated for 'chain 'C' and resid 30 through 33' Processing helix chain 'C' and resid 35 through 41 removed outlier: 3.558A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 59 removed outlier: 4.192A pdb=" N SER R 56 " --> pdb=" O LEU R 52 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE R 57 " --> pdb=" O VAL R 53 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LYS R 58 " --> pdb=" O MET R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 93 removed outlier: 4.837A pdb=" N PHE R 70 " --> pdb=" O ASN R 67 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N SER R 85 " --> pdb=" O GLY R 82 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N MET R 86 " --> pdb=" O ALA R 83 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN R 87 " --> pdb=" O PHE R 84 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL R 91 " --> pdb=" O LEU R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 135 removed outlier: 4.149A pdb=" N TYR R 113 " --> pdb=" O LEU R 109 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL R 114 " --> pdb=" O ALA R 110 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN R 117 " --> pdb=" O TYR R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 143 Processing helix chain 'R' and resid 146 through 164 Processing helix chain 'R' and resid 166 through 175 Processing helix chain 'R' and resid 193 through 223 removed outlier: 4.017A pdb=" N ALA R 202 " --> pdb=" O GLY R 198 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LEU R 206 " --> pdb=" O ALA R 202 " (cutoff:3.500A) Proline residue: R 207 - end of helix removed outlier: 4.386A pdb=" N ARG R 223 " --> pdb=" O SER R 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 392 through 412 removed outlier: 3.654A pdb=" N LEU R 406 " --> pdb=" O ILE R 402 " (cutoff:3.500A) Processing helix chain 'R' and resid 416 through 419 No H-bonds generated for 'chain 'R' and resid 416 through 419' Processing helix chain 'R' and resid 432 through 454 removed outlier: 4.299A pdb=" N CYS R 442 " --> pdb=" O GLY R 438 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N TYR R 443 " --> pdb=" O TYR R 439 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL R 444 " --> pdb=" O TRP R 440 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASN R 445 " --> pdb=" O LEU R 441 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N SER R 446 " --> pdb=" O CYS R 442 " (cutoff:3.500A) Proline residue: R 450 - end of helix Processing helix chain 'R' and resid 458 through 469 removed outlier: 3.742A pdb=" N PHE R 464 " --> pdb=" O PHE R 460 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ARG R 465 " --> pdb=" O LYS R 461 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N HIS R 466 " --> pdb=" O LYS R 462 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LEU R 468 " --> pdb=" O PHE R 464 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 263 through 265 removed outlier: 3.843A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.578A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 178 through 180 removed outlier: 3.513A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 220 through 222 removed outlier: 4.186A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.648A pdb=" N CYS B 233 " --> pdb=" O ALA B 242 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 294 through 298 removed outlier: 3.580A pdb=" N SER B 277 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 327 through 330 removed outlier: 6.183A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.435A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 79 through 82 removed outlier: 3.567A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 250 through 253 removed outlier: 3.740A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 17 through 21 removed outlier: 3.513A pdb=" N ARG S 18 " --> pdb=" O MET S 83 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU S 81 " --> pdb=" O LEU S 20 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 93 through 99 removed outlier: 3.865A pdb=" N TRP S 36 " --> pdb=" O ALA S 49 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'S' and resid 143 through 146 removed outlier: 3.599A pdb=" N VAL S 143 " --> pdb=" O ILE S 204 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'S' and resid 214 through 219 removed outlier: 3.579A pdb=" N TRP S 164 " --> pdb=" O ILE S 177 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE S 177 " --> pdb=" O TRP S 164 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) 330 hydrogen bonds defined for protein. 