Starting phenix.real_space_refine on Fri Aug 7 02:26:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s8l_54664/08_2026/9s8l_54664_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s8l_54664/08_2026/9s8l_54664.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9s8l_54664/08_2026/9s8l_54664.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s8l_54664/08_2026/9s8l_54664.map" model { file = "/net/cci-nas-00/data/ceres_data/9s8l_54664/08_2026/9s8l_54664_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s8l_54664/08_2026/9s8l_54664_trim.cif" } resolution = 3.3 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= 0.000 sd= 0.000 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 4 5.49 5 S 40 5.16 5 C 5842 2.51 5 N 1520 2.21 5 O 1610 1.98 5 H 8997 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 18013 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 7153 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 11, 'TRANS': 422} Chain breaks: 3 Chain: "B" Number of atoms: 7184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 7184 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 11, 'TRANS': 424} Chain breaks: 3 Chain: "C" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1802 Classifications: {'peptide': 117} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain breaks: 1 Chain: "D" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1802 Classifications: {'peptide': 117} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain breaks: 1 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'GDU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'GDU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.26, per 1000 atoms: 0.18 Number of scatterers: 18013 At special positions: 0 Unit cell: (120.414, 107.254, 96.726, 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 40 16.00 P 4 15.00 O 1610 8.00 N 1520 7.00 C 5842 6.00 H 8997 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 407 " - pdb=" SG CYS C 481 " distance=2.03 Simple disulfide: pdb=" SG CYS D 407 " - pdb=" SG CYS D 481 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 568.2 milliseconds 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2060 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 13 sheets defined 52.4% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 3 through 37 removed outlier: 4.298A pdb=" N ASN A 7 " --> pdb=" O HIS A 3 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR A 27 " --> pdb=" O THR A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 44 Processing helix chain 'A' and resid 49 through 69 removed outlier: 3.662A pdb=" N TRP A 57 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 58 " --> pdb=" O GLY A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 106 Processing helix chain 'A' and resid 110 through 139 Proline residue: A 126 - end of helix Processing helix chain 'A' and resid 152 through 165 Processing helix chain 'A' and resid 200 through 205 removed outlier: 3.600A pdb=" N THR A 204 " --> pdb=" O THR A 200 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 205 " --> pdb=" O TRP A 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 200 through 205' Processing helix chain 'A' and resid 216 through 218 No H-bonds generated for 'chain 'A' and resid 216 through 218' Processing helix chain 'A' and resid 219 through 234 Processing helix chain 'A' and resid 273 through 307 Proline residue: A 297 - end of helix Processing helix chain 'A' and resid 372 through 380 Processing helix chain 'A' and resid 382 through 393 removed outlier: 3.771A pdb=" N PHE A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASN A 389 " --> pdb=" O PRO A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 3.649A pdb=" N LEU A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU A 409 " --> pdb=" O THR A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 409' Processing helix chain 'A' and resid 414 through 421 removed outlier: 3.716A pdb=" N TYR A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE A 421 " --> pdb=" O TYR A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 432 Processing helix chain 'A' and resid 442 through 447 Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 454 through 477 Processing helix chain 'B' and resid 4 through 37 removed outlier: 3.932A pdb=" N LEU B 26 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR B 27 " --> pdb=" O THR B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 44 Processing helix chain 'B' and resid 45 through 70 removed outlier: 3.549A pdb=" N GLU B 50 " --> pdb=" O GLN B 46 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N GLY B 51 " --> pdb=" O ASP B 47 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N TRP B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 106 removed outlier: 3.704A pdb=" N VAL B 99 " --> pdb=" O ALA B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 139 removed outlier: 3.796A pdb=" N ALA B 123 " --> pdb=" O VAL B 119 " (cutoff:3.500A) Proline residue: B 126 - end of helix Processing helix chain 'B' and resid 152 through 165 Processing helix chain 'B' and resid 198 through 204 removed outlier: 3.977A pdb=" N LEU B 202 " --> pdb=" O ASP B 198 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR B 203 " --> pdb=" O LYS B 199 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR B 204 " --> pdb=" O THR B 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 198 through 204' Processing helix chain 'B' and resid 216 through 218 No H-bonds generated for 'chain 'B' and resid 216 through 218' Processing helix chain 'B' and resid 219 through 234 Processing helix chain 'B' and resid 273 through 308 Proline residue: B 297 - end of helix Processing helix chain 'B' and resid 322 through 324 No H-bonds generated for 'chain 'B' and resid 322 through 324' Processing helix chain 'B' and resid 372 through 380 Processing helix chain 'B' and resid 381 through 383 No H-bonds generated for 'chain 'B' and resid 381 through 383' Processing helix chain 'B' and resid 384 through 392 removed outlier: 4.113A pdb=" N PHE B 388 " --> pdb=" O LEU B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 removed outlier: 3.799A pdb=" N GLU B 409 " --> pdb=" O ALA B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 420 removed outlier: 3.731A pdb=" N TYR B 418 " --> pdb=" O GLU B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 432 Processing helix chain 'B' and resid 441 through 452 removed outlier: 3.635A pdb=" N LEU B 445 " --> pdb=" O THR B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 477 removed outlier: 3.647A pdb=" N ASP B 458 " --> pdb=" O SER B 454 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE B 459 " --> pdb=" O MET B 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 476 Processing helix chain 'C' and resid 491 through 497 removed outlier: 3.681A pdb=" N TYR C 495 " --> pdb=" O SER C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 501 Processing helix chain 'D' and resid 459 through 461 No H-bonds generated for 'chain 'D' and resid 459 through 461' Processing helix chain 'D' and resid 491 through 497 Processing helix chain 'D' and resid 498 through 501 Processing sheet with id=AA1, first strand: chain 'A' and resid 193 through 195 removed outlier: 3.910A pdb=" N GLN A 193 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ARG A 144 " --> pdb=" O ASN A 171 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL A 173 " --> pdb=" O ARG A 144 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N THR A 146 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N PHE A 175 " --> pdb=" O THR A 146 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE A 148 " --> pdb=" O PHE A 175 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 255 through 257 removed outlier: 3.674A pdb=" N VAL A 262 " --> pdb=" O ILE A 257 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 314 through 320 removed outlier: 3.625A pdb=" N HIS A 317 " --> pdb=" O CYS A 329 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 396 through 398 removed outlier: 6.606A pdb=" N LEU A 397 " --> pdb=" O THR A 426 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 193 through 196 removed outlier: 3.880A pdb=" N GLN B 193 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE B 195 " --> pdb=" O PHE B 175 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N THR B 146 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N PHE B 175 " --> pdb=" O THR B 146 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ILE B 148 " --> pdb=" O PHE B 175 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ASP B 177 " --> pdb=" O ILE B 148 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 255 through 257 Processing sheet with id=AA7, first strand: chain 'B' and resid 314 through 320 Processing sheet with id=AA8, first strand: chain 'B' and resid 396 through 398 removed outlier: 8.643A pdb=" N SER B 396 " --> pdb=" O MET B 425 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 5 through 6 Processing sheet with id=AB1, first strand: chain 'C' and resid 443 through 445 removed outlier: 6.714A pdb=" N TRP C 421 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N SER C 435 " --> pdb=" O MET C 419 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N MET C 419 " --> pdb=" O SER C 435 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR C 503 " --> pdb=" O ALA C 483 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.541A pdb=" N THR D 463 " --> pdb=" O ASP D 458 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 443 through 445 removed outlier: 5.705A pdb=" N PHE D 432 " --> pdb=" O ARG D 423 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ARG D 423 " --> pdb=" O PHE D 432 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA D 434 " --> pdb=" O TRP D 421 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 443 through 445 removed outlier: 5.705A pdb=" N PHE D 432 " --> pdb=" O ARG D 423 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ARG D 423 " --> pdb=" O PHE D 432 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA D 434 " --> pdb=" O TRP D 421 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA D 477 " --> pdb=" O VAL D 510 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL D 510 " --> pdb=" O ALA D 477 " (cutoff:3.500A) 469 hydrogen bonds defined for protein. 1332 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: 4.21 Time building geometry restraints manager: 2.