Starting phenix.real_space_refine on Wed Aug 5 14:31:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vd1_64973/08_2026/9vd1_64973.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vd1_64973/08_2026/9vd1_64973.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vd1_64973/08_2026/9vd1_64973.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vd1_64973/08_2026/9vd1_64973.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vd1_64973/08_2026/9vd1_64973.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vd1_64973/08_2026/9vd1_64973.map" } resolution = 4.16 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= 0.032 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: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 56 5.16 5 C 6361 2.51 5 N 1704 2.21 5 O 1840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 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: 9968 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Classifications: {'RNA': 2} Modifications used: {'rna3p_pyr': 2} Link IDs: {'rna3p': 1} Chain: "B" Number of atoms: 5051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 5051 Classifications: {'peptide': 635} Link IDs: {'PTRANS': 37, 'TRANS': 597} Chain: "A" Number of atoms: 4819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4819 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 32, 'TRANS': 569} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.38, per 1000 atoms: 0.24 Number of scatterers: 9968 At special positions: 0 Unit cell: (97.94, 102.09, 130.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 P 7 15.00 O 1840 8.00 N 1704 7.00 C 6361 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 397.1 milliseconds 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2352 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 6 sheets defined 57.6% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'B' and resid 79 through 85 removed outlier: 3.579A pdb=" N THR B 85 " --> pdb=" O GLY B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 102 Processing helix chain 'B' and resid 103 through 113 Processing helix chain 'B' and resid 116 through 133 Processing helix chain 'B' and resid 138 through 151 Processing helix chain 'B' and resid 158 through 170 removed outlier: 3.706A pdb=" N PHE B 162 " --> pdb=" O LEU B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 183 Processing helix chain 'B' and resid 187 through 191 Processing helix chain 'B' and resid 193 through 198 Processing helix chain 'B' and resid 213 through 224 Processing helix chain 'B' and resid 233 through 248 removed outlier: 3.589A pdb=" N ALA B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 298 removed outlier: 3.579A pdb=" N MET B 295 " --> pdb=" O GLU B 292 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE B 296 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG B 297 " --> pdb=" O GLN B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 310 removed outlier: 3.988A pdb=" N TRP B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 360 through 364 Processing helix chain 'B' and resid 374 through 389 Processing helix chain 'B' and resid 400 through 412 Processing helix chain 'B' and resid 426 through 428 No H-bonds generated for 'chain 'B' and resid 426 through 428' Processing helix chain 'B' and resid 460 through 472 removed outlier: 4.019A pdb=" N GLY B 472 " --> pdb=" O ALA B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 477 Processing helix chain 'B' and resid 488 through 500 removed outlier: 3.608A pdb=" N ARG B 500 " --> pdb=" O GLU B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 524 Processing helix chain 'B' and resid 529 through 539 Processing helix chain 'B' and resid 551 through 562 removed outlier: 3.817A pdb=" N GLN B 562 " --> pdb=" O ALA B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 577 Processing helix chain 'B' and resid 583 through 599 removed outlier: 4.095A pdb=" N CYS B 587 " --> pdb=" O GLN B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 612 Processing helix chain 'B' and resid 622 through 643 Processing helix chain 'B' and resid 651 through 672 Processing helix chain 'B' and resid 672 through 687 Processing helix chain 'A' and resid 89 through 103 Processing helix chain 'A' and resid 103 through 112 removed outlier: 3.804A pdb=" N GLN A 107 " --> pdb=" O ARG A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 133 Processing helix chain 'A' and resid 138 through 151 Processing helix chain 'A' and resid 154 through 170 Proline residue: A 160 - end of helix Processing helix chain 'A' and resid 175 through 183 Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 194 through 198 removed outlier: 4.222A pdb=" N MET A 198 " --> pdb=" O ALA A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 223 Processing helix chain 'A' and resid 233 through 248 Processing helix chain 'A' and resid 276 through 279 Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 301 through 312 removed outlier: 4.180A pdb=" N TRP A 305 " --> pdb=" O ARG