Starting phenix.real_space_refine on Mon Apr 28 07:13:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bls_44675/04_2025/9bls_44675.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bls_44675/04_2025/9bls_44675.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bls_44675/04_2025/9bls_44675.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bls_44675/04_2025/9bls_44675.map" model { file = "/net/cci-nas-00/data/ceres_data/9bls_44675/04_2025/9bls_44675.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bls_44675/04_2025/9bls_44675.cif" } resolution = 2.96 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= 0.009 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: 4 Type Number sf(0) Gaussians S 27 5.16 5 C 4471 2.51 5 N 1229 2.21 5 O 1385 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 7112 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4516 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 21, 'TRANS': 572} Chain: "B" Number of atoms: 1277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1277 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "C" Number of atoms: 1266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1266 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 7, 'TRANS': 151} Chain: "D" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 53 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Time building chain proxies: 5.05, per 1000 atoms: 0.71 Number of scatterers: 7112 At special positions: 0 Unit cell: (73.865, 120.615, 118.745, 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 27 16.00 O 1385 8.00 N 1229 7.00 C 4471 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.42 Conformation dependent library (CDL) restraints added in 1.2 seconds 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1708 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 12 sheets defined 45.9% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 120 through 123 Processing helix chain 'A' and resid 130 through 140 removed outlier: 4.106A pdb=" N LYS A 138 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASN A 139 " --> pdb=" O LYS A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 183 removed outlier: 3.670A pdb=" N GLY A 167 " --> pdb=" O PRO A 163 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR A 181 " --> pdb=" O THR A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 212 Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 258 through 261 Processing helix chain 'A' and resid 274 through 294 removed outlier: 4.224A pdb=" N PHE A 278 " --> pdb=" O GLY A 274 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP A 279 " --> pdb=" O GLY A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 319 Processing helix chain 'A' and resid 348 through 355 Processing helix chain 'A' and resid 355 through 361 Processing helix chain 'A' and resid 363 through 373 Processing helix chain 'A' and resid 387 through 391 removed outlier: 3.740A pdb=" N ARG A 391 " --> pdb=" O GLY A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 404 Processing helix chain 'A' and resid 412 through 415 Processing helix chain 'A' and resid 416 through 429 Processing helix chain 'A' and resid 432 through 437 Processing helix chain 'A' and resid 556 through 561 Processing helix chain 'A' and resid 563 through 568 removed outlier: 3.803A pdb=" N LYS A 567 " --> pdb=" O LYS A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 597 Processing helix chain 'A' and resid 604 through 608 removed outlier: 4.370A pdb=" N GLU A 607 " --> pdb=" O PRO A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 619 removed outlier: 4.035A pdb=" N GLU A 613 " --> pdb=" O ASN A 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 102 removed outlier: 3.640A pdb=" N GLU B 97 " --> pdb=" O GLN B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 125 removed outlier: 4.775A pdb=" N GLU B 113 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL B 114 " --> pdb=" O ASP B 110 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 158 Processing helix chain 'C' and resid 60 through 125 removed outlier: 3.987A pdb=" N LYS C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL C 65 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP C 110 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLU C 113 " --> pdb=" O LYS C 109 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL C 114 " --> pdb=" O ASP C 110 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL C 125 " --> pdb=" O ALA C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 130 removed outlier: 3.787A pdb=" N ILE C 130 " --> pdb=" O LYS C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 158 Processing sheet with id=AA1, first