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 8989 1.03 - 1.23: 12 1.23 - 1.42: 4002 1.42 - 1.62: 5158 1.62 - 1.81: 76 Bond restraints: 18237 Sorted by residual: bond pdb=" N HIS A 3 " pdb=" CA HIS A 3 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.86e+00 bond pdb=" N HIS B 3 " pdb=" CA HIS B 3 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.85e+00 bond pdb=" N HIS B 3 " pdb=" H HIS B 3 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.24e+00 bond pdb=" N HIS A 3 " pdb=" H HIS A 3 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.20e+00 bond pdb=" N GLU C 474 " pdb=" H GLU C 474 " ideal model delta sigma weight residual 0.860 0.833 0.027 2.00e-02 2.50e+03 1.78e+00 ... (remaining 18232 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 32586 1.68 - 3.37: 221 3.37 - 5.05: 22 5.05 - 6.74: 2 6.74 - 8.42: 1 Bond angle restraints: 32832 Sorted by residual: angle pdb=" CA GLU C 474 " pdb=" CB GLU C 474 " pdb=" CG GLU C 474 " ideal model delta sigma weight residual 114.10 120.45 -6.35 2.00e+00 2.50e-01 1.01e+01 angle pdb=" CB GLU C 474 " pdb=" CG GLU C 474 " pdb=" CD GLU C 474 " ideal model delta sigma weight residual 112.60 117.46 -4.86 1.70e+00 3.46e-01 8.18e+00 angle pdb=" CB MET A 254 " pdb=" CG MET A 254 " pdb=" SD MET A 254 " ideal model delta sigma weight residual 112.70 121.12 -8.42 3.00e+00 1.11e-01 7.88e+00 angle pdb=" CA GLU D 429 " pdb=" CB GLU D 429 " pdb=" CG GLU D 429 " ideal model delta sigma weight residual 114.10 118.37 -4.27 2.00e+00 2.50e-01 4.56e+00 angle pdb=" CA MET A 254 " pdb=" CB MET A 254 " pdb=" CG MET A 254 " ideal model delta sigma weight residual 114.10 118.11 -4.01 2.00e+00 2.50e-01 4.02e+00 ... (remaining 32827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 7769 17.83 - 35.67: 605 35.67 - 53.50: 175 53.50 - 71.34: 48 71.34 - 89.17: 10 Dihedral angle restraints: 8607 sinusoidal: 4632 harmonic: 3975 Sorted by residual: dihedral pdb=" CA ALA A 447 " pdb=" C ALA A 447 " pdb=" N TRP A 448 " pdb=" CA TRP A 448 " ideal model delta harmonic sigma weight residual -180.00 -163.24 -16.76 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CB CYS D 407 " pdb=" SG CYS D 407 " pdb=" SG CYS D 481 " pdb=" CB CYS D 481 " ideal model delta sinusoidal sigma weight residual 93.00 65.70 27.30 1 1.00e+01 1.00e-02 1.07e+01 dihedral pdb=" CA TYR C 465 " pdb=" C TYR C 465 " pdb=" N LEU C 466 " pdb=" CA LEU C 466 " ideal model delta harmonic sigma weight residual 180.00 163.76 16.24 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 8604 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 952 0.029 - 0.058: 293 0.058 - 0.087: 87 0.087 - 0.116: 48 0.116 - 0.145: 10 Chirality restraints: 1390 Sorted by residual: chirality pdb=" CA PRO C 473 " pdb=" N PRO C 473 " pdb=" C PRO C 473 " pdb=" CB PRO C 473 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.27e-01 chirality pdb=" CA ILE B 241 " pdb=" N ILE B 241 " pdb=" C ILE B 241 " pdb=" CB ILE B 241 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA ILE A 212 " pdb=" N ILE A 212 " pdb=" C ILE A 212 " pdb=" CB ILE A 212 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 ... (remaining 1387 not shown) Planarity restraints: 2592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 384 " 0.034 5.00e-02 4.00e+02 5.10e-02 4.17e+00 pdb=" N PRO A 385 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 385 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 385 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 428 " 0.008 2.00e-02 2.50e+03 1.46e-02 2.13e+00 pdb=" N GLU D 429 " -0.025 2.00e-02 2.50e+03 pdb=" CA GLU D 429 " 0.006 2.00e-02 2.50e+03 pdb=" H GLU D 429 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 399 " -0.019 5.00e-02 4.00e+02 2.88e-02 1.33e+00 pdb=" N PRO B 400 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 400 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 400 " -0.016 5.00e-02 4.00e+02 ... (remaining 2589 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 5028 2.32 - 2.89: 40791 2.89 - 3.46: 45662 3.46 - 4.03: 60866 4.03 - 4.60: 90967 Nonbonded interactions: 243314 Sorted by model distance: nonbonded pdb=" OE1 GLU C 474 " pdb=" H GLU C 474 " model vdw 1.752 2.450 nonbonded pdb=" HE1 TRP A 448 " pdb=" HE1 PHE B 256 " model vdw 1.767 2.100 nonbonded pdb=" H THR A 465 " pdb=" HG1 THR A 465 " model vdw 1.895 2.100 nonbonded pdb=" H THR B 36 " pdb=" HG1 THR B 36 " model vdw 1.897 2.100 nonbonded pdb=" HD3 ARG A 223 " pdb="HH11 ARG A 223 " model vdw 1.920 2.270 ... (remaining 243309 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 3 and (name N or name CA or name C or name O or name CB o \ r name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA o \ r name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resid 4 through \ 501)) selection = (chain 'B' and (resid 3 through 207 or (resid 208 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 209 through 316 or (resid 317 and (name N or name CA or name C or \ name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or \ name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) \ or resid 318 through 477 or resid 501)) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.410 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: 0.130 Extract box with map and model: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.340 Find NCS groups from input model: 0.290 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: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3030 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9243 Z= 0.126 Angle : 0.478 