A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 324 No H-bonds generated for 'chain 'A' and resid 322 through 324' Processing helix chain 'A' and resid 325 through 337 Processing helix chain 'A' and resid 360 through 364 Processing helix chain 'A' and resid 374 through 389 Processing helix chain 'A' and resid 400 through 413 removed outlier: 3.575A pdb=" N LYS A 404 " --> pdb=" O PRO A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 430 Processing helix chain 'A' and resid 460 through 470 Processing helix chain 'A' and resid 488 through 499 Processing helix chain 'A' and resid 513 through 524 Processing helix chain 'A' and resid 528 through 539 Processing helix chain 'A' and resid 551 through 562 Processing helix chain 'A' and resid 567 through 577 removed outlier: 3.709A pdb=" N ALA A 577 " --> pdb=" O VAL A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 600 Processing helix chain 'A' and resid 604 through 613 Processing helix chain 'A' and resid 621 through 645 Processing helix chain 'A' and resid 651 through 671 Processing helix chain 'A' and resid 672 through 684 Processing sheet with id=AA1, first strand: chain 'B' and resid 251 through 252 removed outlier: 6.619A pdb=" N ASP B 252 " --> pdb=" O SER B 273 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N THR B 275 " --> pdb=" O ASP B 252 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLU B 286 " --> pdb=" O GLU B 316 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N HIS B 318 " --> pdb=" O GLU B 286 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ALA B 288 " --> pdb=" O HIS B 318 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N CYS B 320 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE B 290 " --> pdb=" O CYS B 320 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU B 319 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE B 202 " --> pdb=" O GLU B 341 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ARG B 343 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N PHE B 204 " --> pdb=" O ARG B 343 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 392 through 393 removed outlier: 5.576A pdb=" N ALA B 393 " --> pdb=" O VAL B 422 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N THR B 424 " --> pdb=" O ALA B 393 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU B 421 " --> pdb=" O ASP B 368 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 251 through 254 removed outlier: 6.161A pdb=" N ASP A 252 " --> pdb=" O SER A 273 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLY A 227 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N CYS A 274 " --> pdb=" O GLY A 227 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL A 228 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LYS A 201 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU A 319 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ILE A 203 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ARG A 343 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N PHE A 204 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 351 through 353 removed outlier: 3.731A pdb=" N ASP A 368 " --> pdb=" O LYS A 419 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLU A 391 " --> pdb=" O ILE A 420 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N VAL A 422 " --> pdb=" O GLU A 391 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ALA A 393 " --> pdb=" O VAL A 422 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 444 through 445 Processing sheet with id=AA6, first strand: chain 'A' and resid 508 through 510 removed outlier: 5.433A pdb=" N ALA A 508 " --> pdb=" O PHE A 547 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 503 hydrogen bonds defined for protein. 1446 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.85 Time building geometry restraints manager: 1.53 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: 2543 1.33 - 1.46: 1923 1.46 - 1.58: 5640 1.58 - 1.70: 9 1.70 - 1.82: 87 Bond restraints: 10202 Sorted by residual: bond pdb=" C6 ANP A 801 " pdb=" N6 ANP A 801 " ideal model delta sigma weight residual 1.340 1.447 -0.107 2.00e-02 2.50e+03 2.86e+01 bond pdb=" C6 ANP B 801 " pdb=" N6 ANP B 801 " ideal model delta sigma weight residual 1.340 1.445 -0.105 2.00e-02 2.50e+03 2.76e+01 bond pdb=" C8 ANP A 801 " pdb=" N9 ANP A 801 " ideal model delta sigma weight residual 1.369 1.271 0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" C8 ANP B 801 " pdb=" N9 ANP B 801 " ideal model delta sigma weight residual 1.369 1.271 0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" C4' ANP A 801 " pdb=" O4' ANP A 801 " ideal model delta sigma weight residual 1.431 1.520 -0.089 2.00e-02 2.50e+03 1.97e+01 ... (remaining 10197 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 13515 2.42 - 4.83: 247 4.83 - 7.25: 56 7.25 - 9.66: 15 9.66 - 12.08: 7 Bond angle restraints: 13840 Sorted by residual: angle pdb=" C1' U C 1 " pdb=" N1 U C 1 " pdb=" C2 U C 1 " ideal model delta sigma weight residual 117.70 124.21 -6.51 1.20e+00 6.94e-01 2.94e+01 angle