894 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.41 Time building geometry restraints manager: 4.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2252 1.33 - 1.45: 1739 1.45 - 1.57: 4685 1.57 - 1.70: 0 1.70 - 1.82: 94 Bond restraints: 8770 Sorted by residual: bond pdb=" C19 5XI R 601 " pdb=" N4 5XI R 601 " ideal model delta sigma weight residual 1.351 1.479 -0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" C19 5XI R 601 " pdb=" O3 5XI R 601 " ideal model delta sigma weight residual 1.337 1.428 -0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C8 5XI R 601 " pdb=" N1 5XI R 601 " ideal model delta sigma weight residual 1.439 1.480 -0.041 2.00e-02 2.50e+03 4.22e+00 bond pdb=" C9 5XI R 601 " pdb=" N2 5XI R 601 " ideal model delta sigma weight residual 1.452 1.493 -0.041 2.00e-02 2.50e+03 4.12e+00 bond pdb=" CA THR B 181 " pdb=" CB THR B 181 " ideal model delta sigma weight residual 1.523 1.548 -0.025 1.35e-02 5.49e+03 3.35e+00 ... (remaining 8765 not shown) Histogram of bond angle deviations from ideal: 98.53 - 105.66: 138 105.66 - 112.80: 4702 112.80 - 119.93: 2975 119.93 - 127.06: 4002 127.06 - 134.19: 106 Bond angle restraints: 11923 Sorted by residual: angle pdb=" N VAL R 418 " pdb=" CA VAL R 418 " pdb=" C VAL R 418 " ideal model delta sigma weight residual 112.96 108.07 4.89 1.00e+00 1.00e+00 2.39e+01 angle pdb=" CA TRP R 435 " pdb=" CB TRP R 435 " pdb=" CG TRP R 435 " ideal model delta sigma weight residual 113.60 119.04 -5.44 1.90e+00 2.77e-01 8.20e+00 angle pdb=" N TRP R 435 " pdb=" CA TRP R 435 " pdb=" C TRP R 435 " ideal model delta sigma weight residual 111.33 107.91 3.42 1.21e+00 6.83e-01 8.00e+00 angle pdb=" N ASP B 246 " pdb=" CA ASP B 246 " pdb=" C ASP B 246 " ideal model delta sigma weight residual 113.38 110.13 3.25 1.23e+00 6.61e-01 6.96e+00 angle pdb=" C ARG S 179 " pdb=" N MET S 180 " pdb=" CA MET S 180 " ideal model delta sigma weight residual 122.19 118.54 3.65 1.41e+00 5.03e-01 6.71e+00 ... (remaining 11918 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 4695 17.90 - 35.80: 373 35.80 - 53.70: 78 53.70 - 71.60: 11 71.60 - 89.49: 10 Dihedral angle restraints: 5167 sinusoidal: 1908 harmonic: 3259 Sorted by residual: dihedral pdb=" CB CYS R 426 " pdb=" SG CYS R 426 " pdb=" SG CYS R 429 " pdb=" CB CYS R 429 " ideal model delta sinusoidal sigma weight residual 93.00 136.93 -43.93 1 1.00e+01 1.00e-02 2.69e+01 dihedral pdb=" CA VAL R 434 " pdb=" C VAL R 434 " pdb=" N TRP R 435 " pdb=" CA TRP R 435 " ideal model delta harmonic sigma weight residual 180.00 158.63 21.37 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA MET S 93 " pdb=" C MET S 93 " pdb=" N TYR S 94 " pdb=" CA TYR S 94 " ideal model delta harmonic sigma weight residual -180.00 -160.11 -19.89 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 5164 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1222 0.069 - 0.137: 156 0.137 - 0.206: 7 0.206 - 0.274: 0 0.274 - 0.343: 2 Chirality restraints: 1387 Sorted by residual: chirality pdb=" C9 5XI R 601 " pdb=" C10 5XI R 601 " pdb=" C13 5XI R 601 " pdb=" N2 5XI R 601 " both_signs ideal model delta sigma weight residual False -2.30 -2.65 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" C14 5XI R 601 " pdb=" C15 5XI R 601 " pdb=" C18 5XI R 601 " pdb=" N3 5XI R 601 " both_signs ideal model delta sigma weight residual False -2.29 -2.62 0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CB ILE R 93 " pdb=" CA ILE R 93 " pdb=" CG1 ILE R 93 " pdb=" CG2 ILE R 93 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.34e-01 ... (remaining 1384 not shown) Planarity restraints: 1488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR R 414 " -0.037 5.00e-02 4.00e+02 5.65e-02 5.10e+00 pdb=" N PRO R 415 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO R 415 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO R 415 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA S 40 " 0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO S 41 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO S 41 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO S 41 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 201 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.31e+00 pdb=" C ILE R 201 " 0.031 2.00e-02 2.50e+03 pdb=" O ILE R 201 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA R 202 " -0.011 2.00e-02 2.50e+03 ... (remaining 1485 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 183 2.67 - 3.23: 8667 3.23 - 3.79: 13540 3.79 - 4.34: 17969 4.34 - 4.90: 29295 Nonbonded interactions: 69654 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.113 2.440 nonbonded pdb=" OH TYR A 290 " pdb=" O SER A 293 " model vdw 2.163 2.440 nonbonded pdb=" OH TYR R 439 " pdb=" OH TYR R 443 " model vdw 2.179 2.440 nonbonded pdb=" OG SER B 147 " pdb=" O SER B 160 " model vdw 2.200 2.440 nonbonded pdb=" OG1 THR B 65 " pdb=" O PRO B 107 " model vdw 2.210 2.440 ... (remaining 69649 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 2.040 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 28.130 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 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 : 0.004 0.128 8770 Z= 0.267 Angle : 0.706 7.697 11923 Z= 0.397 Chirality : 0.045 0.343 1387 Planarity : 0.004 0.056 1488 Dihedral : 14.081 89.494 3057 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.88 (0.25), residues: 1104 helix: 0.44 (0.27), residues: 398 sheet: -2.68 (0.30), residues: 230 loop : -1.90 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 82 HIS 0.005 0.001 HIS S 35 PHE 0.029 0.002 PHE B 235 TYR 0.020 0.002 TYR S 103 ARG 0.008 0.001 ARG S 190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 0.945 Fit side-chains REVERT: A 14 GLU cc_start: 0.7249 (tm-30) cc_final: 0.6878 (tm-30) REVERT: A 210 LYS cc_start: 0.7389 (tptt) cc_final: 0.6844 (mmtm) REVERT: A 252 SER cc_start: 0.7474 (p) cc_final: 0.7193 (p) REVERT: A 255 ASN cc_start: 0.6919 (m-40) cc_final: 0.6498 (m-40) REVERT: A 337 ASP cc_start: 0.6790 (t70) cc_final: 0.6584 (t70) REVERT: A 345 LYS cc_start: 0.8149 (tptt) cc_final: 0.7755 (tptt) REVERT: A 353 LEU cc_start: 0.8697 (tp) cc_final: 0.8402 (tp) REVERT: B 110 ASN cc_start: 0.8503 (m110) cc_final: 0.8224 (m110) REVERT: B 125 ASN cc_start: 0.8332 (t0) cc_final: 0.8092 (t0) REVERT: B 161 SER cc_start: 0.8108 (p) cc_final: 0.7846 (p) REVERT: B 228 ASP cc_start: 0.6713 (p0) cc_final: 0.6192 (p0) REVERT: B 239 ASN cc_start: 0.7808 (m110) cc_final: 0.7451 (m-40) REVERT: B 279 SER cc_start: 0.7990 (t) cc_final: 0.7480 (p) REVERT: B 294 CYS cc_start: 0.7277 (t) cc_final: 0.7024 (t) REVERT: B 297 TRP cc_start: 0.8425 (m100) cc_final: 0.8143 (m100) REVERT: C 15 LEU cc_start: 0.8064 (tt) cc_final: 0.7775 (tt) REVERT: S 45 LEU cc_start: 0.7481 (mp) cc_final: 0.7278 (mt) REVERT: S 128 MET cc_start: 0.7325 (mtp) cc_final: 0.6859 (mtp) REVERT: S 179 ARG cc_start: 0.7552 (tpp-160) cc_final: 0.7326 (tpp-160) REVERT: S 214 VAL cc_start: 0.8351 (t) cc_final: 0.8150 (p) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.2342 time to fit residues: 82.4596 Evaluate side-chains 240 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.9980 chunk 82 optimal weight: 0.0470 chunk 45 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 85 optimal weight: 0.0570 chunk 33 optimal weight: 0.0670 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 98 optimal weight: 0.4980 overall best weight: 0.2734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN S 113 GLN S 174 GLN ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 417 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8770 Z= 0.157 Angle : 0.561 10.948 11923 Z= 0.290 Chirality : 0.041 0.205 1387 Planarity : 0.004 0.051 1488 Dihedral : 5.939 61.659 1242 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.56 % Allowed : 12.14 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.70 (0.25), residues: 1104 helix: 0.49 (0.27), residues: 403 sheet: -2.28 (0.30), residues: 251 loop : -1.85 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 339 HIS 0.006 0.001 HIS S 35 PHE 0.013 0.001 PHE A 274 TYR 0.016 0.001 TYR S 163 ARG 0.005 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 241 time to evaluate : 0.972 Fit side-chains REVERT: A 14 GLU cc_start: 0.7357 (tm-30) cc_final: 0.6907 (tm-30) REVERT: A 252 SER cc_start: 0.7511 (p) cc_final: 0.7290 (p) REVERT: B 110 ASN cc_start: 0.8501 (m110) cc_final: 0.8174 (m110) REVERT: B 228 ASP cc_start: 0.6730 (p0) cc_final: 0.6092 (p0) REVERT: B 297 TRP cc_start: 0.8346 (m100) cc_final: 0.7928 (m100) REVERT: S 128 MET cc_start: 0.7509 (mtp) cc_final: 0.6912 (mtp) REVERT: S 190 ARG cc_start: 0.7522 (mtm110) cc_final: 0.7140 (mtp-110) REVERT: S 202 LEU cc_start: 0.8203 (tp) cc_final: 0.7988 (tt) REVERT: R 121 MET cc_start: 0.6896 (mmt) cc_final: 0.6693 (mmt) REVERT: R 152 MET cc_start: 0.5816 (tpt) cc_final: 0.5557 (tpt) REVERT: R 459 THR cc_start: 0.6413 (t) cc_final: 0.6034 (m) outliers start: 14 outliers final: 12 residues processed: 244 average time/residue: 0.2358 time to fit residues: 76.2178 Evaluate side-chains 241 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 229 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain S residue 113 GLN Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain R residue 126 ILE Chi-restraints excluded: chain R residue 398 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 98 optimal weight: 0.0270 chunk 33 optimal weight: 0.2980 chunk 79 optimal weight: 4.