8.420 12536 Z= 0.260 Chirality : 0.037 0.145 1390 Planarity : 0.003 0.051 1530 Dihedral : 13.927 89.172 3400 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.59 % Favored : 97.31 % Rotamer: Outliers : 0.10 % Allowed : 10.35 % Favored : 89.54 % 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: 1.15 (0.26), residues: 1080 helix: 1.96 (0.23), residues: 502 sheet: -0.66 (0.40), residues: 183 loop : 0.02 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 228 TYR 0.011 0.001 TYR D 495 PHE 0.007 0.001 PHE A 19 TRP 0.011 0.001 TRP A 453 HIS 0.002 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 ( 9240) covalent geometry : angle 0.47776 / 0.26 (12532) SS BOND : bond 0.00192 / 0.10 ( 2) SS BOND : angle 0.46271 / 0.39 ( 4) hydrogen bonds : bond 0.18375 / 12.78 ( 458) hydrogen bonds : angle 6.35679 / 4.72 ( 1332) Misc. bond : bond 0.00077 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 0.487 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: 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: A 130 MET cc_start: 0.4163 (mmm) cc_final: 0.3098 (ttt) REVERT: A 145 ASP cc_start: 0.6793 (m-30) cc_final: 0.6531 (m-30) REVERT: A 240 VAL cc_start: 0.4562 (t) cc_final: 0.4314 (t) REVERT: A 245 ARG cc_start: 0.6912 (tpm170) cc_final: 0.6629 (mtp85) REVERT: A 315 TYR cc_start: 0.6767 (t80) cc_final: 0.6517 (t80) REVERT: A 449 TYR cc_start: 0.4969 (t80) cc_final: 0.4252 (t80) REVERT: B 305 LYS cc_start: 0.5515 (mmtt) cc_final: 0.5293 (mmtt) REVERT: B 317 HIS cc_start: 0.4920 (m90) cc_final: 0.4373 (m90) REVERT: B 383 GLU cc_start: 0.6582 (tp30) cc_final: 0.6351 (mt-10) REVERT: B 404 ILE cc_start: 0.6000 (tp) cc_final: 0.5628 (tp) REVERT: C 458 ASP cc_start: 0.3453 (p0) cc_final: 0.3193 (p0) REVERT: C 466 LEU cc_start: 0.2129 (mm) cc_final: 0.1554 (tt) REVERT: D 479 TYR cc_start: 0.5102 (m-80) cc_final: 0.4582 (m-80) REVERT: D 480 TYR cc_start: 0.3904 (m-80) cc_final: 0.3421 (m-80) outliers start: 1 outliers final: 1 residues processed: 209 average time/residue: 0.2659 time to fit residues: 73.7944 Evaluate side-chains 145 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 56 HIS ** 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 = 0.4181 r_free = 0.4181 target = 0.176036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.138229 restraints weight = 41646.502| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.51 r_work: 0.3593 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4154 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 9243 Z= 0.258 Angle : 0.807 6.914 12536 Z= 0.439 Chirality : 0.048 0.219 1390 Planarity : 0.007 0.098 1530 Dihedral : 7.538 68.006 1329 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.61 % Favored : 96.30 % Rotamer: Outliers : 2.17 % Allowed : 13.77 % Favored : 84.06 % 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: 0.07 (0.25), residues: 1080 helix: 1.00 (0.21), residues: 490 sheet: -1.20 (0.37), residues: 180 loop : -0.37 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 497 TYR 0.024 0.003 TYR B 67 PHE 0.040 0.003 PHE B 82 TRP 0.025 0.003 TRP B 147 HIS 0.008 0.002 HIS B 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.26 ( 9240) covalent geometry : angle 0.80715 / 0.44 (12532) SS BOND : bond 0.02891 / 1.38 ( 2) SS BOND : angle 0.52572 / 0.40 ( 4) hydrogen bonds : bond 0.05277 / 3.63 ( 458) hydrogen bonds : angle 4.95781 / 3.73 ( 1332) Misc. bond : bond 0.00050 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 190 time to evaluate : 0.504 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: 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: A 176 VAL cc_start: 0.4691 (t) cc_final: 0.4229 (t) REVERT: A 256 PHE cc_start: 0.1377 (t80) cc_final: 0.1117 (t80) REVERT: A 386 GLN cc_start: 0.4104 (OUTLIER) cc_final: 0.3612 (mm-40) REVERT: A 426 THR cc_start: 0.3734 (p) cc_final: 0.3531 (p) REVERT: A 449 TYR cc_start: 0.5061 (t80) cc_final: 0.3015 (t80) REVERT: B 176 VAL cc_start: 0.4131 (t) cc_final: 0.3678 (t) REVERT: B 262 VAL cc_start: 0.2486 (m) cc_final: 0.2274 (m) REVERT: B 265 PHE cc_start: 0.4572 (OUTLIER) cc_final: 0.4279 (m-10) REVERT: C 419 MET cc_start: 0.3122 (mmp) cc_final: 0.2511 (mmp) REVERT: C 466 LEU cc_start: 0.2008 (mm) cc_final: 0.1614 (tt) REVERT: D 445 TYR cc_start: 0.5680 (m-80) cc_final: 0.5435 (m-80) REVERT: D 454 THR cc_start: 0.4924 (m) cc_final: 0.4442 (m) REVERT: D 467 GLN cc_start: 0.6696 (pm20) cc_final: 0.6278 (mt0) outliers start: 21 outliers final: 8 residues processed: 205 average time/residue: 0.2183 time to fit residues: 62.8118 Evaluate side-chains 159 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 149 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 386 GLN Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 265 PHE Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain D residue 484 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 1 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 101 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 452 ASN ** 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 = 0.4211 r_free = 0.4211 target = 0.179493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.143008 restraints weight = 41967.113| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.51 r_work: 0.3646 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5450 moved from start: 