strand: chain 'A' and resid 74 through 77 removed outlier: 3.946A pdb=" N GLN A 74 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 77 removed outlier: 3.946A pdb=" N GLN A 74 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N MET A 70 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL A 55 " --> pdb=" O MET A 70 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL A 56 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N THR A 192 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE A 58 " --> pdb=" O THR A 192 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ALA A 189 " --> pdb=" O VAL A 216 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ARG A 218 " --> pdb=" O ALA A 189 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 101 Processing sheet with id=AA4, first strand: chain 'A' and resid 143 through 146 removed outlier: 4.494A pdb=" N LYS A 143 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 263 through 270 removed outlier: 5.580A pdb=" N VAL A 264 " --> pdb=" O GLU A 256 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLU A 256 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU A 382 " --> pdb=" O VAL A 239 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 335 removed outlier: 3.849A pdb=" N TYR A 331 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LYS A 340 " --> pdb=" O TYR A 331 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR A 333 " --> pdb=" O GLY A 338 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLY A 338 " --> pdb=" O THR A 333 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 455 through 458 removed outlier: 5.517A pdb=" N LYS A 456 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE A 447 " --> pdb=" O LYS A 456 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY A 501 " --> pdb=" O VAL A 486 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 466 through 473 removed outlier: 3.578A pdb=" N ILE A 524 " --> pdb=" O THR A 466 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 160 through 163 removed outlier: 6.526A pdb=" N TYR B 199 " --> pdb=" O LEU B 206 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 175 through 179 removed outlier: 7.250A pdb=" N VAL B 213 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU B 210 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N VAL B 194 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLY B 212 " --> pdb=" O ALA B 192 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 160 through 163 removed outlier: 6.378A pdb=" N TYR C 199 " --> pdb=" O LEU C 206 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 175 through 180 removed outlier: 7.524A pdb=" N VAL C 213 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N HIS C 180 " --> pdb=" O VAL C 213 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU C 210 " --> pdb=" O VAL C 194 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N VAL C 194 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLY C 212 " --> pdb=" O ALA C 192 " (cutoff:3.500A) 386 hydrogen bonds defined for protein. 1113 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: 2.18 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2408 1.34 - 1.46: 1349 1.46 - 1.58: 3405 1.58 - 1.70: 0 1.70 - 1.82: 45 Bond restraints: 7207 Sorted by residual: bond pdb=" CB GLU B 97 " pdb=" CG GLU B 97 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.03e+00 bond pdb=" SD MET A 174 " pdb=" CE MET A 174 " ideal model delta sigma weight residual 1.791 1.766 0.025 2.50e-02 1.60e+03 9.80e-01 bond pdb=" CB GLU A 374 " pdb=" CG GLU A 374 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.46e-01 bond pdb=" CB GLU C 148 " pdb=" CG GLU C 148 " ideal model delta sigma weight residual 1.520 1.496 0.024 3.00e-02 1.11e+03 6.43e-01 bond pdb=" CG GLU B 97 " pdb=" CD GLU B 97 " ideal model delta sigma weight residual 1.516 1.534 -0.018 2.50e-02 1.60e+03 5.39e-01 ... (remaining 7202 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 9652 2.45 - 4.89: 60 4.89 - 7.34: 8 7.34 - 9.78: 1 9.78 - 12.23: 1 Bond angle restraints: 9722 Sorted by residual: angle pdb=" CB MET A 618 " pdb=" CG MET A 618 " pdb=" SD MET A 618 " ideal model delta sigma weight residual 112.70 124.93 -12.23 3.00e+00 1.11e-01 1.66e+01 angle pdb=" CA GLN A 108 " pdb=" CB GLN A 108 " pdb=" CG GLN A 108 " ideal model delta sigma weight residual 114.10 119.09 -4.99 2.00e+00 2.50e-01 6.24e+00 angle pdb=" CB GLU B 97 " pdb=" CG GLU B 97 " pdb=" CD GLU B 97 " ideal model delta sigma weight residual 112.60 116.77 -4.17 1.70e+00 3.46e-01 6.03e+00 angle pdb=" CB GLU A 374 " pdb=" CG GLU A 374 " pdb=" CD GLU A 374 " ideal model delta sigma weight residual 112.60 116.40 -3.80 1.70e+00 3.46e-01 5.00e+00 