Starting phenix.real_space_refine on Wed Aug 5 04:18:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vb8_43116/08_2026/8vb8_43116.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vb8_43116/08_2026/8vb8_43116.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vb8_43116/08_2026/8vb8_43116.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vb8_43116/08_2026/8vb8_43116.map" model { file = "/net/cci-nas-00/data/ceres_data/8vb8_43116/08_2026/8vb8_43116.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vb8_43116/08_2026/8vb8_43116.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 40 5.49 5 Mg 2 5.21 5 S 13 5.16 5 C 5380 2.51 5 N 1416 2.21 5 O 1660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8511 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4480 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 553, 4473 Classifications: {'peptide': 553} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 515} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 553, 4473 Classifications: {'peptide': 553} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 515} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 4582 Chain: "B" Number of atoms: 3238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3238 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 29, 'TRANS': 368} Chain breaks: 2 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "F" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 761 Classifications: {'DNA': 35, 'RNA': 2} Modifications used: {'rna3p': 2} Link IDs: {'rna3p': 36} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 2, 'DTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.75, per 1000 atoms: 0.32 Number of scatterers: 8511 At special positions: 0 Unit cell: (79.2, 96.525, 124.575, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 13 16.00 P 40 15.00 Mg 2 11.99 O 1660 8.00 N 1416 7.00 C 5380 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: 0.89 Conformation dependent library (CDL) restraints added in 436.9 milliseconds 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1796 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 36.8% alpha, 14.1% beta 13 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 27 through 44 removed outlier: 3.699A pdb=" N GLU A 40 " --> pdb=" O GLU A 36 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A 42 " --> pdb=" O CYS A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 removed outlier: 3.585A pdb=" N ARG A 83 " --> pdb=" O GLU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 114 through 118 Processing helix chain 'A' and resid 121 through 125 Processing helix chain 'A' and resid 155 through 175 Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 194 through 211 Processing helix chain 'A' and resid 217 through 221 removed outlier: 3.615A pdb=" N HIS A 221 " --> pdb=" O ASP A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 268 removed outlier: 3.512A pdb=" N GLN A 258 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 282 removed outlier: 3.647A pdb=" N LEU A 282 " --> pdb=" O GLN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 310 Processing helix chain 'A' and resid 363 through 384 removed outlier: 3.640A pdb=" N VAL A 381 " --> pdb=" O THR A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 403 Processing helix chain 'A' and resid 475 through 488 Processing helix chain 'A' and resid 499 through 508 removed outlier: 4.130A pdb=" N LEU A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 528 removed outlier: 3.637A pdb=" N LYS A 527 " --> pdb=" O GLU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 552 Processing helix chain 'B' and resid 27 through 33 Processing helix chain 'B' and resid 34 through 44 Processing helix chain 'B' and resid 77 through 85 removed outlier: 4.058A pdb=" N GLN B 85 " --> pdb=" O ASN B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 125 removed outlier: 3.507A pdb=" N ARG B 125 " --> pdb=" O GLU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 Processing helix chain 'B' and resid 154 through 160 removed outlier: 4.037A pdb=" N ALA B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 168 removed outlier: 6.029A pdb=" N LYS B 166 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 194 through 213 removed outlier: 3.629A pdb=" N THR B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU B 205 " --> pdb=" O LYS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 239 removed outlier: 3.836A pdb=" N TRP B 239 " --> pdb=" O PRO B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 271 removed outlier: 4.123A pdb=" N GLN B 269 " --> pdb=" O ASN B 265 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE B 270 " --> pdb=" O