0.7704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.140 9243 Z= 0.260 Angle : 0.790 11.846 12536 Z= 0.423 Chirality : 0.045 0.184 1390 Planarity : 0.007 0.098 1530 Dihedral : 7.473 62.286 1328 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.06 % Favored : 96.85 % Rotamer: Outliers : 3.31 % Allowed : 15.42 % Favored : 81.26 % 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: 0.05 (0.25), residues: 1080 helix: 1.14 (0.22), residues: 504 sheet: -0.95 (0.40), residues: 166 loop : -0.84 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 223 TYR 0.014 0.002 TYR A 235 PHE 0.029 0.003 PHE A 120 TRP 0.038 0.002 TRP D 421 HIS 0.009 0.002 HIS A 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.26 ( 9240) covalent geometry : angle 0.78314 / 0.42 (12532) SS BOND : bond 0.02305 / 1.10 ( 2) SS BOND : angle 5.65563 / 5.14 ( 4) hydrogen bonds : bond 0.07049 / 4.76 ( 458) hydrogen bonds : angle 4.97658 / 3.70 ( 1332) Misc. bond : bond 0.00117 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 196 time to evaluate : 0.402 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: symmetry clash REVERT: A 10 CYS cc_start: 0.5689 (m) cc_final: 0.5469 (t) REVERT: A 82 PHE cc_start: 0.7294 (m-80) cc_final: 0.7042 (m-80) REVERT: A 87 ILE cc_start: 0.5411 (mt) cc_final: 0.5186 (mt) REVERT: A 120 PHE cc_start: 0.3955 (m-10) cc_final: 0.3742 (m-80) REVERT: A 162 ILE cc_start: 0.5249 (tp) cc_final: 0.5037 (tp) REVERT: A 176 VAL cc_start: 0.5481 (t) cc_final: 0.4986 (t) REVERT: A 249 LEU cc_start: 0.5552 (OUTLIER) cc_final: 0.5342 (tp) REVERT: A 446 ASP cc_start: 0.3441 (t0) cc_final: 0.2775 (p0) REVERT: B 146 THR cc_start: 0.7479 (OUTLIER) cc_final: 0.7218 (p) REVERT: B 285 ILE cc_start: 0.6269 (tt) cc_final: 0.6038 (mt) REVERT: B 398 VAL cc_start: 0.6545 (t) cc_final: 0.6167 (t) REVERT: C 419 MET cc_start: 0.3924 (mmp) cc_final: 0.3017 (mmp) REVERT: D 467 GLN cc_start: 0.6685 (pm20) cc_final: 0.6318 (mt0) REVERT: D 479 TYR cc_start: 0.5185 (m-80) cc_final: 0.4746 (m-80) outliers start: 32 outliers final: 11 residues processed: 215 average time/residue: 0.1681 time to fit residues: 51.4855 Evaluate side-chains 170 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 481 CYS Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 484 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 63 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 72 optimal weight: 0.5980 chunk 12 optimal weight: 0.3980 chunk 59 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 30 optimal weight: 0.0670 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 56 HIS A 386 GLN ** B 156 HIS ** 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 = 0.4217 r_free = 0.4217 target = 0.180233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.144244 restraints weight = 41790.379| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.48 r_work: 0.3663 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5721 moved from start: 0.8804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 9243 Z= 0.145 Angle : 0.575 8.157 12536 Z= 0.308 Chirality : 0.039 0.166 1390 Planarity : 0.004 0.049 1530 Dihedral : 7.262 63.180 1328 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.41 % Favored : 97.50 % Rotamer: Outliers : 1.35 % Allowed : 17.60 % Favored : 81.06 % 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: 0.44 (0.26), residues: 1080 helix: 1.54 (0.22), residues: 504 sheet: -0.82 (0.41), residues: 169 loop : -0.74 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 497 TYR 0.010 0.001 TYR C 465 PHE 0.020 0.001 PHE B 109 TRP 0.011 0.001 TRP B 118 HIS 0.008 0.001 HIS A 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 9240) covalent geometry : angle 0.57013 / 0.31 (12532) SS BOND : bond 0.00432 / 0.22 ( 2) SS BOND : angle 4.21352 / 3.21 ( 4) hydrogen bonds : bond 0.04158 / 2.86 ( 458) hydrogen bonds : angle 4.48732 / 3.34 ( 1332) Misc. bond : bond 0.00046 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 171 time to evaluate : 0.422 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: A 82 PHE cc_start: 0.7589 (m-80) cc_final: 0.7293 (m-10) REVERT: A 120 PHE cc_start: 0.4381 (m-10) cc_final: 0.3953 (m-80) REVERT: A 176 VAL cc_start: 0.5626 (t) cc_final: 0.5168 (t) REVERT: B 146 THR cc_start: 0.7690 (OUTLIER) cc_final: 0.7486 (p) REVERT: B 147 TRP cc_start: 0.7918 (m100) cc_final: 0.7627 (m100) REVERT: B 398 VAL cc_start: 0.6877 (t) cc_final: 0.6392 (t) REVERT: D 467 GLN cc_start: 0.6746 (pm20) cc_final: 0.6456 (mt0) outliers start: 13 outliers final: 9 residues processed: 180 average time/residue: 0.1867 time to fit residues: 48.2626 Evaluate side-chains 160 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 150 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 484 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 81 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 102 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 ASN B 210 GLN C 459 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.179296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.142641 restraints weight = 42461.760| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.82 r_work: 0.3619 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 1.