angle pdb=" CG MET A 618 " pdb=" SD MET A 618 " pdb=" CE MET A 618 " ideal model delta sigma weight residual 100.90 105.78 -4.88 2.20e+00 2.07e-01 4.92e+00 ... (remaining 9717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 3654 17.10 - 34.20: 550 34.20 - 51.30: 196 51.30 - 68.40: 55 68.40 - 85.50: 12 Dihedral angle restraints: 4467 sinusoidal: 1823 harmonic: 2644 Sorted by residual: dihedral pdb=" CA GLY B 103 " pdb=" C GLY B 103 " pdb=" N ILE B 104 " pdb=" CA ILE B 104 " ideal model delta harmonic sigma weight residual 180.00 162.63 17.37 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA GLY A 528 " pdb=" C GLY A 528 " pdb=" N ILE A 529 " pdb=" CA ILE A 529 " ideal model delta harmonic sigma weight residual -180.00 -162.97 -17.03 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CG ARG A 309 " pdb=" CD ARG A 309 " pdb=" NE ARG A 309 " pdb=" CZ ARG A 309 " ideal model delta sinusoidal sigma weight residual -180.00 -136.24 -43.76 2 1.50e+01 4.44e-03 1.02e+01 ... (remaining 4464 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 733 0.031 - 0.063: 274 0.063 - 0.094: 77 0.094 - 0.126: 45 0.126 - 0.157: 3 Chirality restraints: 1132 Sorted by residual: chirality pdb=" CB ILE A 257 " pdb=" CA ILE A 257 " pdb=" CG1 ILE A 257 " pdb=" CG2 ILE A 257 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.16 2.00e-01 2.50e+01 6.15e-01 chirality pdb=" CA VAL A 193 " pdb=" N VAL A 193 " pdb=" C VAL A 193 " pdb=" CB VAL A 193 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.97e-01 chirality pdb=" CA VAL B 125 " pdb=" N VAL B 125 " pdb=" C VAL B 125 " pdb=" CB VAL B 125 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.95e-01 ... (remaining 1129 not shown) Planarity restraints: 1265 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 103 " 0.036 5.00e-02 4.00e+02 5.49e-02 4.83e+00 pdb=" N PRO A 104 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 104 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 104 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 374 " 0.007 2.00e-02 2.50e+03 1.53e-02 2.33e+00 pdb=" CD GLU A 374 " -0.026 2.00e-02 2.50e+03 pdb=" OE1 GLU A 374 " 0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU A 374 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 120 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.93e+00 pdb=" C THR A 120 " -0.024 2.00e-02 2.50e+03 pdb=" O THR A 120 " 0.009 2.00e-02 2.50e+03 pdb=" N LYS A 121 " 0.008 2.00e-02 2.50e+03 ... (remaining 1262 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1084 2.76 - 3.29: 6665 3.29 - 3.83: 11707 3.83 - 4.36: 13334 4.36 - 4.90: 24319 Nonbonded interactions: 57109 Sorted by model distance: nonbonded pdb=" OG1 THR A 474 " pdb=" OE1 GLN A 479 " model vdw 2.224 3.040 nonbonded pdb=" OG1 THR A 441 " pdb=" O ARG A 460 " model vdw 2.252 3.040 nonbonded pdb=" NH1 ARG A 578 " pdb=" OH TYR C 173 " model vdw 2.260 3.120 nonbonded pdb=" OD2 ASP B 116 " pdb=" NH1 ARG B 207 " model vdw 2.278 3.120 nonbonded pdb=" O GLU A 352 " pdb=" OG1 THR A 356 " model vdw 2.278 3.040 ... (remaining 57104 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 59 through 217) selection = chain 'C' } 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: 2.710 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.420 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:13.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 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 : 0.003 0.035 7207 Z= 0.134 Angle : 0.510 12.229 9722 Z= 0.254 Chirality : 0.040 0.157 1132 Planarity : 0.003 0.055 1265 Dihedral : 19.379 85.504 2759 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.62 % Allowed : 36.18 % Favored : 60.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.28), residues: 913 helix: 1.53 (0.26), residues: 389 sheet: -0.05 (0.49), residues: 125 loop : -1.11 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 126 HIS 0.003 0.001 HIS B 136 PHE 0.008 0.001 PHE A 142 TYR 0.014 0.001 TYR B 102 ARG 0.002 0.000 ARG A 578 Details of bonding type rmsd hydrogen bonds : bond 0.15852 ( 383) hydrogen bonds : angle 6.24754 ( 1113) covalent geometry : bond 0.00319 ( 7207) covalent geometry : angle 0.51018 ( 9722) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 68 time to evaluate : 0.645 Fit side-chains REVERT: A 155 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.6783 (tm-30) REVERT: A 258 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.6529 (pm20) REVERT: A 498 LYS cc_start: 0.6947 (OUTLIER) cc_final: 0.6474 (mptt) REVERT: A 547 ILE cc_start: 0.7436 (OUTLIER) cc_final: 0.6908 (tp) REVERT: B 93 GLN cc_start: 0.7350 (mt0) cc_final: 0.7034 (mp10) REVERT: B 201 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.7974 (pt) REVERT: D 438 LEU cc_start: 0.7903 (mt) cc_final: 0.7339 (mp) outliers start: 28 outliers final: 20 residues processed: 91 average time/residue: 1.1792 time to fit residues: 114.3711 Evaluate side-chains 93 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 68 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 488 GLN Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 625 LYS Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 197 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 0.1980 chunk 68 optimal weight: 0.0870 chunk 37 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 27 optimal weight: 0.0050 chunk 42 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.3972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.182005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.132268 restraints weight = 7160.793| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.75 r_work: 0.3238 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.0668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7207 Z= 0.123 Angle : 0.502 8.350 9722 Z= 0.261 Chirality : 0.040 0.138 1132 Planarity : 0.003 0.053 1265 Dihedral : 7.887 59.244 1025 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 6.85 % Allowed : 31.40 % Favored : 61.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.28), residues: 913 helix: 1.84 (0.26), residues: 391 sheet: -0.25 (0.46), residues: 134 loop : -1.06 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 126 HIS 0.004 0.001 HIS B 136 PHE 0.009 0.001 PHE A 503 TYR 0.013 0.001 TYR A 243 ARG 0.004 0.000 ARG A 578 Details of bonding type rmsd hydrogen bonds : bond 0.04451 ( 383) hydrogen bonds : angle 4.77185 ( 1113) covalent geometry : bond 0.00274 ( 7207) covalent geometry : angle 0.50156 ( 9722) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 73 time to evaluate : 0.928 Fit side-chains REVERT: A 155 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7271 (tm-30) REVERT: A 340 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7238 (mmmt) REVERT: A 498 LYS cc_start: 0.7148 (mttt) cc_final: 0.6546 (mptt) REVERT: A 523 ASP cc_start: 0.7369 (t70) cc_final: 0.7148 (m-30) REVERT: B 86 GLU cc_start: 0.7461 (tp30) cc_final: 0.6412 (mm-30) REVERT: B 93 GLN cc_start: 0.7212 (OUTLIER) cc_final: 0.6910 (mp10) REVERT: B 148 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7089 (tt0) REVERT: B 201 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8194 (pt) REVERT: D 438 LEU cc_start: 0.7689 (mt) cc_final: 0.7140 (mp) REVERT: D 439 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7652 (t0) outliers start: 53 outliers final: 18 residues processed: 116 average time/residue: 1.4792 time to fit residues: 182.7258 Evaluate side-chains 92 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 488 GLN Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 439 ASP Chi-restraints excluded: chain D residue 441 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 32 optimal weight: 0.0770 chunk 71 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 35 optimal weight: 0.0980 chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 0.3980 chunk 79 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN B 123 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.182963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.134636 restraints weight = 7242.717| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.95 r_work: 0.3221 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7207 Z= 0.117 Angle : 0.488 8.578 9722 Z= 0.251 Chirality : 0.040 0.134 1132 Planarity : 0.003 0.050 1265 Dihedral : 6.639 59.432 997 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 7.88 % Allowed : 30.10 % Favored : 62.02 % 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: 0.63 (0.28), residues: 913 helix: 1.99 (0.26), residues: 393 sheet: -0.19 (0.45), residues: 134 loop : -1.02 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 126 HIS 0.004 0.001 HIS B 136 PHE 0.010 0.001 PHE A 503 TYR 0.012 0.001 TYR A 243 ARG 0.003 0.000 ARG A 578 Details of bonding type rmsd hydrogen bonds : bond 0.04154 ( 383) hydrogen bonds : angle 4.49268 ( 1113) covalent geometry : bond 0.00263 ( 7207) covalent geometry : angle 0.48812 ( 9722) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 72 time to evaluate : 0.860 Fit side-chains REVERT: A 155 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7358 (tm-30) REVERT: A 259 LYS cc_start: 0.7983 (tmtt) cc_final: 0.7746 (tmtt) REVERT: A 314 LYS cc_start: 0.7509 (mptt) cc_final: 0.7176 (mptt) REVERT: A 340 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.7277 (mmmt) REVERT: A 405 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.7158 (ttm-80) REVERT: A 498 LYS cc_start: 0.7217 (mttt) cc_final: 0.6608 (mptt) REVERT: A 502 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.8064 (tt0) REVERT: A 613 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6248 (tp30) REVERT: B 93 GLN cc_start: 0.7167 (OUTLIER) cc_final: 0.6903 (mp10) REVERT: B 148 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7173 (tt0) REVERT: B 201 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8240 (pt) REVERT: C 131 LYS cc_start: 0.7996 (mtmm) cc_final: 0.7765 (pttp) REVERT: D 438 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7045 (mp) outliers start: 61 outliers final: 28 residues processed: 119 average time/residue: 1.4748 time to fit residues: 186.8941 Evaluate side-chains 108 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 71 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 488 GLN Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 502 GLN Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 441 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 0.0870 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 55 optimal weight: 0.0070 chunk 71 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.5776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN B 123 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.181460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.132110 restraints weight = 7288.247| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.94 r_work: 0.3207 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7207 Z= 0.140 Angle : 0.506 8.866 9722 Z= 0.260 Chirality : 0.041 0.137 1132 Planarity : 0.003 0.050 1265 Dihedral : 6.716 59.347 997 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 7.36 % Allowed : 30.23 % Favored : 62.40 % 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: 0.59 (0.28), residues: 913 helix: 1.93 (0.26), residues: 391 sheet: -0.28 (0.44), residues: 131 loop : -0.97 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 126 HIS 0.004 0.001 HIS B 136 PHE 0.010 0.001 PHE A 503 TYR 0.013 0.001 TYR A 243 ARG 0.002 0.000 ARG A 578 Details of bonding type rmsd hydrogen bonds : bond 0.04323 ( 383) hydrogen bonds : angle 4.45166 ( 1113) covalent geometry : bond 0.00328 ( 7207) covalent geometry : angle 0.50630 ( 9722) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 77 time to evaluate : 0.829 Fit side-chains REVERT: A 155 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.6733 (tm-30) REVERT: A 259 LYS cc_start: 0.8032 (tmtt) cc_final: 0.7791 (tmtt) REVERT: A 314 LYS cc_start: 0.7530 (mptt) cc_final: 0.7260 (mptt) REVERT: A 334 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.7086 (tpt) REVERT: A 340 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.7456 (mmmt) REVERT: A 498 LYS cc_start: 0.7255 (mttt) cc_final: 0.6649 (mptt) REVERT: A 499 LEU cc_start: 0.6704 (OUTLIER) cc_final: 0.6398 (tm) REVERT: A 613 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.6247 (tp30) REVERT: B 86 GLU cc_start: 0.7458 (tp30) cc_final: 0.6408 (mm-30) REVERT: B 93 GLN cc_start: 0.7184 (OUTLIER) cc_final: 0.6868 (mp10) REVERT: B 148 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.7152 (tt0) REVERT: B 201 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8202 (pt) REVERT: C 131 LYS cc_start: 0.7984 (mtmm) cc_final: 0.7784 (pttp) REVERT: D 438 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7048 (mp) outliers start: 57 outliers final: 32 residues processed: 119 average time/residue: 1.0998 time to fit residues: 138.8678 Evaluate side-chains 115 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 74 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 441 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 17 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 7 optimal weight: 0.3980 chunk 36 optimal weight: 0.2980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.181900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.132844 restraints weight = 7189.134| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.83 r_work: 0.3219 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7207 Z= 0.132 Angle : 0.504 8.729 9722 Z= 0.256 Chirality : 0.041 0.208 1132 Planarity : 0.003 0.049 1265 Dihedral : 6.611 59.778 994 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 6.98 % Allowed : 30.49 % Favored : 62.