pdb=" N1 U C 1 " pdb=" C2 U C 1 " pdb=" O2 U C 1 " ideal model delta sigma weight residual 122.80 126.19 -3.39 7.00e-01 2.04e+00 2.34e+01 angle pdb=" C ARG B 477 " pdb=" CA ARG B 477 " pdb=" CB ARG B 477 " ideal model delta sigma weight residual 115.79 110.48 5.31 1.19e+00 7.06e-01 1.99e+01 angle pdb=" O2 U C 1 " pdb=" C2 U C 1 " pdb=" N3 U C 1 " ideal model delta sigma weight residual 122.20 119.10 3.10 7.00e-01 2.04e+00 1.96e+01 angle pdb=" O3A ANP B 801 " pdb=" PA ANP B 801 " pdb=" O5' ANP B 801 " ideal model delta sigma weight residual 98.09 110.17 -12.08 3.00e+00 1.11e-01 1.62e+01 ... (remaining 13835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.75: 5989 28.75 - 57.50: 221 57.50 - 86.25: 30 86.25 - 115.00: 0 115.00 - 143.75: 2 Dihedral angle restraints: 6242 sinusoidal: 2615 harmonic: 3627 Sorted by residual: dihedral pdb=" O4' U C 1 " pdb=" C1' U C 1 " pdb=" N1 U C 1 " pdb=" C2 U C 1 " ideal model delta sinusoidal sigma weight residual 200.00 75.57 124.43 1 1.50e+01 4.44e-03 6.68e+01 dihedral pdb=" CA ASN B 600 " pdb=" C ASN B 600 " pdb=" N GLU B 601 " pdb=" CA GLU B 601 " ideal model delta harmonic sigma weight residual -180.00 -149.93 -30.07 0 5.00e+00 4.00e-02 3.62e+01 dihedral pdb=" O4' U C 2 " pdb=" C1' U C 2 " pdb=" N1 U C 2 " pdb=" C2 U C 2 " ideal model delta sinusoidal sigma weight residual -160.00 -83.60 -76.40 1 1.50e+01 4.44e-03 3.26e+01 ... (remaining 6239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1254 0.054 - 0.107: 244 0.107 - 0.161: 43 0.161 - 0.215: 3 0.215 - 0.268: 2 Chirality restraints: 1546 Sorted by residual: chirality pdb=" C2' ANP A 801 " pdb=" C1' ANP A 801 " pdb=" C3' ANP A 801 " pdb=" O2' ANP A 801 " both_signs ideal model delta sigma weight residual False -2.72 -2.46 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C2' ANP B 801 " pdb=" C1' ANP B 801 " pdb=" C3' ANP B 801 " pdb=" O2' ANP B 801 " both_signs ideal model delta sigma weight residual False -2.72 -2.49 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA LYS B 613 " pdb=" N LYS B 613 " pdb=" C LYS B 613 " pdb=" CB LYS B 613 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.90e-01 ... (remaining 1543 not shown) Planarity restraints: 1767 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 188 " -0.039 5.00e-02 4.00e+02 5.96e-02 5.67e+00 pdb=" N PRO B 189 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 189 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 189 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 120 " 0.021 2.00e-02 2.50e+03 1.73e-02 5.21e+00 pdb=" CG PHE B 120 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE B 120 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE B 120 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 120 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 120 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 120 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 188 " 0.037 5.00e-02 4.00e+02 5.49e-02 4.83e+00 pdb=" N PRO A 189 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 189 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 189 " 0.031 5.00e-02 4.00e+02 ... (remaining 1764 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 296 2.69 - 3.24: 11031 3.24 - 3.80: 17348 3.80 - 4.35: 22506 4.35 - 4.90: 34406 Nonbonded interactions: 85587 Sorted by model distance: nonbonded pdb=" OG SER B 75 " pdb=" O GLY B 78 " model vdw 2.139 3.040 nonbonded pdb=" O LEU B 332 " pdb=" OG1 THR B 335 " model vdw 2.173 3.040 nonbonded pdb=" NH2 ARG A 347 " pdb=" O ALA A 471 " model vdw 2.186 3.120 nonbonded pdb=" NZ LYS A 234 " pdb=" OD2 ASP A 636 " model vdw 2.195 3.120 nonbonded pdb=" O ARG A 595 " pdb=" OG SER A 598 " model vdw 2.209 3.040 ... (remaining 85582 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 87 through 688 or (resid 801 and (name C1' or name C2 or n \ ame C2' or name C3' or name C4 or name C4' or name C5 or name C5' or name C6 or \ name C8 or name N1 or name N3 or name N3B or name N6 or name N7 or name N9 or na \ me O1A or name O1B or name O2' or name O2A or name O2B or name O3' or name O3A o \ r name O4' or name O5' or name PA or name PB )))) selection = (chain 'B' and resid 87 through 801) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.560 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:1.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6399 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 0.107 10202 Z= 0.248 Angle : 0.883 12.077 13840 Z= 0.459 Chirality : 0.044 0.268 1546 Planarity : 0.005 0.069 1767 Dihedral : 14.712 143.754 3890 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 22.