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.115 9243 Z= 0.268 Angle : 0.826 10.625 12536 Z= 0.445 Chirality : 0.048 0.245 1390 Planarity : 0.007 0.067 1530 Dihedral : 7.404 59.642 1328 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.19 % Favored : 94.72 % Rotamer: Outliers : 3.11 % Allowed : 16.56 % Favored : 80.33 % 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: -0.57 (0.25), residues: 1080 helix: 0.66 (0.22), residues: 502 sheet: -1.02 (0.41), residues: 168 loop : -1.32 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 77 TYR 0.034 0.002 TYR C 445 PHE 0.053 0.003 PHE A 19 TRP 0.026 0.002 TRP B 52 HIS 0.020 0.004 HIS A 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.27 ( 9240) covalent geometry : angle 0.82491 / 0.44 (12532) SS BOND : bond 0.01868 / 0.89 ( 2) SS BOND : angle 2.67219 / 2.36 ( 4) hydrogen bonds : bond 0.06036 / 4.13 ( 458) hydrogen bonds : angle 4.90456 / 3.65 ( 1332) Misc. bond : bond 0.00082 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 0.508 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: A 192 VAL cc_start: 0.2129 (OUTLIER) cc_final: 0.1731 (p) REVERT: A 315 TYR cc_start: 0.6255 (t80) cc_final: 0.5883 (t80) REVERT: A 389 ASN cc_start: 0.7643 (t0) cc_final: 0.7183 (t0) REVERT: A 394 GLU cc_start: 0.6015 (mt-10) cc_final: 0.5223 (mt-10) REVERT: A 446 ASP cc_start: 0.4011 (t0) cc_final: 0.3304 (p0) REVERT: B 83 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8380 (tt0) REVERT: B 252 THR cc_start: 0.7641 (p) cc_final: 0.7393 (m) REVERT: B 454 SER cc_start: 0.8035 (p) cc_final: 0.7652 (p) REVERT: C 419 MET cc_start: 0.6409 (mmp) cc_final: 0.5830 (mmp) REVERT: C 444 TYR cc_start: 0.6130 (m-80) cc_final: 0.5914 (m-80) REVERT: D 486 ARG cc_start: 0.5883 (tpp80) cc_final: 0.5440 (tpp-160) outliers start: 30 outliers final: 16 residues processed: 218 average time/residue: 0.2197 time to fit residues: 65.3293 Evaluate side-chains 164 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 484 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 105 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 GLN B 7 ASN ** B 156 HIS ** 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 = 0.4167 r_free = 0.4167 target = 0.175670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.137327 restraints weight = 41837.502| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.94 r_work: 0.3537 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 1.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 9243 Z= 0.164 Angle : 0.580 6.030 12536 Z= 0.315 Chirality : 0.041 0.182 1390 Planarity : 0.005 0.064 1530 Dihedral : 6.831 57.512 1328 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.78 % Favored : 97.13 % Rotamer: Outliers : 2.59 % Allowed : 19.46 % Favored : 77.95 % 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: -0.01 (0.25), residues: 1080 helix: 1.23 (0.22), residues: 498 sheet: -1.03 (0.40), residues: 168 loop : -1.02 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 129 TYR 0.020 0.002 TYR D 479 PHE 0.015 0.002 PHE A 104 TRP 0.015 0.001 TRP B 118 HIS 0.006 0.001 HIS A 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 9240) covalent geometry : angle 0.57806 / 0.31 (12532) SS BOND : bond 0.00282 / 0.15 ( 2) SS BOND : angle 2.52636 / 1.89 ( 4) hydrogen bonds : bond 0.04672 / 3.21 ( 458) hydrogen bonds : angle 4.51072 / 3.36 ( 1332) Misc. bond : bond 0.00033 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 0.332 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: symmetry clash REVERT: A 192 VAL cc_start: 0.2411 (OUTLIER) cc_final: 0.2030 (p) REVERT: A 446 ASP cc_start: 0.4121 (t0) cc_final: 0.3428 (p0) REVERT: B 62 CYS cc_start: 0.7476 (p) cc_final: 0.6962 (t) REVERT: B 83 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8237 (tt0) REVERT: B 143 MET cc_start: 0.9023 (mmm) cc_final: 0.8813 (mmp) REVERT: B 252 THR cc_start: 0.7775 (p) cc_final: 0.7521 (m) REVERT: B 454 SER cc_start: 0.8005 (p) cc_final: 0.7618 (p) REVERT: C 419 MET cc_start: 0.6677 (mmp) cc_final: 0.6179 (mmp) REVERT: C 437 MET cc_start: 0.8188 (ttt) cc_final: 0.7922 (ttt) REVERT: C 463 THR cc_start: 0.4517 (m) cc_final: 0.4009 (p) REVERT: D 486 ARG cc_start: 0.6141 (tpp80) cc_final: 0.5653 (tpp-160) outliers start: 25 outliers final: 15 residues processed: 184 average time/residue: 0.1925 time to fit residues: 49.6004 Evaluate side-chains 170 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 218 HIS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 492 SER Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 484 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 26 optimal weight: 0.1980 chunk 42 optimal weight: 0.0980 chunk 15 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 4 optimal weight: 0.4980 chunk 18 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 GLN B 7 ASN ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN C 459 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.175899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.137102 restraints weight = 41874.006| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.93 r_work: 0.3533 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 1.