Starting phenix.real_space_refine on Thu Jul 2 11:36:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vb8_43116/07_2026/8vb8_43116.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vb8_43116/07_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_43116/07_2026/8vb8_43116.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vb8_43116/07_2026/8vb8_43116.map" model { file = "/net/cci-nas-00/data/ceres_data/8vb8_43116/07_2026/8vb8_43116.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vb8_43116/07_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-dev-6108/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: 2.61, per 1000 atoms: 0.31 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: 0.94 Conformation dependent library (CDL) restraints added in 443.1 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: 1.07 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: 1.40 Time building geometry restraints manager: 1.13 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=" 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 bond pdb=" CA SER A 134 " pdb=" CB SER A 134 " ideal model delta sigma weight residual 1.535 1.490 0.045 1.51e-02 4.39e+03 8.75e+00 ... (remaining 8806 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 11749 1.71 - 3.43: 329 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: 4.100 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: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.840 Find NCS groups from input model: 0.040 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:6.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.040 ------------------------------------------------------------------------------- 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= 0.286 Angle : 0.693 8.573 12151 Z= 0.444 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 0.69304 / 0.44 (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 : 0.324 Fit side-chains outliers start: 41 outliers final: 36 residues processed: 102 average time/residue: 0.4713 time to fit residues: 51.8462 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 : 0.324 ------------------------------------------------------------------------------- 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 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 = 0.3699 r_free = 0.3699 target = 0.116805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.078845 restraints weight = 19356.225| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 3.23 r_work: 0.2928 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.0701 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 : 0.579 8.632 12151 Z= 0.314 Chirality : 0.043 0.159 1334 Planarity : 0.005 0.089 1399 Dihedral : 17.242 161.116 1472 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.30 % Favored : 94.49 % Rotamer: Outliers : 4.40 % Allowed : 31.31 % Favored : 64.29 % 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: -0.73 (0.28), residues: 944 helix: 0.71 (0.31), residues: 316 sheet: -0.81 (0.39), residues: 182 loop : -1.19 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 277 TYR 0.029 0.001 TYR A 457 PHE 0.017 0.001 PHE B 87 TRP 0.024 0.001 TRP A 414 HIS 0.004 0.001 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 8811) covalent geometry : angle 0.57934 / 0.31 (12151) hydrogen bonds : bond 0.04329 / 2.83 ( 324) hydrogen bonds : angle 4.88197 / 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 112 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 75 time to evaluate : 0.321 Fit side-chains REVERT: A 358 ARG cc_start: 0.8405 (mtp85) cc_final: 0.7976 (mtp85) REVERT: A 535 TRP cc_start: 0.8179 (t60) cc_final: 0.7564 (t60) REVERT: B 186 ASP cc_start: 0.7291 (m-30) cc_final: 0.7087 (m-30) REVERT: B 353 LYS cc_start: 0.9009 (tttp) cc_final: 0.8417 (ttpp) outliers start: 37 outliers final: 21 residues processed: 111 average time/residue: 0.4804 time to fit residues: 57.5744 Evaluate side-chains 85 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 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 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 202 ILE 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: 2.9990 chunk 82 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.3692 r_free = 0.3692 target = 0.114853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.078644 restraints weight = 16165.198| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.78 r_work: 0.2939 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 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 = 0.2954 r_free = 0.2954 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: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 8811 Z= 0.224 Angle : 0.592 7.563 12151 Z= 0.318 Chirality : 0.044 0.165 1334 Planarity : 0.005 0.082 1399 Dihedral : 17.124 154.457 1445 Min Nonbonded Distance : 2.043 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: -0.68 (0.28), residues: 944 helix: 0.82 (0.31), residues: 324 sheet: -0.82 (0.38), residues: 188 loop : -1.22 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 358 TYR 0.034 0.001 TYR A 457 PHE 0.014 0.002 PHE B 61 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 0.00521 / 0.22 ( 8811) covalent geometry : angle 0.59200 / 0.32 (12151) hydrogen bonds : bond 0.04050 / 2.67 ( 324) hydrogen bonds : angle 4.55860 / 3.24 ( 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 : 0.268 Fit side-chains revert: symmetry clash REVERT: A 358 ARG cc_start: 0.8463 (mtp85) cc_final: 0.8081 (mtp85) REVERT: A 535 TRP cc_start: 0.8353 (t60) cc_final: 0.7729 (t60) REVERT: B 186 ASP cc_start: 0.7335 (m-30) cc_final: 0.7116 (m-30) REVERT: B 305 GLU cc_start: 0.9130 (tp30) cc_final: 0.8921 (tp30) REVERT: B 334 GLN cc_start: 0.8852 (mp10) cc_final: 0.8530 (mp10) REVERT: B 353 LYS cc_start: 0.9046 (tttp) cc_final: 0.8451 (ttpp) outliers start: 33 outliers final: 23 residues processed: 92 average time/residue: 0.4834 time to fit residues: 48.0151 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 : 0.353 ------------------------------------------------------------------------------- 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 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 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: 0.0870 chunk 19 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 81 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 24 optimal weight: 0.2980 chunk 1 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.123415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.083486 restraints weight = 18866.062| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 3.00 r_work: 0.2956 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 8811 Z= 0.138 Angle : 0.554 7.304 12151 Z= 0.298 Chirality : 0.042 0.156 1334 Planarity : 0.005 0.074 1399 Dihedral : 16.982 151.079 1440 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.98 % Favored : 94.80 % Rotamer: Outliers : 4.29 % Allowed : 30.95 % 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: -0.49 (0.28), residues: 944 helix: 1.04 (0.31), residues: 318 sheet: -0.75 (0.40), residues: 177 loop : -1.12 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 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 0.00308 / 0.14 ( 8811) covalent geometry : angle 0.55416 / 0.30 (12151) hydrogen bonds : bond 0.03488 / 2.26 ( 324) hydrogen bonds : angle 4.31640 / 3.09 ( 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 98 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 62 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 358 ARG cc_start: 0.8479 (mtp85) cc_final: 0.8106 (mtp85) REVERT: A 535 TRP cc_start: 0.8284 (t60) cc_final: 0.7672 (t60) REVERT: B 44 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8195 (mt-10) REVERT: B 270 ILE cc_start: 0.8599 (tt) cc_final: 0.8132 (pt) REVERT: B 334 GLN cc_start: 0.8870 (mp10) cc_final: 0.8571 (mp10) REVERT: B 336 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.8081 (mp10) REVERT: B 353 LYS cc_start: 0.9027 (tttp) cc_final: 0.8406 (ttpp) outliers start: 36 outliers final: 22 residues processed: 96 average time/residue: 0.4426 time to fit residues: 45.8183 Evaluate side-chains 78 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 55 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 442 VAL Chi-restraints excluded: chain A residue 484 LEU 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 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 418 ASN 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: 1.9990 chunk 52 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 0.0870 chunk 41 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- 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 336 GLN B 418 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.114617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.077395 restraints weight = 25354.648| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 3.44 r_work: 0.2894 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2906 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2906 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 8811 Z= 0.218 Angle : 0.579 7.034 12151 Z= 0.311 Chirality : 0.043 0.160 1334 Planarity : 0.005 0.066 1399 Dihedral : 16.943 148.475 1436 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.04 % Favored : 93.74 % Rotamer: Outliers : 4.05 % Allowed : 31.43 % 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: -0.48 (0.28), residues: 944 helix: 1.01 (0.31), residues: 318 sheet: -0.68 (0.40), residues: 172 loop : -1.12 (0.29), residues: 454 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 0.012 0.001 PHE A 160 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 0.00505 / 0.22 ( 8811) covalent geometry : angle 0.57898 / 0.31 (12151) hydrogen bonds : bond 0.03651 / 2.41 ( 324) hydrogen bonds : angle 4.29768 / 3.08 ( 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 87 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 53 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: A 373 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7102 (mp10) REVERT: A 484 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9123 (tp) REVERT: A 535 TRP cc_start: 0.8400 (t60) cc_final: 0.7893 (t60) REVERT: B 270 ILE cc_start: 0.8620 (tt) cc_final: 0.8170 (pt) REVERT: B 353 LYS cc_start: 0.9075 (tttp) cc_final: 0.8458 (ttpp) outliers start: 34 outliers final: 20 residues processed: 85 average time/residue: 0.4378 time to fit residues: 40.2975 Evaluate side-chains 76 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 54 time to evaluate : 0.204 ------------------------------------------------------------------------------- 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 258 GLN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 373 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 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 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: 2.9990 chunk 31 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 69 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3720 r_free = 0.3720 target = 0.123151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.083090 restraints weight = 18831.558| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.98 r_work: 0.2951 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 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 = 0.2963 r_free = 0.2963 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: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8811 Z= 0.140 Angle : 0.553 7.291 12151 Z= 0.296 Chirality : 0.042 0.142 1334 Planarity : 0.004 0.050 1399 Dihedral : 16.825 145.176 1432 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.20 % Favored : 94.70 % Rotamer: Outliers : 3.45 % Allowed : 31.19 % 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: -0.40 (0.28), residues: 944 helix: 1.09 (0.31), residues: 318 sheet: -0.59 (0.40), residues: 165 loop : -1.09 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 358 TYR 