TRP B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 312 removed outlier: 3.612A pdb=" N GLU B 312 " --> pdb=" O GLU B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 383 Processing helix chain 'B' and resid 394 through 406 removed outlier: 3.530A pdb=" N THR B 400 " --> pdb=" O GLU B 396 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TRP B 401 " --> pdb=" O THR B 397 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N THR B 403 " --> pdb=" O GLU B 399 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLU B 404 " --> pdb=" O THR B 400 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR B 405 " --> pdb=" O TRP B 401 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 64 Processing sheet with id=AA3, first strand: chain 'A' and resid 105 through 110 Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 229 Processing sheet with id=AA5, first strand: chain 'A' and resid 252 through 253 removed outlier: 4.175A pdb=" N TRP A 252 " --> pdb=" O ILE A 293 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 347 through 354 removed outlier: 8.611A pdb=" N ASN A 348 " --> pdb=" O GLN A 343 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLN A 343 " --> pdb=" O ASN A 348 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A 329 " --> pdb=" O LYS A 390 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 Processing sheet with id=AA8, first strand: chain 'A' and resid 439 through 441 Processing sheet with id=AA9, first strand: chain 'A' and resid 443 through 446 Processing sheet with id=AB1, first strand: chain 'B' and resid 47 through 49 Processing sheet with id=AB2, first strand: chain 'B' and resid 60 through 64 Processing sheet with id=AB3, first strand: chain 'B' and resid 105 through 110 removed outlier: 3.861A pdb=" N SER B 105 " --> pdb=" O SER B 191 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 329 through 331 removed outlier: 7.204A pdb=" N GLN B 343 " --> pdb=" O ASN B 348 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N ASN B 348 " --> pdb=" O GLN B 343 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 389 through 391 removed outlier: 6.218A pdb=" N PHE B 389 " --> pdb=" O GLU B 415 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 288 hydrogen bonds defined for protein. 798 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 1.69 Time building geometry restraints manager: 1.12 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: 2152 1.33 - 1.45: 1739 1.45 - 1.57: 4818 1.57 - 1.69: 79 1.69 - 1.80: 23 Bond restraints: 8811 Sorted by residual: bond pdb=" C1' DTP A 701 " pdb=" N9 DTP A 701 " ideal model delta sigma weight residual 1.457 1.408 0.049 1.20e-02 6.94e+03 1.64e+01 bond pdb=" O2B DTP A 701 " pdb=" PB DTP A 701 " ideal model delta sigma weight residual 1.529 1.460 0.069 2.20e-02 2.07e+03 9.98e+00 bond pdb=" O3' DG F 32 " pdb=" P DG F 33 " ideal model delta sigma weight residual 1.607 1.569 0.038 1.20e-02 6.94e+03 9.86e+00 bond pdb=" N ILE B 94 " pdb=" CA ILE B 94 " ideal model delta sigma weight residual 1.461 1.499 -0.038 1.23e-02 6.61e+03 9.48e+00 bond pdb=" N ILE A 135 " pdb=" CA ILE A 135 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.30e+00 ... (remaining 8806 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 11748 1.71 - 3.43: 330 3.43 - 5.14: 54 5.14 - 6.86: 14 6.86 - 8.57: 5 Bond angle restraints: 12151 Sorted by residual: angle pdb=" PB DTP A 701 " pdb=" O3B DTP A 701 " pdb=" PG DTP A 701 " ideal model delta sigma weight residual 139.87 134.07 5.80 1.00e+00 1.00e+00 3.36e+01 angle pdb=" O4' DG F 31 " pdb=" C4' DG F 31 " pdb=" C3' DG F 31 " ideal model delta sigma weight residual 106.00 103.04 2.96 6.00e-01 2.78e+00 2.43e+01 angle pdb=" N3 DT F 13 " pdb=" C4 DT F 13 " pdb=" O4 DT F 13 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT F 8 " pdb=" C4 DT F 8 " pdb=" O4 DT F 8 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" CA GLU A 297 " pdb=" CB GLU A 297 " pdb=" CG GLU A 297 " ideal model delta sigma weight residual 114.10 122.45 -8.35 2.00e+00 2.50e-01 1.74e+01 ... (remaining 12146 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.61: 4683 30.61 - 61.22: 462 61.22 - 91.83: 30 91.83 - 122.44: 0 122.44 - 153.06: 1 Dihedral angle restraints: 5176 sinusoidal: 2393 harmonic: 2783 Sorted by residual: dihedral pdb=" CA PRO A 420 " pdb=" C PRO A 420 " pdb=" N PRO A 421 " pdb=" CA PRO A 421 " ideal model delta harmonic sigma weight residual -180.00 -156.77 -23.23 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" O1B DTP A 701 " pdb=" O3B DTP A 701 " pdb=" PB DTP A 701 " pdb=" PG DTP A 701 " ideal model delta sinusoidal sigma weight residual 299.93 146.87 153.06 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" C