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9243 Z= 0.122 Angle : 0.529 6.344 12536 Z= 0.281 Chirality : 0.038 0.146 1390 Planarity : 0.004 0.051 1530 Dihedral : 6.328 56.193 1328 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.41 % Favored : 97.50 % Rotamer: Outliers : 1.76 % Allowed : 20.29 % Favored : 77.95 % 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: 0.52 (0.26), residues: 1080 helix: 1.79 (0.23), residues: 498 sheet: -0.97 (0.41), residues: 166 loop : -0.83 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 457 TYR 0.020 0.001 TYR C 445 PHE 0.022 0.001 PHE D 422 TRP 0.014 0.001 TRP B 118 HIS 0.006 0.001 HIS A 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 9240) covalent geometry : angle 0.52852 / 0.28 (12532) SS BOND : bond 0.01413 / 0.68 ( 2) SS BOND : angle 1.19787 / 0.87 ( 4) hydrogen bonds : bond 0.04051 / 2.76 ( 458) hydrogen bonds : angle 4.17198 / 3.09 ( 1332) Misc. bond : bond 0.00048 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 0.529 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: A 192 VAL cc_start: 0.2597 (OUTLIER) cc_final: 0.2201 (p) REVERT: A 446 ASP cc_start: 0.4223 (t0) cc_final: 0.3561 (p0) REVERT: B 62 CYS cc_start: 0.7343 (p) cc_final: 0.7130 (t) REVERT: B 130 MET cc_start: 0.7204 (mmt) cc_final: 0.6961 (mmt) REVERT: B 143 MET cc_start: 0.9097 (mmm) cc_final: 0.8767 (mmp) REVERT: B 252 THR cc_start: 0.7678 (p) cc_final: 0.7352 (m) REVERT: B 314 ILE cc_start: 0.7464 (pt) cc_final: 0.7226 (mp) REVERT: C 414 PHE cc_start: 0.7643 (t80) cc_final: 0.7250 (t80) REVERT: C 419 MET cc_start: 0.6766 (mmp) cc_final: 0.6208 (mmp) REVERT: C 437 MET cc_start: 0.8163 (ttt) cc_final: 0.7894 (ttt) REVERT: D 423 ARG cc_start: 0.7403 (mpp80) cc_final: 0.7035 (mpp80) REVERT: D 486 ARG cc_start: 0.6211 (tpp80) cc_final: 0.5812 (tpp-160) outliers start: 17 outliers final: 10 residues processed: 174 average time/residue: 0.2042 time to fit residues: 50.6141 Evaluate side-chains 162 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 151 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 260 HIS Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain D residue 510 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 15 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 76 optimal weight: 0.0470 chunk 66 optimal weight: 0.0970 chunk 40 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 7 ASN B 156 HIS D 467 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.174328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.135082 restraints weight = 41697.062| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.87 r_work: 0.3505 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 1.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9243 Z= 0.119 Angle : 0.517 5.999 12536 Z= 0.275 Chirality : 0.038 0.160 1390 Planarity : 0.004 0.048 1530 Dihedral : 6.026 55.894 1328 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.50 % Favored : 97.41 % Rotamer: Outliers : 1.14 % Allowed : 21.01 % Favored : 77.85 % 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: 0.70 (0.26), residues: 1080 helix: 1.90 (0.23), residues: 504 sheet: -0.77 (0.41), residues: 172 loop : -0.77 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 6 TYR 0.012 0.001 TYR C 445 PHE 0.012 0.001 PHE B 109 TRP 0.013 0.001 TRP B 118 HIS 0.003 0.001 HIS A 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 9240) covalent geometry : angle 0.51671 / 0.27 (12532) SS BOND : bond 0.00715 / 0.34 ( 2) SS BOND : angle 0.87266 / 0.60 ( 4) hydrogen bonds : bond 0.03873 / 2.65 ( 458) hydrogen bonds : angle 4.06823 / 3.03 ( 1332) Misc. bond : bond 0.00041 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 171 time to evaluate : 0.359 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: A 389 ASN cc_start: 0.7743 (t0) cc_final: 0.7474 (t0) REVERT: A 394 GLU cc_start: 0.6252 (mt-10) cc_final: 0.5779 (mt-10) REVERT: A 446 ASP cc_start: 0.4232 (t0) cc_final: 0.3707 (p0) REVERT: B 143 MET cc_start: 0.9148 (mmm) cc_final: 0.8638 (mmp) REVERT: B 252 THR cc_start: 0.7655 (p) cc_final: 0.7374 (m) REVERT: B 307 LYS cc_start: 0.5921 (tptp) cc_final: 0.5509 (ttpp) REVERT: B 314 ILE cc_start: 0.7529 (pt) cc_final: 0.7309 (mp) REVERT: B 454 SER cc_start: 0.7820 (OUTLIER) cc_final: 0.7535 (p) REVERT: C 414 PHE cc_start: 0.7682 (t80) cc_final: 0.7298 (t80) REVERT: C 419 MET cc_start: 0.6909 (mmp) cc_final: 0.6403 (mmp) REVERT: D 423 ARG cc_start: 0.7487 (mpp80) cc_final: 0.7044 (mpp80) REVERT: D 459 ASN cc_start: 0.7509 (p0) cc_final: 0.6718 (t0) REVERT: D 486 ARG cc_start: 0.6249 (tpp80) cc_final: 0.5892 (tpp-160) outliers start: 11 outliers final: 8 residues processed: 176 average time/residue: 0.1958 time to fit residues: 49.0093 Evaluate side-chains 170 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 161 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 HIS Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain D residue 510 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 57 optimal weight: 0.9990 chunk 63 optimal weight: 0.3980 chunk 92 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 68 optimal weight: 0.4980 chunk 13 optimal weight: 0.6980 chunk 4 optimal weight: 0.0050 chunk 62 optimal weight: 0.6980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 7 ASN C 442 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.173428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.134015 restraints weight = 41365.304| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.93 r_work: 0.3492 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 1.