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.28), residues: 913 helix: 1.97 (0.26), residues: 391 sheet: -0.32 (0.44), residues: 131 loop : -0.96 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 126 HIS 0.003 0.001 HIS B 136 PHE 0.010 0.001 PHE A 503 TYR 0.013 0.001 TYR A 243 ARG 0.005 0.000 ARG A 578 Details of bonding type rmsd hydrogen bonds : bond 0.04197 ( 383) hydrogen bonds : angle 4.36080 ( 1113) covalent geometry : bond 0.00308 ( 7207) covalent geometry : angle 0.50364 ( 9722) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 76 time to evaluate : 0.756 Fit side-chains REVERT: A 155 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.6704 (tm-30) REVERT: A 259 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7803 (tmtt) REVERT: A 314 LYS cc_start: 0.7473 (mptt) cc_final: 0.7218 (mptt) REVERT: A 340 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.7397 (mmmt) REVERT: A 498 LYS cc_start: 0.7192 (mttt) cc_final: 0.6587 (mptt) REVERT: A 613 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6253 (tp30) REVERT: B 86 GLU cc_start: 0.7437 (tp30) cc_final: 0.6390 (mm-30) REVERT: B 93 GLN cc_start: 0.7145 (OUTLIER) cc_final: 0.6828 (mp10) REVERT: B 148 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.7106 (tt0) REVERT: B 201 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8177 (pt) REVERT: D 438 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7136 (mp) outliers start: 54 outliers final: 30 residues processed: 116 average time/residue: 1.0321 time to fit residues: 127.3984 Evaluate side-chains 109 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 71 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 438 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 5 optimal weight: 0.1980 chunk 48 optimal weight: 7.9990 chunk 73 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN B 123 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.179401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.122586 restraints weight = 7221.982| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.66 r_work: 0.3195 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7207 Z= 0.200 Angle : 0.563 9.171 9722 Z= 0.286 Chirality : 0.043 0.173 1132 Planarity : 0.004 0.050 1265 Dihedral : 7.000 61.579 994 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 7.11 % Allowed : 30.88 % Favored : 62.02 % 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: 0.38 (0.28), residues: 913 helix: 1.67 (0.25), residues: 397 sheet: -0.34 (0.44), residues: 131 loop : -1.03 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 126 HIS 0.004 0.001 HIS B 136 PHE 0.011 0.002 PHE A 503 TYR 0.015 0.002 TYR B 102 ARG 0.004 0.000 ARG A 578 Details of bonding type rmsd hydrogen bonds : bond 0.04887 ( 383) hydrogen bonds : angle 4.51109 ( 1113) covalent geometry : bond 0.00489 ( 7207) covalent geometry : angle 0.56303 ( 9722) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 75 time to evaluate : 0.761 Fit side-chains REVERT: A 155 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.6723 (tm-30) REVERT: A 259 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7840 (tmtt) REVERT: A 314 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.6993 (mptt) REVERT: A 340 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7332 (mmmt) REVERT: A 498 LYS cc_start: 0.7184 (mttt) cc_final: 0.6574 (mptt) REVERT: A 613 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.6282 (tp30) REVERT: B 86 GLU cc_start: 0.7297 (tp30) cc_final: 0.6209 (mm-30) REVERT: B 93 GLN cc_start: 0.7199 (OUTLIER) cc_final: 0.6808 (mp10) REVERT: B 148 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6995 (tt0) REVERT: D 438 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7016 (mp) outliers start: 55 outliers final: 33 residues processed: 117 average time/residue: 1.0235 time to fit residues: 127.5731 Evaluate side-chains 113 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 72 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 519 GLU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 441 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 18 optimal weight: 0.9980 chunk 63 optimal weight: 0.0670 chunk 76 optimal weight: 6.9990 chunk 86 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 35 optimal weight: 0.0870 chunk 78 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.181922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.131901 restraints weight = 7163.639| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.90 r_work: 0.3185 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7207 Z= 0.126 Angle : 0.512 9.762 9722 Z= 0.259 Chirality : 0.041 0.163 1132 Planarity : 0.003 0.049 1265 Dihedral : 6.850 59.979 994 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 5.68 % Allowed : 32.43 % Favored : 61.89 % 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: 0.59 (0.28), residues: 913 helix: 2.00 (0.26), residues: 385 sheet: -0.33 (0.44), residues: 131 loop : -0.99 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 126 HIS 0.003 0.001 HIS B 136 PHE 0.010 0.001 