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.97 (0.24), residues: 1233 helix: -0.06 (0.20), residues: 643 sheet: -0.95 (0.54), residues: 105 loop : -1.23 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 383 TYR 0.021 0.002 TYR B 379 PHE 0.039 0.002 PHE B 120 TRP 0.035 0.002 TRP B 607 HIS 0.006 0.001 HIS B 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.25 (10202) covalent geometry : angle 0.88335 / 0.46 (13840) hydrogen bonds : bond 0.15180 / 9.82 ( 503) hydrogen bonds : angle 6.15793 / 4.32 ( 1446) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 296 ILE cc_start: 0.9471 (tt) cc_final: 0.9247 (tp) REVERT: B 539 PHE cc_start: 0.7427 (m-80) cc_final: 0.6739 (m-80) REVERT: B 603 LEU cc_start: 0.8155 (mm) cc_final: 0.7524 (mm) REVERT: B 605 PHE cc_start: 0.8331 (t80) cc_final: 0.7385 (t80) REVERT: B 627 ASP cc_start: 0.8981 (m-30) cc_final: 0.8419 (m-30) REVERT: B 641 LEU cc_start: 0.9494 (mt) cc_final: 0.9197 (mt) REVERT: B 651 ASP cc_start: 0.6777 (m-30) cc_final: 0.6241 (t0) REVERT: B 663 ASP cc_start: 0.8423 (m-30) cc_final: 0.8206 (m-30) REVERT: A 295 MET cc_start: 0.6736 (mmm) cc_final: 0.6401 (tpp) REVERT: A 395 ILE cc_start: 0.6805 (pt) cc_final: 0.6592 (pt) REVERT: A 466 GLN cc_start: 0.8220 (mm110) cc_final: 0.8002 (mm110) REVERT: A 493 LEU cc_start: 0.9702 (tp) cc_final: 0.9400 (tp) REVERT: A 648 MET cc_start: 0.9281 (mmp) cc_final: 0.8869 (mmp) REVERT: A 678 LYS cc_start: 0.8501 (mmpt) cc_final: 0.7961 (tppt) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.0917 time to fit residues: 23.4401 Evaluate side-chains 139 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.7980 chunk 123 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN A 121 HIS A 210 ASN ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.134379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.107820 restraints weight = 39254.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.110911 restraints weight = 27888.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.112616 restraints weight = 21384.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.114258 restraints weight = 18241.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.115022 restraints weight = 15780.960| |-----------------------------------------------------------------------------| r_work (final): 0.4389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10202 Z= 0.200 Angle : 0.693 10.004 13840 Z= 0.358 Chirality : 0.044 0.152 1546 Planarity : 0.005 0.061 1767 Dihedral : 10.067 140.515 1433 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 24.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 0.18 % Allowed : 6.33 % Favored : 93.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.03 (0.24), residues: 1233 helix: -0.10 (0.19), residues: 661 sheet: -0.80 (0.59), residues: 94 loop : -1.36 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 609 TYR 0.016 0.002 TYR A 229 PHE 0.027 0.002 PHE B 120 TRP 0.017 0.003 TRP B 607 HIS 0.011 0.001 HIS B 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.20 (10202) covalent geometry : angle 0.69330 / 0.36 (13840) hydrogen bonds : bond 0.04537 / 2.99 ( 503) hydrogen bonds : angle 5.40838 / 3.81 ( 1446) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 166 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 116 ASP cc_start: 0.6803 (OUTLIER) cc_final: 0.6336 (t0) REVERT: B 539 PHE cc_start: 0.6857 (m-80) cc_final: 0.6510 (m-80) REVERT: B 605 PHE cc_start: 0.8281 (t80) cc_final: 0.7460 (t80) REVERT: B 626 MET cc_start: 0.7782 (ppp) cc_final: 0.7541 (ppp) REVERT: B 627 ASP cc_start: 0.8862 (m-30) cc_final: 0.8538 (m-30) REVERT: B 641 LEU cc_start: 0.9462 (mt) cc_final: 0.9210 (mt) REVERT: B 651 ASP cc_start: 0.6724 (m-30) cc_final: 0.6068 (t0) REVERT: A 295 MET cc_start: 0.7093 (mmm) cc_final: 0.6604 (tpp) REVERT: A 609 ARG cc_start: 0.8942 (ptm-80) cc_final: 0.8735 (ptm-80) outliers start: 2 outliers final: 1 residues processed: 167 average time/residue: 0.0951 time to fit residues: 22.7663 Evaluate side-chains 134 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 132 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 87 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 chunk 35 optimal weight: 20.0000 chunk 79 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 667 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 = 0.4632 r_free = 0.4632 target = 0.135653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.107736 restraints weight = 41469.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.111077 restraints weight = 29090.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.113442 restraints weight = 22266.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.115095 restraints weight = 18283.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.115818 restraints weight = 15793.128| |-----------------------------------------------------------------------------| r_work (final): 0.4327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6486 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10202 Z= 0.165 Angle : 0.655 7.924 13840 Z= 0.336 Chirality : 0.043 0.147 1546 Planarity : 0.006 0.078 1767 Dihedral : 9.726 142.311 1433 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 21.