ILE B 94 " pdb=" N ILE B 94 " pdb=" CA ILE B 94 " pdb=" CB ILE B 94 " ideal model delta harmonic sigma weight residual -122.00 -131.06 9.06 0 2.50e+00 1.60e-01 1.31e+01 ... (remaining 5173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 1293 0.106 - 0.211: 39 0.211 - 0.317: 1 0.317 - 0.422: 0 0.422 - 0.528: 1 Chirality restraints: 1334 Sorted by residual: chirality pdb=" P DT F 17 " pdb=" OP1 DT F 17 " pdb=" OP2 DT F 17 " pdb=" O5' DT F 17 " both_signs ideal model delta sigma weight residual True 2.34 -2.86 -0.53 2.00e-01 2.50e+01 6.96e+00 chirality pdb=" CB ILE B 94 " pdb=" CA ILE B 94 " pdb=" CG1 ILE B 94 " pdb=" CG2 ILE B 94 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA ILE A 135 " pdb=" N ILE A 135 " pdb=" C ILE A 135 " pdb=" CB ILE A 135 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.57e-01 ... (remaining 1331 not shown) Planarity restraints: 1399 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 419 " -0.064 5.00e-02 4.00e+02 9.58e-02 1.47e+01 pdb=" N PRO A 420 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO A 420 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 420 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 420 " -0.045 5.00e-02 4.00e+02 6.73e-02 7.24e+00 pdb=" N PRO A 421 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 421 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 421 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 414 " -0.018 2.00e-02 2.50e+03 1.52e-02 5.74e+00 pdb=" CG TRP A 414 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP A 414 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 414 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 414 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 414 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 414 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 414 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 414 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 414 " -0.003 2.00e-02 2.50e+03 ... (remaining 1396 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 91 2.60 - 3.17: 6694 3.17 - 3.75: 13546 3.75 - 4.32: 18910 4.32 - 4.90: 30801 Nonbonded interactions: 70042 Sorted by model distance: nonbonded pdb=" OD1 ASP A 110 " pdb="MG MG A 702 " model vdw 2.019 2.170 nonbonded pdb=" O VAL A 111 " pdb="MG MG A 702 " model vdw 2.119 2.170 nonbonded pdb=" O THR A 439 " pdb=" OG1 THR A 459 " model vdw 2.241 3.040 nonbonded pdb=" O VAL B 372 " pdb=" OG1 THR B 376 " model vdw 2.253 3.040 nonbonded pdb=" OG SER A 280 " pdb=" O3' DC F 7 " model vdw 2.254 3.040 ... (remaining 70037 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 ========== 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=0.50 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: 5.280 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.790 Find NCS groups from input model: 0.040 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:8.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 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 : 0.005 0.086 8811 Z= 0.287 Angle : 0.694 8.573 12151 Z= 0.445 Chirality : 0.048 0.528 1334 Planarity : 0.006 0.096 1399 Dihedral : 21.076 153.056 3380 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.20 % Favored : 94.59 % Rotamer: Outliers : 4.88 % Allowed : 32.02 % Favored : 63.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.28), residues: 944 helix: 0.26 (0.31), residues: 317 sheet: -0.95 (0.38), residues: 188 loop : -1.26 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 277 TYR 0.020 0.001 TYR B 354 PHE 0.010 0.001 PHE B 87 TRP 0.041 0.001 TRP A 414 HIS 0.003 0.001 HIS A 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.29 ( 8811) covalent geometry : angle 0.69390 / 0.45 (12151) hydrogen bonds : bond 0.19058 / 12.75 ( 324) hydrogen bonds : angle 6.67212 / 4.65 ( 870) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 62 time to evaluate : 0.326 Fit side-chains outliers start: 41 outliers final: 36 residues processed: 102 average time/residue: 0.5054 time to fit residues: 55.6440 Evaluate side-chains 97 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 61 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 TRP Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 422 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.0170 chunk 51 optimal weight: 0.0170 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 GLN ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.116762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.080441 restraints weight = 19306.472| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 3.04 r_work: 0.2962 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.0697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 8811 Z= 0.142 Angle : 0.581 8.586 12151 Z= 0.314 Chirality : 0.043 0.158 1334 Planarity : 0.005 0.090 1399 Dihedral : 17.220 160.661 1472 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.30 % Favored : 94.49 % Rotamer: Outliers : 4.29 % Allowed : 31.31 % Favored : 64.