0.032 0.001 TYR A 457 PHE 0.013 0.001 PHE B 87 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 0.00313 / 0.14 ( 8811) covalent geometry : angle 0.55330 / 0.30 (12151) hydrogen bonds : bond 0.03321 / 2.16 ( 324) hydrogen bonds : angle 4.17766 / 3.00 ( 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 86 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 57 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 358 ARG cc_start: 0.8530 (mtp85) cc_final: 0.8080 (mtp85) REVERT: A 373 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7010 (mp10) REVERT: A 535 TRP cc_start: 0.8351 (t60) cc_final: 0.7731 (t60) REVERT: B 270 ILE cc_start: 0.8665 (tt) cc_final: 0.8234 (pt) REVERT: B 353 LYS cc_start: 0.9030 (tttp) cc_final: 0.8421 (ttpp) outliers start: 29 outliers final: 18 residues processed: 84 average time/residue: 0.4295 time to fit residues: 39.1723 Evaluate side-chains 74 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 258 GLN 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 425 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 35 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 33 optimal weight: 0.3980 chunk 70 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 340 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 = 0.3712 r_free = 0.3712 target = 0.121883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.081826 restraints weight = 18407.668| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.98 r_work: 0.2946 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 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 = 0.2958 r_free = 0.2958 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: 0.2958 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8811 Z= 0.163 Angle : 0.556 7.580 12151 Z= 0.296 Chirality : 0.042 0.141 1334 Planarity : 0.004 0.047 1399 Dihedral : 16.747 143.504 1430 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.51 % Favored : 94.38 % Rotamer: Outliers : 2.98 % Allowed : 31.55 % 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: -0.39 (0.28), residues: 944 helix: 1.12 (0.31), residues: 316 sheet: -0.63 (0.40), residues: 172 loop : -1.07 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 358 TYR 0.037 0.001 TYR A 457 PHE 0.010 0.001 PHE A 160 TRP 0.013 0.001 TRP A 24 HIS 0.003 0.001 HIS A 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 8811) covalent geometry : angle 0.55605 / 0.30 (12151) hydrogen bonds : bond 0.03308 / 2.17 ( 324) hydrogen bonds : angle 4.15802 / 2.99 ( 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 81 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 56 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 358 ARG cc_start: 0.8559 (mtp85) cc_final: 0.8127 (mtp85) REVERT: A 373 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.6992 (mp10) REVERT: A 535 TRP cc_start: 0.8392 (t60) cc_final: 0.7782 (t60) REVERT: B 270 ILE cc_start: 0.8685 (tt) cc_final: 0.8255 (pt) REVERT: B 353 LYS cc_start: 0.9026 (tttp) cc_final: 0.8427 (ttpp) outliers start: 25 outliers final: 18 residues processed: 79 average time/residue: 0.4656 time to fit residues: 39.7301 Evaluate side-chains 74 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 0.249 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 53 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 95 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 340 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 = 0.3711 r_free = 0.3711 target = 0.121807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.081742 restraints weight = 18206.730| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.98 r_work: 0.2934 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2964 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 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 = 0.2964 r_free = 0.2964 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: 0.2964 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8811 Z= 0.166 Angle : 0.551 7.785 12151 Z= 0.293 Chirality : 0.042 0.139 1334 Planarity : 0.004 0.047 1399 Dihedral : 16.712 141.747 1429 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.30 % Favored : 94.59 % Rotamer: Outliers : 3.21 % Allowed : 30.83 % Favored : 65.95 % 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: -0.37 (0.28), residues: 944 helix: 1.15 (0.31), residues: 316 sheet: -0.64 (0.39), residues: 172 loop : -1.07 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 358 TYR 0.037 0.001 TYR A 457 PHE 0.014 0.001 PHE B 87 TRP 0.013 0.001 TRP A 24 HIS 0.003 0.001 HIS A 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 ( 8811) covalent geometry : angle 0.55127 / 0.29 (12151) hydrogen bonds : bond 0.03270 / 2.14 ( 324) hydrogen bonds : angle 4.14034 / 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: 27 poor density : 55 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 373 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7007 (mp10) REVERT: A 535 TRP cc_start: 0.8414 (t60) cc_final: 0.7822 (t60) REVERT: B 270 ILE cc_start: 0.8716 (tt) cc_final: 0.8310 (pt) REVERT: B 353 LYS cc_start: 0.9020 (tttp) cc_final: 0.8508 (ttmm) outliers start: 27 outliers final: 21 residues processed: 80 average time/residue: 0.5162 time to fit residues: 44.3994 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 : 0.362 ------------------------------------------------------------------------------- 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 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 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 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: 0.9980 chunk 49 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 17 optimal weight: 0.0770 chunk 34 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 21 optimal weight: 0.1980 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.122383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.082379 restraints weight = 18303.151| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.98 r_work: 0.2945 