PHE A 503 TYR 0.013 0.001 TYR A 243 ARG 0.003 0.000 ARG A 578 Details of bonding type rmsd hydrogen bonds : bond 0.04182 ( 383) hydrogen bonds : angle 4.36134 ( 1113) covalent geometry : bond 0.00290 ( 7207) covalent geometry : angle 0.51165 ( 9722) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 73 time to evaluate : 0.893 Fit side-chains REVERT: A 155 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.6811 (tm-30) REVERT: A 259 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7907 (tmtt) REVERT: A 340 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.7464 (mmmt) REVERT: A 498 LYS cc_start: 0.7099 (mttt) cc_final: 0.6489 (mptt) REVERT: A 519 GLU cc_start: 0.6511 (OUTLIER) cc_final: 0.5619 (tt0) REVERT: A 613 GLU cc_start: 0.6875 (OUTLIER) cc_final: 0.6290 (tp30) REVERT: B 93 GLN cc_start: 0.7234 (OUTLIER) cc_final: 0.6911 (mp10) REVERT: B 148 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7215 (tt0) REVERT: D 438 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7132 (mp) outliers start: 44 outliers final: 27 residues processed: 106 average time/residue: 1.0430 time to fit residues: 118.1540 Evaluate side-chains 105 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 70 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 519 GLU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 441 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 29 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 63 optimal weight: 0.0870 chunk 58 optimal weight: 0.3980 chunk 7 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 33 optimal weight: 0.0870 chunk 47 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.179786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.130997 restraints weight = 7235.002| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.94 r_work: 0.3146 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7207 Z= 0.191 Angle : 0.568 10.511 9722 Z= 0.286 Chirality : 0.043 0.193 1132 Planarity : 0.004 0.051 1265 Dihedral : 6.841 61.798 993 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 6.46 % Allowed : 32.04 % Favored : 61.50 % 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: 0.38 (0.28), residues: 913 helix: 1.65 (0.25), residues: 398 sheet: -0.34 (0.44), residues: 131 loop : -1.03 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 126 HIS 0.004 0.001 HIS B 136 PHE 0.010 0.002 PHE A 503 TYR 0.017 0.002 TYR A 128 ARG 0.003 0.000 ARG A 578 Details of bonding type rmsd hydrogen bonds : bond 0.04767 ( 383) hydrogen bonds : angle 4.47287 ( 1113) covalent geometry : bond 0.00467 ( 7207) covalent geometry : angle 0.56821 ( 9722) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 74 time to evaluate : 0.757 Fit side-chains REVERT: A 155 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.6866 (tm-30) REVERT: A 340 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.7565 (mmmt) REVERT: A 498 LYS cc_start: 0.7273 (mttt) cc_final: 0.6699 (mptt) REVERT: A 523 ASP cc_start: 0.7507 (t70) cc_final: 0.7239 (m-30) REVERT: A 613 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.6303 (tp30) REVERT: B 86 GLU cc_start: 0.7573 (tp30) cc_final: 0.7355 (tp30) REVERT: B 93 GLN cc_start: 0.7423 (OUTLIER) cc_final: 0.7079 (mp10) REVERT: B 148 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7228 (tt0) REVERT: D 438 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7264 (mp) outliers start: 50 outliers final: 31 residues processed: 115 average time/residue: 1.0493 time to fit residues: 128.4405 Evaluate side-chains 110 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 73 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 519 GLU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 441 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 84 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 81 optimal weight: 0.0270 chunk 75 optimal weight: 8.9990 chunk 14 optimal weight: 0.1980 chunk 51 optimal weight: 10.0000 chunk 25 optimal weight: 0.0040 chunk 12 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.2450 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.183761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.134473 restraints weight = 7227.586| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.83 r_work: 0.3222 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7207 Z= 0.105 Angle : 0.509 11.829 9722 Z= 0.256 Chirality : 0.040 0.195 1132 Planarity : 0.003 0.048 1265 Dihedral : 6.460 59.709 993 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.88 % Allowed : 34.24 % Favored : 61.89 % 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: 0.68 (0.28), residues: 913 helix: 2.06 (0.26), residues: 390 sheet: -0.34 (0.44), residues: 