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.23), residues: 1233 helix: -0.13 (0.19), residues: 663 sheet: -1.07 (0.59), residues: 92 loop : -1.33 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 383 TYR 0.017 0.002 TYR B 611 PHE 0.022 0.002 PHE B 162 TRP 0.029 0.002 TRP B 607 HIS 0.008 0.001 HIS A 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (10202) covalent geometry : angle 0.65539 / 0.34 (13840) hydrogen bonds : bond 0.04139 / 2.73 ( 503) hydrogen bonds : angle 5.27494 / 3.73 ( 1446) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 376 ASN cc_start: 0.9303 (m-40) cc_final: 0.9034 (p0) REVERT: B 539 PHE cc_start: 0.6888 (m-80) cc_final: 0.6598 (m-80) REVERT: B 605 PHE cc_start: 0.8315 (t80) cc_final: 0.7565 (t80) REVERT: B 626 MET cc_start: 0.7732 (ppp) cc_final: 0.7506 (ppp) REVERT: B 627 ASP cc_start: 0.8909 (m-30) cc_final: 0.8581 (m-30) REVERT: B 641 LEU cc_start: 0.9424 (mt) cc_final: 0.9185 (mt) REVERT: B 651 ASP cc_start: 0.6866 (m-30) cc_final: 0.6186 (t0) REVERT: A 295 MET cc_start: 0.6874 (mmm) cc_final: 0.6384 (tpp) REVERT: A 466 GLN cc_start: 0.8252 (mm110) cc_final: 0.7980 (mm110) REVERT: A 637 LEU cc_start: 0.9371 (tp) cc_final: 0.9141 (tt) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.0920 time to fit residues: 22.5073 Evaluate side-chains 132 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 71 optimal weight: 8.9990 chunk 119 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 67 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 114 optimal weight: 7.9990 chunk 13 optimal weight: 20.0000 chunk 21 optimal weight: 0.2980 chunk 110 optimal weight: 0.3980 chunk 82 optimal weight: 20.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 HIS ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 667 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 = 0.4691 r_free = 0.4691 target = 0.138458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.111037 restraints weight = 41764.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.114465 restraints weight = 28525.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.116880 restraints weight = 21643.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.118513 restraints weight = 17646.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.119685 restraints weight = 15207.962| |-----------------------------------------------------------------------------| r_work (final): 0.4381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6380 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10202 Z= 0.135 Angle : 0.628 8.718 13840 Z= 0.319 Chirality : 0.042 0.169 1546 Planarity : 0.005 0.062 1767 Dihedral : 9.474 142.252 1433 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.09 % Allowed : 3.76 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.08 (0.23), residues: 1233 helix: -0.06 (0.19), residues: 663 sheet: -1.54 (0.53), residues: 104 loop : -1.34 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 383 TYR 0.012 0.001 TYR A 334 PHE 0.022 0.002 PHE B 204 TRP 0.023 0.002 TRP B 607 HIS 0.006 0.001 HIS A 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (10202) covalent geometry : angle 0.62773 / 0.32 (13840) hydrogen bonds : bond 0.03799 / 2.48 ( 503) hydrogen bonds : angle 5.06669 / 3.60 ( 1446) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 174 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 376 ASN cc_start: 0.9272 (m-40) cc_final: 0.8969 (p0) REVERT: B 539 PHE cc_start: 0.6861 (m-80) cc_final: 0.6448 (m-80) REVERT: B 605 PHE cc_start: 0.8530 (t80) cc_final: 0.7803 (t80) REVERT: B 616 LEU cc_start: 0.6155 (mm) cc_final: 0.5825 (pt) REVERT: B 626 MET cc_start: 0.7749 (ppp) cc_final: 0.7515 (ppp) REVERT: B 627 ASP cc_start: 0.8911 (m-30) cc_final: 0.8577 (m-30) REVERT: B 641 LEU cc_start: 0.9494 (mt) cc_final: 0.9232 (mt) REVERT: B 651 ASP cc_start: 0.7033 (m-30) cc_final: 0.6249 (t0) REVERT: A 295 MET cc_start: 0.6757 (mmm) cc_final: 0.6276 (tpp) REVERT: A 326 ILE cc_start: 0.9254 (pt) cc_final: 0.8942 (pt) REVERT: A 395 ILE cc_start: 0.7013 (pt) cc_final: 0.6785 (pt) outliers start: 1 outliers final: 1 residues processed: 175 average time/residue: 0.0872 time to fit residues: 22.0547 Evaluate side-chains 140 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 5 optimal weight: 8.9990 chunk 113 optimal weight: 0.5980 chunk 105 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 117 optimal weight: 0.0030 chunk 72 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 overall best weight: 3.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 667 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 = 0.4579 r_free = 0.4579 target = 0.133179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.105474 restraints weight = 40475.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.108714 restraints weight = 28620.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.110978 restraints weight = 22091.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.112598 restraints weight = 18218.