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2975 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8811 Z= 0.139 Angle : 0.548 8.407 12151 Z= 0.292 Chirality : 0.042 0.138 1334 Planarity : 0.004 0.050 1399 Dihedral : 16.664 138.945 1429 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.20 % Favored : 94.70 % Rotamer: Outliers : 2.62 % Allowed : 31.67 % Favored : 65.71 % 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: -0.36 (0.28), residues: 944 helix: 1.23 (0.31), residues: 316 sheet: -0.63 (0.39), residues: 175 loop : -1.12 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 83 TYR 0.032 0.001 TYR A 457 PHE 0.009 0.001 PHE A 160 TRP 0.013 0.001 TRP A 24 HIS 0.003 0.001 HIS A 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 8811) covalent geometry : angle 0.54837 / 0.29 (12151) hydrogen bonds : bond 0.03150 / 2.05 ( 324) hydrogen bonds : angle 4.08686 / 2.94 ( 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 76 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 54 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 373 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7039 (mp10) REVERT: A 535 TRP cc_start: 0.8427 (t60) cc_final: 0.7779 (t60) REVERT: B 270 ILE cc_start: 0.8710 (tt) cc_final: 0.8307 (pt) REVERT: B 353 LYS cc_start: 0.9000 (tttp) cc_final: 0.8488 (ttmm) outliers start: 22 outliers final: 18 residues processed: 74 average time/residue: 0.5199 time to fit residues: 41.4045 Evaluate side-chains 73 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 54 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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: 1.9990 chunk 81 optimal weight: 0.0970 chunk 70 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 90 optimal weight: 0.4980 chunk 61 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 77 optimal weight: 0.0770 chunk 89 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 GLN B 269 GLN B 418 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.116667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.078227 restraints weight = 25167.831| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 3.61 r_work: 0.2930 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2952 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 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 = 0.2952 r_free = 0.2952 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: 0.2952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8811 Z= 0.126 Angle : 0.544 8.552 12151 Z= 0.289 Chirality : 0.042 0.144 1334 Planarity : 0.004 0.054 1399 Dihedral : 16.569 133.767 1428 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.98 % Favored : 94.91 % Rotamer: Outliers : 2.62 % Allowed : 31.67 % Favored : 65.71 % 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: -0.20 (0.28), residues: 944 helix: 1.37 (0.31), residues: 313 sheet: -0.56 (0.39), residues: 175 loop : -1.02 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 358 TYR 0.043 0.001 TYR B 354 PHE 0.017 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 0.00276 / 0.13 ( 8811) covalent geometry : angle 0.54412 / 0.29 (12151) hydrogen bonds : bond 0.03016 / 1.95 ( 324) hydrogen bonds : angle 4.03186 / 2.90 ( 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 80 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 357 MET cc_start: 0.8761 (mmt) cc_final: 0.8519 (mmm) REVERT: A 373 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7073 (mp10) REVERT: A 535 TRP cc_start: 0.8413 (t60) cc_final: 0.7732 (t60) REVERT: A 536 VAL cc_start: 0.8530 (OUTLIER) cc_final: 0.8190 (m) REVERT: B 193 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8525 (pp) REVERT: B 353 LYS cc_start: 0.8988 (tttp) cc_final: 0.8470 (ttmm) REVERT: B 354 TYR cc_start: 0.7654 (t80) cc_final: 0.7405 (t80) outliers start: 22 outliers final: 16 residues processed: 78 average time/residue: 0.5318 time to fit residues: 44.7458 Evaluate side-chains 72 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 53 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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 280 SER Chi-restraints excluded: chain A residue 317 VAL 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 94 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 59 optimal weight: 0.0980 chunk 6 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 77 optimal weight: 0.0060 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 0.1980 chunk 56 optimal weight: 0.7980 chunk 90 optimal weight: 0.0970 chunk 52 optimal weight: 0.9980 overall best weight: 0.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 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 = 0.3710 r_free = 0.3710 target = 0.116743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.079533 restraints weight = 18684.088| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.13 r_work: 0.2946 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 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 = 0.2960 r_free = 0.2960 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: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8811 Z= 0.116 Angle : 0.549 8.911 12151 Z= 0.291 Chirality : 0.041 0.138 1334 Planarity : 0.004 0.059 1399 Dihedral : 16.459 127.884 1427 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.88 % Favored : 95.02 % Rotamer: Outliers : 2.50 % Allowed : 31.90 % 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: -0.09 (0.28), residues: 944 helix: 1.50 (0.31), residues: 307 sheet: -0.48 (0.39), residues: 175 loop : -0.95 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 83 TYR 0.035 0.001 TYR B 354 PHE 0.015 0.001 PHE B 116 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 0.00250 / 0.12 ( 8811) covalent geometry : angle 0.54946 / 0.29 (12151) hydrogen bonds : bond 0.02913 / 1.88 ( 324) hydrogen bonds : angle 4.00464 / 2.87 ( 870) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2807.69 seconds wall clock time: 48 minutes 46.52 seconds (2926.52 seconds total)