131 loop : -0.95 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 126 HIS 0.003 0.001 HIS B 136 PHE 0.009 0.001 PHE A 503 TYR 0.013 0.001 TYR C 78 ARG 0.004 0.000 ARG A 578 Details of bonding type rmsd hydrogen bonds : bond 0.03813 ( 383) hydrogen bonds : angle 4.24897 ( 1113) covalent geometry : bond 0.00230 ( 7207) covalent geometry : angle 0.50931 ( 9722) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 76 time to evaluate : 0.884 Fit side-chains REVERT: A 155 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.6689 (tm-30) REVERT: A 340 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.7222 (mmmt) REVERT: A 498 LYS cc_start: 0.7019 (mttt) cc_final: 0.6437 (mptt) REVERT: B 93 GLN cc_start: 0.7059 (OUTLIER) cc_final: 0.6752 (mp10) REVERT: B 148 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.7060 (tt0) REVERT: D 438 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7007 (mp) outliers start: 30 outliers final: 17 residues processed: 99 average time/residue: 1.1144 time to fit residues: 117.8849 Evaluate side-chains 94 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 441 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 66 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 33 optimal weight: 0.0980 chunk 50 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 68 optimal weight: 0.3980 chunk 40 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN C 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.181312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.131954 restraints weight = 7356.062| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.82 r_work: 0.3212 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7207 Z= 0.147 Angle : 0.537 12.095 9722 Z= 0.271 Chirality : 0.042 0.182 1132 Planarity : 0.003 0.049 1265 Dihedral : 6.290 59.779 992 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.36 % Allowed : 35.27 % Favored : 61.37 % 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: 0.60 (0.28), residues: 913 helix: 1.92 (0.25), residues: 394 sheet: -0.31 (0.44), residues: 131 loop : -0.95 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 126 HIS 0.003 0.001 HIS B 136 PHE 0.010 0.001 PHE A 503 TYR 0.015 0.001 TYR A 243 ARG 0.005 0.000 ARG A 578 Details of bonding type rmsd hydrogen bonds : bond 0.04295 ( 383) hydrogen bonds : angle 4.30695 ( 1113) covalent geometry : bond 0.00353 ( 7207) covalent geometry : angle 0.53703 ( 9722) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 74 time to evaluate : 0.764 Fit side-chains REVERT: A 155 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.6740 (tm-30) REVERT: A 340 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.7374 (mmmt) REVERT: A 498 LYS cc_start: 0.7082 (mttt) cc_final: 0.6527 (mptt) REVERT: B 86 GLU cc_start: 0.7422 (tp30) cc_final: 0.6336 (mm-30) REVERT: B 93 GLN cc_start: 0.7147 (OUTLIER) cc_final: 0.6832 (mp10) REVERT: B 148 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.7080 (tt0) REVERT: D 438 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7119 (mp) outliers start: 26 outliers final: 15 residues processed: 94 average time/residue: 1.2716 time to fit residues: 128.0298 Evaluate side-chains 94 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 441 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 29 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 14 optimal weight: 0.4980 chunk 87 optimal weight: 8.9990 chunk 53 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 0 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN C 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.180490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.130796 restraints weight = 7208.073| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.88 r_work: 0.3193 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7207 Z= 0.163 Angle : 0.545 11.752 9722 Z= 0.277 Chirality : 0.042 0.178 1132 Planarity : 0.003 0.049 1265 Dihedral : 6.191 59.953 988 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.49 % Allowed : 34.88 % Favored : 61.63 % 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: 0.49 (0.28), residues: 913 helix: 1.81 (0.25), residues: 394 sheet: -0.37 (0.44), residues: 131 loop : -0.99 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 126 HIS 0.004 0.001 HIS B 136 PHE 0.010 0.001 PHE A 503 TYR 0.014 0.001 TYR A 243 ARG 0.005 0.000 ARG A 578 Details of bonding type rmsd hydrogen bonds : bond 0.04465 ( 383) hydrogen bonds : angle 4.34670 ( 1113) covalent geometry : bond 0.00395 ( 7207) covalent geometry : angle 0.54501 ( 9722) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6805.37 seconds wall clock time: 120 minutes 47.39 seconds (7247.39 seconds total)