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.113745 restraints weight = 15768.910| |-----------------------------------------------------------------------------| r_work (final): 0.4284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6537 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10202 Z= 0.198 Angle : 0.683 7.377 13840 Z= 0.350 Chirality : 0.044 0.160 1546 Planarity : 0.005 0.062 1767 Dihedral : 9.494 142.491 1433 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 23.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.12 (0.23), residues: 1233 helix: -0.12 (0.19), residues: 666 sheet: -1.23 (0.58), residues: 92 loop : -1.42 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 610 TYR 0.015 0.002 TYR A 229 PHE 0.025 0.002 PHE B 162 TRP 0.040 0.003 TRP B 614 HIS 0.010 0.001 HIS A 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.20 (10202) covalent geometry : angle 0.68279 / 0.35 (13840) hydrogen bonds : bond 0.03979 / 2.64 ( 503) hydrogen bonds : angle 5.23072 / 3.69 ( 1446) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 376 ASN cc_start: 0.9328 (m-40) cc_final: 0.9001 (p0) REVERT: B 539 PHE cc_start: 0.7023 (m-80) cc_final: 0.6751 (m-80) REVERT: B 616 LEU cc_start: 0.6343 (mm) cc_final: 0.5897 (pt) REVERT: B 627 ASP cc_start: 0.8931 (m-30) cc_final: 0.8550 (m-30) REVERT: B 641 LEU cc_start: 0.9472 (mt) cc_final: 0.9217 (mt) REVERT: A 295 MET cc_start: 0.6987 (mmm) cc_final: 0.6390 (tpp) REVERT: A 466 GLN cc_start: 0.8285 (mm110) cc_final: 0.7975 (mm110) REVERT: A 648 MET cc_start: 0.9337 (mmp) cc_final: 0.8938 (mmm) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.0897 time to fit residues: 22.1945 Evaluate side-chains 131 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 10.0000 chunk 123 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 68 optimal weight: 30.0000 chunk 61 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 3 optimal weight: 30.0000 chunk 102 optimal weight: 9.9990 chunk 73 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 GLN ** A 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 667 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 = 0.4596 r_free = 0.4596 target = 0.132685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.104925 restraints weight = 41802.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.108191 restraints weight = 29279.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.110482 restraints weight = 22547.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.112095 restraints weight = 18520.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.113232 restraints weight = 16057.177| |-----------------------------------------------------------------------------| r_work (final): 0.4314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10202 Z= 0.191 Angle : 0.679 7.561 13840 Z= 0.351 Chirality : 0.044 0.200 1546 Planarity : 0.005 0.060 1767 Dihedral : 9.528 143.388 1433 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 24.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.11 (0.23), residues: 1233 helix: -0.10 (0.19), residues: 664 sheet: -1.30 (0.58), residues: 91 loop : -1.41 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 383 TYR 0.015 0.002 TYR B 229 PHE 0.028 0.002 PHE B 120 TRP 0.036 0.003 TRP B 614 HIS 0.009 0.001 HIS B 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 (10202) covalent geometry : angle 0.67870 / 0.35 (13840) hydrogen bonds : bond 0.04020 / 2.65 ( 503) hydrogen bonds : angle 5.25262 / 3.73 ( 1446) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 376 ASN cc_start: 0.9335 (m-40) cc_final: 0.9022 (p0) REVERT: B 627 ASP cc_start: 0.8924 (m-30) cc_final: 0.8568 (m-30) REVERT: B 641 LEU cc_start: 0.9530 (mt) cc_final: 0.9278 (mt) REVERT: A 295 MET cc_start: 0.6951 (mmm) cc_final: 0.6421 (tpp) REVERT: A 466 GLN cc_start: 0.8333 (mm110) cc_final: 0.7999 (mm110) REVERT: A 637 LEU cc_start: 0.9395 (tt) cc_final: 0.9186 (tt) REVERT: A 648 MET cc_start: 0.9334 (mmp) cc_final: 0.8949 (mmm) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.0986 time to fit residues: 24.0927 Evaluate side-chains 134 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 112 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 chunk 102 optimal weight: 10.0000 chunk 38 optimal weight: 0.0030 chunk 69 optimal weight: 0.2980 chunk 123 optimal weight: 10.0000 overall best weight: 1.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 GLN ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 667 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 = 0.4688 r_free = 0.4688 target = 0.139768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.115735 restraints weight = 42168.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.119031 restraints weight = 28619.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.121308 restraints weight = 21391.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.122898 restraints weight = 17195.