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 113 GLN ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8770 Z= 0.192 Angle : 0.566 11.419 11923 Z= 0.290 Chirality : 0.041 0.190 1387 Planarity : 0.004 0.050 1488 Dihedral : 5.918 61.297 1242 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.78 % Allowed : 16.37 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.59 (0.25), residues: 1104 helix: 0.53 (0.27), residues: 400 sheet: -2.13 (0.30), residues: 255 loop : -1.77 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 435 HIS 0.006 0.001 HIS S 35 PHE 0.012 0.001 PHE B 234 TYR 0.011 0.001 TYR S 163 ARG 0.003 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 237 time to evaluate : 0.957 Fit side-chains REVERT: A 14 GLU cc_start: 0.7380 (tm-30) cc_final: 0.6891 (tm-30) REVERT: A 210 LYS cc_start: 0.7447 (tptt) cc_final: 0.7054 (mmtm) REVERT: A 252 SER cc_start: 0.7479 (p) cc_final: 0.7228 (p) REVERT: A 253 ILE cc_start: 0.7841 (tp) cc_final: 0.7589 (tp) REVERT: A 351 CYS cc_start: 0.7205 (m) cc_final: 0.6716 (m) REVERT: B 105 TYR cc_start: 0.8063 (t80) cc_final: 0.7801 (t80) REVERT: B 228 ASP cc_start: 0.6790 (p0) cc_final: 0.6163 (p0) REVERT: B 297 TRP cc_start: 0.8393 (m100) cc_final: 0.8105 (m100) REVERT: S 77 ASN cc_start: 0.7023 (m-40) cc_final: 0.6819 (t0) REVERT: S 110 PHE cc_start: 0.7893 (t80) cc_final: 0.7590 (t80) REVERT: S 128 MET cc_start: 0.7536 (mtp) cc_final: 0.7022 (mtp) REVERT: S 190 ARG cc_start: 0.7509 (mtm110) cc_final: 0.7264 (mtm110) REVERT: S 202 LEU cc_start: 0.8187 (tp) cc_final: 0.7986 (tt) REVERT: R 459 THR cc_start: 0.6485 (t) cc_final: 0.6079 (m) outliers start: 25 outliers final: 19 residues processed: 245 average time/residue: 0.2294 time to fit residues: 74.1835 Evaluate side-chains 243 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 224 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain R residue 126 ILE Chi-restraints excluded: chain R residue 398 VAL Chi-restraints excluded: chain R residue 421 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 66 optimal weight: 0.0670 chunk 99 optimal weight: 0.9990 chunk 105 optimal weight: 0.3980 chunk 94 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.6122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8770 Z= 0.195 Angle : 0.584 11.439 11923 Z= 0.293 Chirality : 0.042 0.180 1387 Planarity : 0.003 0.051 1488 Dihedral : 5.858 58.226 1242 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.12 % Allowed : 18.26 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.45 (0.25), residues: 1104 helix: 0.54 (0.27), residues: 401 sheet: -1.98 (0.30), residues: 266 loop : -1.60 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 435 HIS 0.005 0.001 HIS S 35 PHE 0.014 0.001 PHE S 29 TYR 0.011 0.001 TYR S 102 ARG 0.003 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 233 time to evaluate : 1.002 Fit side-chains REVERT: A 14 GLU cc_start: 0.7301 (tm-30) cc_final: 0.6876 (tm-30) REVERT: A 252 SER cc_start: 0.6746 (p) cc_final: 0.6414 (p) REVERT: A 255 ASN cc_start: 0.6929 (m-40) cc_final: 0.6620 (m-40) REVERT: A 270 LYS cc_start: 0.7221 (mmmt) cc_final: 0.6919 (mmtp) REVERT: A 317 LYS cc_start: 0.7880 (ptmt) cc_final: 0.7645 (ptmt) REVERT: A 351 CYS cc_start: 0.7246 (m) cc_final: 0.6752 (m) REVERT: B 112 VAL cc_start: 0.8523 (p) cc_final: 0.8127 (t) REVERT: B 169 TRP cc_start: 0.8261 (m100) cc_final: 0.7840 (m100) REVERT: B 228 ASP cc_start: 0.6868 (p0) cc_final: 0.6259 (p0) REVERT: B 239 ASN cc_start: 0.7783 (m110) cc_final: 0.7567 (m-40) REVERT: B 280 LYS cc_start: 0.7604 (tptt) cc_final: 0.7343 (mptt) REVERT: S 29 PHE cc_start: 0.7966 (t80) cc_final: 0.7454 (t80) REVERT: S 110 PHE cc_start: 0.8001 (t80) cc_final: 0.7611 (t80) REVERT: S 128 MET cc_start: 0.7575 (mtp) cc_final: 0.7064 (mtp) REVERT: S 174 GLN cc_start: 0.7558 (OUTLIER) cc_final: 0.7226 (pm20) REVERT: S 190 ARG cc_start: 0.7498 (mtm110) cc_final: 0.7205 (mtm110) REVERT: S 202 LEU cc_start: 0.8190 (tp) cc_final: 0.7966 (tt) REVERT: R 152 MET cc_start: 0.5878 (tpt) cc_final: 0.5644 (tpt) REVERT: R 421 LEU cc_start: 0.5671 (OUTLIER) cc_final: 0.5058 (mt) REVERT: R 459 THR cc_start: 0.6505 (t) cc_final: 0.6204 (m) outliers start: 37 outliers final: 26 residues processed: 250 average time/residue: 0.2400 time to fit residues: 80.1639 Evaluate side-chains 258 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 230 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 126 ILE Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 398 VAL Chi-restraints excluded: chain R residue 421 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 78 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 130 GLN ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8770 Z= 0.232 Angle : 0.606 11.431 11923 Z= 0.307 Chirality : 0.042 0.168 1387 Planarity : 0.004 0.052 1488 Dihedral : 5.960 54.751 1242 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 5.68 % Allowed : 19.15 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.41 (0.25), residues: 1104 helix: 0.51 (0.27), residues: 399 sheet: -1.85 (0.30), residues: 266 loop : -1.59 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 339 HIS 0.003 0.001 HIS S 35 PHE 0.011 0.001 PHE B 234 TYR 0.015 0.001 TYR S 102 ARG 0.003 0.000 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 231 time to evaluate : 0.933 Fit side-chains REVERT: A 14 GLU cc_start: 0.7306 (tm-30) cc_final: 0.6869 (tm-30) REVERT: A 252 SER cc_start: 0.6642 (p) cc_final: 0.6340 (p) REVERT: A 255 ASN cc_start: 0.6964 (m-40) cc_final: 0.6649 (m-40) REVERT: A 270 LYS cc_start: 0.7246 (mmmt) cc_final: 0.6965 (mmtp) REVERT: A 317 LYS cc_start: 0.7902 (ptmt) cc_final: 0.7676 (ptmt) REVERT: A 330 LYS cc_start: 0.7315 (OUTLIER) cc_final: 0.7033 (tptp) REVERT: A 351 CYS cc_start: 0.7274 (m) cc_final: 0.6797 (m) REVERT: B 84 SER cc_start: 0.7556 (m) cc_final: 0.7126 (p) REVERT: B 112 VAL cc_start: 0.8515 (p) cc_final: 0.8118 (t) REVERT: B 169 TRP cc_start: 0.8287 (m100) cc_final: 0.7799 (m100) REVERT: B 186 ASP cc_start: 0.7547 (p0) cc_final: 0.7100 (p0) REVERT: B 228 ASP cc_start: 0.6863 (p0) cc_final: 0.6384 (p0) REVERT: B 239 ASN cc_start: 0.7862 (m110) cc_final: 0.7567 (m-40) REVERT: B 280 LYS cc_start: 0.7795 (tptt) cc_final: 0.7572 (tptt) REVERT: B 308 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7060 (mp) REVERT: S 27 PHE cc_start: 0.7720 (p90) cc_final: 0.7454 (p90) REVERT: S 79 LEU cc_start: 0.6633 (OUTLIER) cc_final: 0.6370 (tp) REVERT: S 128 MET cc_start: 0.7576 (mtp) cc_final: 0.7117 (mtp) REVERT: S 174 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.7122 (pm20) REVERT: S 190 ARG cc_start: 0.7468 (mtm110) cc_final: 0.7224 (mtm110) REVERT: S 202 LEU cc_start: 0.8225 (tp) cc_final: 0.8014 (tt) REVERT: R 121 MET cc_start: 0.7073 (mmt) cc_final: 0.6856 (mmt) REVERT: R 138 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.6986 (mt) REVERT: R 152 MET cc_start: 0.5922 (tpt) cc_final: 0.5703 (tpt) REVERT: R 421 LEU cc_start: 0.5684 (OUTLIER) cc_final: 0.5098 (mt) REVERT: R 459 THR cc_start: 0.6640 (t) cc_final: 0.6222 (m) outliers start: 51 outliers final: 37 residues processed: 252 average time/residue: 0.2377 time to fit residues: 79.2442 Evaluate side-chains 276 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 233 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 126 ILE Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 217 CYS Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 68 ASN Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 398 VAL Chi-restraints excluded: chain R residue 421 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8770 Z= 0.246 Angle : 0.621 11.395 11923 Z= 0.312 Chirality : 0.043 0.246 1387 Planarity : 0.003 0.055 1488 Dihedral : 6.015 52.499 1242 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 5.68 % Allowed : 20.27 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.41 (0.26), residues: 1104 helix: 0.52 (0.27), residues: 398 sheet: -1.86 (0.30), residues: 269 loop : -1.58 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 435 HIS 0.004 0.001 HIS S 35 PHE 0.014 0.001 PHE S 29 TYR 0.013 0.001 TYR S 102 ARG 0.003 0.000 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 234 time to evaluate : 0.972 Fit side-chains REVERT: A 14 GLU cc_start: 0.7338 (tm-30) cc_final: 0.6895 (tm-30) REVERT: A 252 SER cc_start: 0.6607 (p) cc_final: 0.6308 (p) REVERT: A 255 ASN cc_start: 0.6968 (m-40) cc_final: 0.6614 (m-40) REVERT: A 270 LYS cc_start: 0.7254 (mmmt) cc_final: 0.7015 (mmtp) REVERT: B 84 SER cc_start: 0.7556 (m) cc_final: 0.7198 (p) REVERT: B 112 VAL cc_start: 0.8549 (p) cc_final: 0.8141 (t) REVERT: B 169 TRP cc_start: 0.8274 (m100) cc_final: 0.7874 (m100) REVERT: B 186 ASP cc_start: 0.7543 (p0) cc_final: 0.7095 (p0) REVERT: B 228 ASP cc_start: 0.6963 (p0) cc_final: 0.6381 (p0) REVERT: B 280 LYS cc_start: 0.7847 (tptt) cc_final: 0.7639 (tptt) REVERT: B 308 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.6892 (mp) REVERT: S 79 LEU cc_start: 0.6616 (OUTLIER) cc_final: 0.6356 (tp) REVERT: S 108 PHE cc_start: 0.7817 (m-80) cc_final: 0.7511 (m-80) REVERT: S 110 PHE cc_start: 0.7968 (t80) cc_final: 0.7755 (t80) REVERT: S 128 MET cc_start: 0.7619 (mtp) cc_final: 0.7170 (mtp) REVERT: S 174 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.7132 (pm20) REVERT: S 190 ARG cc_start: 0.7513 (mtm110) cc_final: 0.7301 (mtm110) REVERT: S 202 LEU cc_start: 0.8229 (tp) cc_final: 0.8015 (tt) REVERT: R 121 MET cc_start: 0.7094 (mmt) cc_final: 0.6865 (mmt) REVERT: R 421 LEU cc_start: 0.5708 (OUTLIER) cc_final: 0.5112 (mt) REVERT: R 459 THR cc_start: 0.6733 (t) cc_final: 0.6322 (m) outliers start: 51 outliers final: 38 residues processed: 254 average time/residue: 0.2322 time to fit residues: 77.5456 Evaluate side-chains 275 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 233 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 77 ASN Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 126 ILE Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 217 CYS Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 398 VAL Chi-restraints excluded: chain R residue 421 LEU Chi-restraints excluded: chain R residue 434 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 58 optimal weight: 0.0670 chunk 105 optimal weight: 6.9990 chunk 65 optimal weight: 0.0470 chunk 64 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 overall best weight: 0.5616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8770 Z= 0.194 Angle : 0.608 11.850 11923 Z= 0.301 Chirality : 0.042 0.173 1387 Planarity : 0.003 0.054 1488 Dihedral : 5.887 51.811 1242 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.68 % Allowed : 21.83 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.30 (0.26), residues: 1104 helix: 0.61 (0.27), residues: 398 sheet: -1.74 (0.31), residues: 270 loop : -1.54 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 435 HIS 0.004 0.001 HIS S 35 PHE 0.016 0.001 PHE S 29 TYR 0.011 0.001 TYR S 102 ARG 0.004 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 241 time to evaluate : 0.996 Fit side-chains REVERT: A 252 SER cc_start: 0.6556 (p) cc_final: 0.6215 (p) REVERT: A 255 ASN cc_start: 0.6904 (m-40) cc_final: 0.6446 (m110) REVERT: B 84 SER cc_start: 0.7600 (m) cc_final: 0.7181 (p) REVERT: B 112 VAL cc_start: 0.8528 (p) cc_final: 0.8134 (t) REVERT: B 169 TRP cc_start: 0.8225 (m100) cc_final: 0.7689 (m100) REVERT: B 186 ASP cc_start: 0.7494 (p0) cc_final: 0.7054 (p0) REVERT: B 228 ASP cc_start: 0.6931 (p0) cc_final: 0.6339 (p0) REVERT: B 280 LYS cc_start: 0.7825 (tptt) cc_final: 0.7625 (tptt) REVERT: B 308 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7080 (mt) REVERT: B 316 SER cc_start: 0.7143 (t) cc_final: 0.6939 (t) REVERT: S 79 LEU cc_start: 0.6578 (OUTLIER) cc_final: 0.6339 (tp) REVERT: S 128 MET cc_start: 0.7530 (mtp) cc_final: 0.7264 (mtt) REVERT: S 174 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.7212 (pm20) REVERT: S 190 ARG cc_start: 0.7510 (mtm110) cc_final: 0.7269 (mtm110) REVERT: S 202 LEU cc_start: 0.8215 (tp) cc_final: 0.8014 (tt) REVERT: R 121 MET cc_start: 0.7001 (mmt) cc_final: 0.6797 (mmt) REVERT: R 152 MET cc_start: 0.5765 (tpt) cc_final: 0.5530 (tpt) REVERT: R 190 LEU cc_start: 0.6722 (mm) cc_final: 0.6518 (mp) REVERT: R 421 LEU cc_start: 0.5657 (OUTLIER) cc_final: 0.5083 (mt) REVERT: R 459 THR cc_start: 0.6776 (t) cc_final: 0.6329 (m) outliers start: 42 outliers final: 34 residues processed: 256 average time/residue: 0.2398 time to fit residues: 80.7387 Evaluate side-chains 281 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 243 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 77 ASN Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 126 ILE Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 217 CYS Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 398 VAL Chi-restraints excluded: chain R residue 421 LEU Chi-restraints excluded: chain R residue 434 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 82 optimal weight: 0.0170 chunk 95 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 68 ASN R 423 ASN ** R 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8770 Z= 0.203 Angle : 0.618 11.656 11923 Z= 0.305 Chirality : 0.042 0.178 1387 Planarity : 0.003 0.054 1488 Dihedral : 5.831 48.758 1242 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 5.35 % Allowed : 21.71 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.26), residues: 1104 helix: 0.67 (0.27), residues: 391 sheet: -1.64 (0.31), residues: 269 loop : -1.54 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 435 HIS 0.005 0.001 HIS S 35 PHE 0.017 0.001 PHE S 29 TYR 0.012 0.001 TYR S 102 ARG 0.004 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 247 time to evaluate : 0.997 Fit side-chains REVERT: A 252 SER cc_start: 0.6344 (p) cc_final: 0.6040 (p) REVERT: A 255 ASN cc_start: 0.6930 (m-40) cc_final: 0.6517 (m110) REVERT: B 70 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8091 (mp) REVERT: B 84 SER cc_start: 0.7559 (m) cc_final: 0.7162 (p) REVERT: B 112 VAL cc_start: 0.8532 (p) cc_final: 0.8136 (t) REVERT: B 169 TRP cc_start: 0.8212 (m100) cc_final: 0.7699 (m100) REVERT: B 186 ASP cc_start: 0.7478 (p0) cc_final: 0.7048 (p0) REVERT: B 228 ASP cc_start: 0.6936 (p0) cc_final: 0.6315 (p0) REVERT: B 280 LYS cc_start: 0.7834 (tptt) cc_final: 0.7627 (tptt) REVERT: B 308 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7123 (mt) REVERT: S 38 ARG cc_start: 0.8166 (ptt180) cc_final: 0.7835 (ptp90) REVERT: S 174 GLN cc_start: 0.7469 (OUTLIER) cc_final: 0.7200 (pm20) REVERT: S 190 ARG cc_start: 0.7489 (mtm110) cc_final: 0.7246 (mtm110) REVERT: S 202 LEU cc_start: 0.8221 (tp) cc_final: 0.8007 (tt) REVERT: R 152 MET cc_start: 0.5785 (tpt) cc_final: 0.5564 (tpt) REVERT: R 409 PHE cc_start: 0.6517 (t80) cc_final: 0.6275 (t80) REVERT: R 419 MET cc_start: 0.5070 (OUTLIER) cc_final: 0.4648 (ppp) REVERT: R 459 THR cc_start: 0.6777 (t) cc_final: 0.6330 (m) outliers start: 48 outliers final: 40 residues processed: 266 average time/residue: 0.2317 time to fit residues: 80.9213 Evaluate side-chains 291 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 247 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain S residue 3 GLN Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 77 ASN Chi-restraints excluded: chain S residue 126 ILE Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 217 CYS Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 81 ILE Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 398 VAL Chi-restraints excluded: chain R residue 419 MET Chi-restraints excluded: chain R residue 421 LEU Chi-restraints excluded: chain R residue 434 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 42 optimal weight: 0.0170 chunk 76 optimal weight: 0.0870 chunk 30 optimal weight: 0.3980 chunk 88 optimal weight: 0.9980 chunk 92 optimal weight: 0.1980 chunk 64 optimal weight: 0.8980 chunk 103 optimal weight: 0.0870 chunk 63 optimal weight: 0.5980 overall best weight: 0.1574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 417 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8770 Z= 0.153 Angle : 0.610 12.020 11923 Z= 0.299 Chirality : 0.041 0.172 1387 Planarity : 0.003 0.053 1488 Dihedral : 5.660 50.486 1242 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.01 % Allowed : 23.39 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.26), residues: 1104 helix: 0.78 (0.28), residues: 392 sheet: -1.61 (0.30), residues: 290 loop : -1.32 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 82 HIS 0.005 0.001 HIS S 35 PHE 0.022 0.001 PHE S 29 TYR 0.009 0.001 TYR S 95 ARG 0.009 0.000 ARG S 168 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 246 time to evaluate : 0.996 Fit side-chains REVERT: A 14 GLU cc_start: 0.7307 (tm-30) cc_final: 0.6857 (tm-30) REVERT: A 252 SER cc_start: 0.6507 (p) cc_final: 0.6255 (p) REVERT: B 70 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7982 (mp) REVERT: B 112 VAL cc_start: 0.8472 (p) cc_final: 0.8052 (t) REVERT: B 186 ASP cc_start: 0.7362 (p0) cc_final: 0.6916 (p0) REVERT: B 228 ASP cc_start: 0.6971 (p0) cc_final: 0.6460 (p0) REVERT: B 255 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7208 (mm) REVERT: B 280 LYS cc_start: 0.7665 (tptt) cc_final: 0.7340 (mptt) REVERT: B 308 LEU cc_start: 0.7475 (tp) cc_final: 0.6927 (mt) REVERT: S 38 ARG cc_start: 0.8100 (ptt180) cc_final: 0.7837 (ptp90) REVERT: S 108 PHE cc_start: 0.7879 (m-80) cc_final: 0.7587 (m-80) REVERT: S 168 ARG cc_start: 0.7033 (mtt90) cc_final: 0.6811 (mpt180) REVERT: S 174 GLN cc_start: 0.7547 (pm20) cc_final: 0.7177 (pm20) REVERT: S 190 