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.28), residues: 944 helix: 0.70 (0.31), residues: 316 sheet: -0.82 (0.39), residues: 182 loop : -1.18 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 277 TYR 0.028 0.001 TYR A 457 PHE 0.016 0.001 PHE B 87 TRP 0.025 0.001 TRP A 414 HIS 0.004 0.001 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 8811) covalent geometry : angle 0.58113 / 0.31 (12151) hydrogen bonds : bond 0.04436 / 2.90 ( 324) hydrogen bonds : angle 4.88898 / 3.45 ( 870) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 75 time to evaluate : 0.340 Fit side-chains REVERT: A 535 TRP cc_start: 0.8229 (t60) cc_final: 0.7607 (t60) REVERT: B 353 LYS cc_start: 0.8998 (tttp) cc_final: 0.8415 (ttpp) outliers start: 36 outliers final: 20 residues processed: 110 average time/residue: 0.4870 time to fit residues: 57.9017 Evaluate side-chains 83 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 TRP Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 422 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 18 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 53 optimal weight: 0.0770 chunk 76 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 480 GLN ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.114763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.078791 restraints weight = 16072.589| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.75 r_work: 0.2942 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2952 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 8811 Z= 0.225 Angle : 0.592 7.539 12151 Z= 0.318 Chirality : 0.044 0.169 1334 Planarity : 0.005 0.082 1399 Dihedral : 17.114 154.062 1443 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.62 % Favored : 94.17 % Rotamer: Outliers : 3.93 % Allowed : 31.07 % Favored : 65.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.28), residues: 944 helix: 0.81 (0.31), residues: 323 sheet: -0.83 (0.38), residues: 188 loop : -1.22 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 358 TYR 0.034 0.001 TYR A 457 PHE 0.014 0.002 PHE B 61 TRP 0.015 0.001 TRP A 414 HIS 0.003 0.001 HIS A 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.23 ( 8811) covalent geometry : angle 0.59202 / 0.32 (12151) hydrogen bonds : bond 0.04082 / 2.69 ( 324) hydrogen bonds : angle 4.54837 / 3.23 ( 870) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 62 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: A 358 ARG cc_start: 0.8469 (mtp85) cc_final: 0.8058 (mtp85) REVERT: A 535 TRP cc_start: 0.8378 (t60) cc_final: 0.7751 (t60) REVERT: B 305 GLU cc_start: 0.9135 (tp30) cc_final: 0.8921 (tp30) REVERT: B 353 LYS cc_start: 0.9045 (tttp) cc_final: 0.8459 (ttpp) outliers start: 33 outliers final: 22 residues processed: 92 average time/residue: 0.5231 time to fit residues: 51.9078 Evaluate side-chains 81 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 TRP Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 70 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 GLN ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 HIS ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN B 336 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.114767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.078494 restraints weight = 18231.648| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.96 r_work: 0.2932 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2941 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2941 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 8811 Z= 0.194 Angle : 0.571 7.085 12151 Z= 0.306 Chirality : 0.043 0.163 1334 Planarity : 0.005 0.075 1399 Dihedral : 17.027 150.813 1437 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.62 % Favored : 94.17 % Rotamer: Outliers : 4.29 % Allowed : 31.19 % Favored : 64.