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.123999 restraints weight = 14614.031| |-----------------------------------------------------------------------------| r_work (final): 0.4430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6334 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10202 Z= 0.137 Angle : 0.658 8.579 13840 Z= 0.336 Chirality : 0.044 0.202 1546 Planarity : 0.005 0.068 1767 Dihedral : 9.379 147.780 1433 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.98 (0.24), residues: 1233 helix: 0.02 (0.20), residues: 663 sheet: -1.26 (0.58), residues: 91 loop : -1.37 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 383 TYR 0.028 0.002 TYR A 334 PHE 0.036 0.002 PHE B 162 TRP 0.028 0.003 TRP B 607 HIS 0.006 0.001 HIS B 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (10202) covalent geometry : angle 0.65772 / 0.34 (13840) hydrogen bonds : bond 0.03697 / 2.44 ( 503) hydrogen bonds : angle 5.03533 / 3.55 ( 1446) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 376 ASN cc_start: 0.9214 (m-40) cc_final: 0.8948 (p0) REVERT: B 627 ASP cc_start: 0.8853 (m-30) cc_final: 0.8526 (m-30) REVERT: B 638 TYR cc_start: 0.8548 (t80) cc_final: 0.8064 (t80) REVERT: B 641 LEU cc_start: 0.9403 (mt) cc_final: 0.9092 (mt) REVERT: B 651 ASP cc_start: 0.7054 (m-30) cc_final: 0.6742 (m-30) REVERT: A 295 MET cc_start: 0.6821 (mmm) cc_final: 0.6315 (tpp) REVERT: A 394 VAL cc_start: 0.6060 (m) cc_final: 0.5852 (p) REVERT: A 466 GLN cc_start: 0.8212 (mm110) cc_final: 0.7979 (mm110) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.0973 time to fit residues: 24.2795 Evaluate side-chains 141 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 20 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 24 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 86 optimal weight: 0.0050 chunk 26 optimal weight: 5.9990 chunk 81 optimal weight: 0.2980 chunk 92 optimal weight: 20.0000 chunk 57 optimal weight: 0.0970 chunk 93 optimal weight: 5.9990 overall best weight: 1.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 190 ASN ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 HIS ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.137342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.110381 restraints weight = 38106.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.113948 restraints weight = 26494.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.116293 restraints weight = 19770.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.117953 restraints weight = 15849.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.119113 restraints weight = 13507.508| |-----------------------------------------------------------------------------| r_work (final): 0.4411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6376 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10202 Z= 0.137 Angle : 0.649 8.577 13840 Z= 0.332 Chirality : 0.044 0.211 1546 Planarity : 0.005 0.062 1767 Dihedral : 9.278 149.720 1433 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.99 (0.24), residues: 1233 helix: 0.08 (0.20), residues: 664 sheet: -1.48 (0.54), residues: 103 loop : -1.42 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 383 TYR 0.022 0.002 TYR A 334 PHE 0.020 0.001 PHE B 162 TRP 0.028 0.002 TRP B 607 HIS 0.006 0.001 HIS B 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (10202) covalent geometry : angle 0.64895 / 0.33 (13840) hydrogen bonds : bond 0.03598 / 2.38 ( 503) hydrogen bonds : angle 4.97652 / 3.51 ( 1446) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 376 ASN cc_start: 0.9283 (m-40) cc_final: 0.8985 (p0) REVERT: B 539 PHE cc_start: 0.6881 (m-80) cc_final: 0.6512 (m-80) REVERT: B 603 LEU cc_start: 0.8504 (mm) cc_final: 0.8294 (mm) REVERT: B 627 ASP cc_start: 0.8867 (m-30) cc_final: 0.8525 (m-30) REVERT: A 295 MET cc_start: 0.6783 (mmm) cc_final: 0.6283 (tpp) REVERT: A 648 MET cc_start: 0.9263 (mmp) cc_final: 0.8860 (mmt) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.0942 time to fit residues: 23.3634 Evaluate side-chains 142 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 79 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 55 optimal weight: 0.8980 chunk 24 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 HIS A 407 GLN ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.138462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.111531 restraints weight = 37229.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.114915 restraints weight = 25531.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.117241 restraints weight = 19302.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.118397 restraints weight = 15652.