ARG cc_start: 0.7572 (mtm110) cc_final: 0.7338 (mtm110) REVERT: S 202 LEU cc_start: 0.8191 (tp) cc_final: 0.7973 (tt) REVERT: R 215 TYR cc_start: 0.7562 (m-10) cc_final: 0.7183 (m-80) REVERT: R 419 MET cc_start: 0.4865 (OUTLIER) cc_final: 0.4540 (ppp) REVERT: R 459 THR cc_start: 0.6691 (t) cc_final: 0.6226 (m) outliers start: 36 outliers final: 27 residues processed: 263 average time/residue: 0.2281 time to fit residues: 79.9359 Evaluate side-chains 275 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 245 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 217 CYS Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 398 VAL Chi-restraints excluded: chain R residue 419 MET Chi-restraints excluded: chain R residue 421 LEU Chi-restraints excluded: chain R residue 434 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.7980 chunk 71 optimal weight: 0.0570 chunk 108 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 8 optimal weight: 0.0870 chunk 66 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 230 ASN ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8770 Z= 0.187 Angle : 0.625 11.809 11923 Z= 0.305 Chirality : 0.042 0.175 1387 Planarity : 0.004 0.053 1488 Dihedral : 5.663 47.081 1242 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.90 % Allowed : 24.05 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.26), residues: 1104 helix: 0.77 (0.27), residues: 392 sheet: -1.47 (0.31), residues: 272 loop : -1.38 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 339 HIS 0.006 0.001 HIS B 91 PHE 0.021 0.001 PHE S 29 TYR 0.010 0.001 TYR S 102 ARG 0.009 0.000 ARG S 168 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 241 time to evaluate : 0.963 Fit side-chains REVERT: A 14 GLU cc_start: 0.7309 (tm-30) cc_final: 0.6855 (tm-30) REVERT: A 255 ASN cc_start: 0.6877 (m-40) cc_final: 0.6463 (m110) REVERT: B 70 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8090 (mp) REVERT: B 112 VAL cc_start: 0.8493 (p) cc_final: 0.8083 (t) REVERT: B 186 ASP cc_start: 0.7420 (p0) cc_final: 0.6770 (p0) REVERT: B 228 ASP cc_start: 0.6956 (p0) cc_final: 0.6463 (p0) REVERT: B 308 LEU cc_start: 0.7589 (tp) cc_final: 0.7029 (mt) REVERT: S 38 ARG cc_start: 0.8108 (ptt180) cc_final: 0.7900 (ptp90) REVERT: S 108 PHE cc_start: 0.7899 (m-80) cc_final: 0.7617 (m-80) REVERT: S 174 GLN cc_start: 0.7587 (pm20) cc_final: 0.7164 (pm20) REVERT: S 190 ARG cc_start: 0.7560 (mtm110) cc_final: 0.7313 (mtm110) REVERT: S 202 LEU cc_start: 0.8212 (tp) cc_final: 0.7990 (tt) REVERT: R 419 MET cc_start: 0.4948 (OUTLIER) cc_final: 0.4618 (ppp) REVERT: R 459 THR cc_start: 0.6776 (t) cc_final: 0.6329 (m) outliers start: 35 outliers final: 29 residues processed: 256 average time/residue: 0.2313 time to fit residues: 77.9938 Evaluate side-chains 271 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 240 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 126 ILE Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 217 CYS Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 398 VAL Chi-restraints excluded: chain R residue 419 MET Chi-restraints excluded: chain R residue 421 LEU Chi-restraints excluded: chain R residue 434 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 10 optimal weight: 0.1980 chunk 15 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 4 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN C 11 GLN ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 64 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 = 0.3872 r_free = 0.3872 target = 0.149513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.132690 restraints weight = 13493.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.136133 restraints weight = 6257.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.138345 restraints weight = 3492.889| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8770 Z= 0.217 Angle : 0.652 11.698 11923 Z= 0.321 Chirality : 0.043 0.177 1387 Planarity : 0.003 0.054 1488 Dihedral : 5.790 45.682 1242 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.45 % Allowed : 25.06 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.04 (0.26), residues: 1104 helix: 0.78 (0.27), residues: 389 sheet: -1.53 (0.31), residues: 274 loop : -1.36 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 169 HIS 0.005 0.001 HIS B 91 PHE 0.020 0.001 PHE S 29 TYR 0.014 0.001 TYR R 113 ARG 0.005 0.000 ARG S 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2277.80 seconds wall clock time: 41 minutes 41.95 seconds (2501.95 seconds total)