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.28), residues: 944 helix: 0.94 (0.31), residues: 318 sheet: -0.73 (0.40), residues: 172 loop : -1.15 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 83 TYR 0.013 0.001 TYR B 354 PHE 0.014 0.001 PHE B 87 TRP 0.014 0.001 TRP A 414 HIS 0.003 0.001 HIS A 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 ( 8811) covalent geometry : angle 0.57058 / 0.31 (12151) hydrogen bonds : bond 0.03693 / 2.42 ( 324) hydrogen bonds : angle 4.38198 / 3.14 ( 870) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 58 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 535 TRP cc_start: 0.8351 (t60) cc_final: 0.7716 (t60) REVERT: B 270 ILE cc_start: 0.8648 (tt) cc_final: 0.8183 (pt) REVERT: B 334 GLN cc_start: 0.8826 (mp10) cc_final: 0.8512 (mp10) REVERT: B 336 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8089 (mp10) REVERT: B 353 LYS cc_start: 0.9042 (tttp) cc_final: 0.8426 (ttpp) outliers start: 36 outliers final: 21 residues processed: 92 average time/residue: 0.4944 time to fit residues: 49.3839 Evaluate side-chains 75 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 53 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 TRP Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 25 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 GLN ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN B 336 GLN B 418 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.113123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.074680 restraints weight = 25020.010| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.53 r_work: 0.2832 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 8811 Z= 0.271 Angle : 0.603 6.940 12151 Z= 0.322 Chirality : 0.044 0.160 1334 Planarity : 0.005 0.068 1399 Dihedral : 17.035 149.216 1436 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.15 % Favored : 93.64 % Rotamer: Outliers : 3.93 % Allowed : 31.31 % Favored : 64.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.28), residues: 944 helix: 0.82 (0.31), residues: 324 sheet: -0.74 (0.39), residues: 177 loop : -1.20 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 83 TYR 0.033 0.001 TYR A 457 PHE 0.013 0.001 PHE A 61 TRP 0.017 0.001 TRP A 414 HIS 0.003 0.001 HIS A 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00630 / 0.27 ( 8811) covalent geometry : angle 0.60274 / 0.32 (12151) hydrogen bonds : bond 0.03871 / 2.56 ( 324) hydrogen bonds : angle 4.39478 / 3.14 ( 870) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 53 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 484 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9112 (tp) REVERT: A 535 TRP cc_start: 0.8413 (t60) cc_final: 0.7719 (t60) REVERT: B 270 ILE cc_start: 0.8598 (tt) cc_final: 0.8151 (pt) REVERT: B 353 LYS cc_start: 0.9081 (tttp) cc_final: 0.8458 (ttpp) outliers start: 33 outliers final: 23 residues processed: 85 average time/residue: 0.4786 time to fit residues: 44.2649 Evaluate side-chains 77 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 53 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 24 TRP Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 38 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 9 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 69 optimal weight: 0.0170 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN B 418 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.121679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.081617 restraints weight = 18561.569| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.00 r_work: 0.2939 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 8811 Z= 0.138 Angle : 0.556 7.195 12151 Z= 0.299 Chirality : 0.042 0.149 1334 Planarity : 0.005 0.059 1399 Dihedral : 16.909 145.494 1434 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.20 % Favored : 94.59 % Rotamer: Outliers : 4.05 % Allowed : 30.95 % Favored : 65.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.28), residues: 944 helix: 1.08 (0.31), residues: 318 sheet: -0.66 (0.40), residues: 166 loop : -1.08 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 358 TYR 0.032 0.001 TYR A 457 PHE 0.013 0.001 PHE B 87 TRP 0.016 0.001 TRP A 414 HIS 0.003 0.001 HIS A 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 8811) covalent geometry : angle 0.55610 / 0.30 (12151) hydrogen bonds : bond 0.03375 / 2.19 ( 324) hydrogen bonds : angle 4.22441 / 3.03 ( 870) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 60 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 373 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.6938 (mp10) REVERT: A 535 TRP cc_start: 0.8364 (t60) cc_final: 0.7655 (t60) REVERT: B 270 ILE cc_start: 0.8669 (tt) cc_final: 0.8242 (pt) REVERT: B 353 LYS cc_start: 0.9039 (tttp) cc_final: 0.8520 (ttmm) outliers start: 34 outliers final: 20 residues processed: 92 average time/residue: 0.4802 time to fit residues: 48.0305 Evaluate side-chains 77 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 56 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 TRP Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 35 optimal weight: 2.9990 chunk 71 optimal weight: 0.4980 chunk 33 optimal weight: 0.1980 chunk 70 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 80 optimal weight: 0.0030 chunk 96 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.122168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.082174 restraints weight = 18396.289| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.00 r_work: 0.2949 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8811 Z= 0.134 Angle : 0.555 7.540 12151 Z= 0.296 Chirality : 0.042 0.144 1334 Planarity : 0.004 0.052 1399 Dihedral : 16.719 142.504 1429 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.41 % Favored : 94.49 % Rotamer: Outliers : 3.69 % Allowed : 30.95 % Favored : 65.