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.120006 restraints weight = 13664.707| |-----------------------------------------------------------------------------| r_work (final): 0.4422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6345 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10202 Z= 0.131 Angle : 0.650 7.927 13840 Z= 0.332 Chirality : 0.043 0.195 1546 Planarity : 0.005 0.064 1767 Dihedral : 9.197 151.315 1433 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.90 (0.24), residues: 1233 helix: 0.15 (0.20), residues: 660 sheet: -1.38 (0.54), residues: 101 loop : -1.39 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 609 TYR 0.021 0.002 TYR A 334 PHE 0.022 0.002 PHE B 162 TRP 0.028 0.002 TRP B 607 HIS 0.012 0.001 HIS B 671 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (10202) covalent geometry : angle 0.64998 / 0.33 (13840) hydrogen bonds : bond 0.03501 / 2.32 ( 503) hydrogen bonds : angle 4.92349 / 3.47 ( 1446) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 263 GLN cc_start: 0.7721 (tt0) cc_final: 0.6902 (mp10) REVERT: B 376 ASN cc_start: 0.9285 (m-40) cc_final: 0.9002 (p0) REVERT: B 627 ASP cc_start: 0.8879 (m-30) cc_final: 0.8534 (m-30) REVERT: B 638 TYR cc_start: 0.8635 (t80) cc_final: 0.8079 (t80) REVERT: A 295 MET cc_start: 0.6599 (mmm) cc_final: 0.6167 (tpp) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.0957 time to fit residues: 23.2131 Evaluate side-chains 137 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 3 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 70 optimal weight: 40.0000 chunk 42 optimal weight: 9.9990 chunk 49 optimal weight: 0.6980 chunk 34 optimal weight: 0.1980 chunk 20 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 ASN ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 667 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 = 0.4704 r_free = 0.4704 target = 0.138399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.111472 restraints weight = 37166.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.114785 restraints weight = 26121.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.117004 restraints weight = 19548.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.118770 restraints weight = 15814.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.119989 restraints weight = 13414.498| |-----------------------------------------------------------------------------| r_work (final): 0.4430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10202 Z= 0.137 Angle : 0.659 9.392 13840 Z= 0.337 Chirality : 0.044 0.195 1546 Planarity : 0.005 0.063 1767 Dihedral : 9.142 151.578 1433 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.85 (0.24), residues: 1233 helix: 0.19 (0.20), residues: 665 sheet: -1.25 (0.54), residues: 101 loop : -1.40 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 569 TYR 0.022 0.002 TYR A 334 PHE 0.021 0.002 PHE B 162 TRP 0.028 0.002 TRP B 607 HIS 0.009 0.001 HIS B 671 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (10202) covalent geometry : angle 0.65944 / 0.34 (13840) hydrogen bonds : bond 0.03524 / 2.35 ( 503) hydrogen bonds : angle 4.92276 / 3.47 ( 1446) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 156 ASP cc_start: 0.7753 (t0) cc_final: 0.7462 (m-30) REVERT: B 263 GLN cc_start: 0.7715 (tt0) cc_final: 0.6898 (mp10) REVERT: B 376 ASN cc_start: 0.9241 (m-40) cc_final: 0.8967 (p0) REVERT: B 539 PHE cc_start: 0.5954 (m-80) cc_final: 0.5438 (m-80) REVERT: B 603 LEU cc_start: 0.8447 (mm) cc_final: 0.8054 (mm) REVERT: B 605 PHE cc_start: 0.8297 (t80) cc_final: 0.7513 (t80) REVERT: B 627 ASP cc_start: 0.8863 (m-30) cc_final: 0.8520 (m-30) REVERT: B 651 ASP cc_start: 0.7005 (m-30) cc_final: 0.6778 (t0) REVERT: A 295 MET cc_start: 0.6650 (mmm) cc_final: 0.6188 (tpp) REVERT: A 541 GLN cc_start: 0.8535 (mm-40) cc_final: 0.8171 (mt0) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.0883 time to fit residues: 21.5789 Evaluate side-chains 138 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 116 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 43 optimal weight: 20.0000 chunk 26 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 667 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 = 0.4706 r_free = 0.4706 target = 0.138335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.111371 restraints weight = 37497.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.114869 restraints weight = 25960.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.117235 restraints weight = 19606.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.118874 restraints weight = 15854.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.120085 restraints weight = 13519.495| |-----------------------------------------------------------------------------| r_work (final): 0.4426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6359 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10202 Z= 0.137 Angle : 0.649 8.420 13840 Z= 0.332 Chirality : 0.044 0.194 1546 Planarity : 0.005 0.064 1767 Dihedral : 9.076 151.314 1433 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.88 (0.24), residues: 1233 helix: 0.19 (0.20), residues: 665 sheet: -1.36 (0.54), residues: 103 loop : -1.42 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 569 TYR 0.019 0.002 TYR A 334 PHE 0.021 0.002 PHE B 162 TRP 0.027 0.002 TRP B 607 HIS 0.009 0.001 HIS B 671 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (10202) covalent geometry : angle 0.64891 / 0.33 (13840) hydrogen bonds : bond 0.03474 / 2.32 ( 503) hydrogen bonds : angle 4.89653 / 3.45 ( 1446) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1893.88 seconds wall clock time: 33 minutes 39.07 seconds (2019.07 seconds total)