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.28), residues: 944 helix: 1.15 (0.31), residues: 316 sheet: -0.58 (0.40), residues: 165 loop : -1.09 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 358 TYR 0.040 0.001 TYR A 457 PHE 0.009 0.001 PHE B 87 TRP 0.013 0.001 TRP A 414 HIS 0.003 0.001 HIS A 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 8811) covalent geometry : angle 0.55453 / 0.30 (12151) hydrogen bonds : bond 0.03229 / 2.10 ( 324) hydrogen bonds : angle 4.13645 / 2.97 ( 870) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 56 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 373 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.6988 (mp10) REVERT: A 535 TRP cc_start: 0.8387 (t60) cc_final: 0.7766 (t60) REVERT: B 353 LYS cc_start: 0.9017 (tttp) cc_final: 0.8510 (ttmm) outliers start: 31 outliers final: 20 residues processed: 85 average time/residue: 0.5265 time to fit residues: 48.5179 Evaluate side-chains 75 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 54 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 TRP Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 19 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 56 optimal weight: 0.8980 chunk 63 optimal weight: 8.9990 chunk 95 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.114840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.078661 restraints weight = 17837.395| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.91 r_work: 0.2917 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8811 Z= 0.180 Angle : 0.562 7.726 12151 Z= 0.299 Chirality : 0.043 0.143 1334 Planarity : 0.004 0.048 1399 Dihedral : 16.717 141.259 1429 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.73 % Favored : 94.17 % Rotamer: Outliers : 3.10 % Allowed : 31.55 % Favored : 65.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.28), residues: 944 helix: 1.16 (0.31), residues: 316 sheet: -0.66 (0.39), residues: 172 loop : -1.07 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 358 TYR 0.032 0.001 TYR A 457 PHE 0.012 0.001 PHE B 87 TRP 0.029 0.001 TRP A 414 HIS 0.003 0.001 HIS A 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 ( 8811) covalent geometry : angle 0.56192 / 0.30 (12151) hydrogen bonds : bond 0.03311 / 2.17 ( 324) hydrogen bonds : angle 4.13894 / 2.98 ( 870) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 56 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 373 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.6985 (mp10) REVERT: A 535 TRP cc_start: 0.8456 (t60) cc_final: 0.7858 (t60) REVERT: B 270 ILE cc_start: 0.8795 (tt) cc_final: 0.8400 (pt) REVERT: B 353 LYS cc_start: 0.9024 (tttp) cc_final: 0.8533 (ttmm) outliers start: 26 outliers final: 20 residues processed: 80 average time/residue: 0.4915 time to fit residues: 42.3876 Evaluate side-chains 75 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 54 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 TRP Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 59 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 58 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 21 optimal weight: 0.0770 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 GLN ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.116200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.078145 restraints weight = 18060.845| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 3.10 r_work: 0.2921 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2936 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2936 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8811 Z= 0.141 Angle : 0.553 8.262 12151 Z= 0.293 Chirality : 0.042 0.136 1334 Planarity : 0.004 0.053 1399 Dihedral : 16.634 136.927 1428 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.20 % Favored : 94.70 % Rotamer: Outliers : 2.62 % Allowed : 31.90 % Favored : 65.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.28), residues: 944 helix: 1.30 (0.31), residues: 313 sheet: -0.58 (0.40), residues: 165 loop : -1.02 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 358 TYR 0.033 0.001 TYR A 457 PHE 0.008 0.001 PHE A 160 TRP 0.029 0.001 TRP A 414 HIS 0.003 0.001 HIS A 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 8811) covalent geometry : angle 0.55305 / 0.29 (12151) hydrogen bonds : bond 0.03118 / 2.03 ( 324) hydrogen bonds : angle 4.06670 / 2.92 ( 870) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 56 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 357 MET cc_start: 0.8712 (mmt) cc_final: 0.8469 (mmm) REVERT: A 373 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.6997 (mp10) REVERT: A 535 TRP cc_start: 0.8452 (t60) cc_final: 0.7867 (t60) REVERT: A 536 VAL cc_start: 0.8519 (OUTLIER) cc_final: 0.8281 (p) REVERT: B 193 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8540 (pp) REVERT: B 353 LYS cc_start: 0.9016 (tttp) cc_final: 0.8521 (ttmm) outliers start: 22 outliers final: 16 residues processed: 76 average time/residue: 0.5041 time to fit residues: 41.4107 Evaluate side-chains 75 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 TRP Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 46 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 74 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 91 optimal weight: 0.0670 chunk 77 optimal weight: 7.9990 chunk 89 optimal weight: 0.5980 chunk 40 optimal weight: 0.2980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 GLN B 269 GLN B 336 GLN B 418 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.116851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.077752 restraints weight = 24991.353| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 3.65 r_work: 0.2892 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2918 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8811 Z= 0.130 Angle : 0.541 8.306 12151 Z= 0.287 Chirality : 0.042 0.135 1334 Planarity : 0.004 0.059 1399 Dihedral : 16.508 130.796 1428 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.98 % Favored : 94.91 % Rotamer: Outliers : 2.74 % Allowed : 31.67 % Favored : 65.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.28), residues: 944 helix: 1.44 (0.31), residues: 313 sheet: -0.61 (0.39), residues: 175 loop : -1.03 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 358 TYR 0.034 0.001 TYR A 457 PHE 0.020 0.001 PHE B 87 TRP 0.027 0.001 TRP A 414 HIS 0.003 0.001 HIS A 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 8811) covalent geometry : angle 0.54142 / 0.29 (12151) hydrogen bonds : bond 0.02952 / 1.93 ( 324) hydrogen bonds : angle 3.99109 / 2.87 ( 870) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 60 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 357 MET cc_start: 0.8754 (mmt) cc_final: 0.8500 (mmm) REVERT: A 373 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7024 (mp10) REVERT: A 535 TRP cc_start: 0.8444 (t60) cc_final: 0.7846 (t60) REVERT: A 536 VAL cc_start: 0.8504 (OUTLIER) cc_final: 0.8199 (m) REVERT: B 193 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8518 (pp) REVERT: B 353 LYS cc_start: 0.9008 (tttp) cc_final: 0.8470 (ttmm) outliers start: 23 outliers final: 16 residues processed: 81 average time/residue: 0.4970 time to fit residues: 43.2897 Evaluate side-chains 76 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 TRP Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 94 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 77 optimal weight: 0.0670 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 56 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.6722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.115889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.080073 restraints weight = 17422.620| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.86 r_work: 0.2952 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.173 8811 Z= 0.222 Angle : 0.905 59.190 12151 Z= 0.540 Chirality : 0.046 0.700 1334 Planarity : 0.004 0.060 1399 Dihedral : 16.513 130.779 1427 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.88 % Favored : 95.02 % Rotamer: Outliers : 2.38 % Allowed : 32.26 % Favored : 65.36 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.28), residues: 944 helix: 1.44 (0.31), residues: 313 sheet: -0.61 (0.39), residues: 175 loop : -1.02 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 358 TYR 0.033 0.001 TYR A 457 PHE 0.011 0.001 PHE B 87 TRP 0.024 0.001 TRP A 414 HIS 0.003 0.001 HIS A 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.22 ( 8811) covalent geometry : angle 0.90475 / 0.54 (12151) hydrogen bonds : bond 0.02966 / 1.94 ( 324) hydrogen bonds : angle 3.98944 / 2.87 ( 870) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2797.15 seconds wall clock time: 48 minutes 30.76 seconds (2910.76 seconds total)