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9243 Z= 0.116 Angle : 0.522 6.271 12536 Z= 0.277 Chirality : 0.038 0.172 1390 Planarity : 0.004 0.048 1530 Dihedral : 5.866 56.160 1328 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.31 % Favored : 97.59 % Rotamer: Outliers : 1.86 % Allowed : 20.70 % Favored : 77.43 % 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: 0.80 (0.26), residues: 1080 helix: 2.00 (0.23), residues: 503 sheet: -0.74 (0.41), residues: 172 loop : -0.75 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 497 TYR 0.033 0.001 TYR C 490 PHE 0.011 0.001 PHE B 109 TRP 0.013 0.001 TRP B 118 HIS 0.002 0.001 HIS A 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 9240) covalent geometry : angle 0.52195 / 0.28 (12532) SS BOND : bond 0.00501 / 0.25 ( 2) SS BOND : angle 1.40779 / 1.04 ( 4) hydrogen bonds : bond 0.03908 / 2.66 ( 458) hydrogen bonds : angle 3.99452 / 2.97 ( 1332) Misc. bond : bond 0.00054 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.535 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: A 192 VAL cc_start: 0.3063 (OUTLIER) cc_final: 0.2679 (p) REVERT: A 446 ASP cc_start: 0.4524 (t0) cc_final: 0.3974 (p0) REVERT: A 472 LYS cc_start: 0.6753 (mmtm) cc_final: 0.6173 (ttmt) REVERT: B 143 MET cc_start: 0.9148 (mmm) cc_final: 0.8493 (mmp) REVERT: B 252 THR cc_start: 0.7746 (p) cc_final: 0.7496 (m) REVERT: B 307 LYS cc_start: 0.5893 (tptp) cc_final: 0.5482 (ttpp) REVERT: B 454 SER cc_start: 0.7848 (OUTLIER) cc_final: 0.7565 (p) REVERT: C 414 PHE cc_start: 0.7685 (t80) cc_final: 0.7308 (t80) REVERT: C 419 MET cc_start: 0.7021 (mmp) cc_final: 0.6503 (mmp) outliers start: 18 outliers final: 14 residues processed: 172 average time/residue: 0.2257 time to fit residues: 54.2087 Evaluate side-chains 168 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 260 HIS Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain D residue 510 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 13 optimal weight: 0.9980 chunk 103 optimal weight: 0.4980 chunk 89 optimal weight: 0.3980 chunk 102 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 105 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 389 ASN C 469 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.170497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.129970 restraints weight = 41560.206| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 3.01 r_work: 0.3428 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 1.5658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9243 Z= 0.154 Angle : 0.560 7.884 12536 Z= 0.299 Chirality : 0.040 0.167 1390 Planarity : 0.005 0.047 1530 Dihedral : 5.916 55.079 1328 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.70 % Favored : 96.20 % Rotamer: Outliers : 1.76 % Allowed : 20.60 % Favored : 77.64 % 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: 0.67 (0.26), residues: 1080 helix: 1.85 (0.23), residues: 505 sheet: -0.65 (0.40), residues: 177 loop : -0.82 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 497 TYR 0.024 0.002 TYR C 490 PHE 0.015 0.002 PHE B 109 TRP 0.013 0.001 TRP B 147 HIS 0.004 0.001 HIS B 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 9240) covalent geometry : angle 0.55950 / 0.30 (12532) SS BOND : bond 0.00401 / 0.20 ( 2) SS BOND : angle 1.38606 / 1.03 ( 4) hydrogen bonds : bond 0.04444 / 3.06 ( 458) hydrogen bonds : angle 4.10670 / 3.07 ( 1332) Misc. bond : bond 0.00044 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 0.501 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: A 192 VAL cc_start: 0.3299 (OUTLIER) cc_final: 0.2968 (p) REVERT: A 446 ASP cc_start: 0.4771 (t0) cc_final: 0.4167 (p0) REVERT: A 472 LYS cc_start: 0.6838 (mmtm) cc_final: 0.6248 (ttmt) REVERT: B 307 LYS cc_start: 0.5838 (tptp) cc_final: 0.5442 (ttpp) REVERT: B 425 MET cc_start: 0.7573 (mtp) cc_final: 0.7293 (mtt) REVERT: B 453 TRP cc_start: 0.6191 (t60) cc_final: 0.5520 (t60) REVERT: B 454 SER cc_start: 0.8059 (OUTLIER) cc_final: 0.7831 (p) REVERT: C 414 PHE cc_start: 0.7813 (t80) cc_final: 0.7466 (t80) REVERT: C 419 MET cc_start: 0.7366 (mmp) cc_final: 0.6872 (mmp) REVERT: D 454 THR cc_start: 0.5555 (m) cc_final: 0.5197 (p) outliers start: 17 outliers final: 14 residues processed: 166 average time/residue: 0.2228 time to fit residues: 51.8622 Evaluate side-chains 163 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 260 HIS Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 492 SER Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain D residue 510 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 65 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 33 optimal weight: 0.0770 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 181 ASN C 459 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.169860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.129924 restraints weight = 40993.451| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.75 r_work: 0.3426 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 1.6214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9243 Z= 0.130 Angle : 0.542 4.745 12536 Z= 0.289 Chirality : 0.039 0.158 1390 Planarity : 0.005 0.082 1530 Dihedral : 5.895 58.563 1328 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.78 % Favored : 97.13 % Rotamer: Outliers : 1.55 % Allowed : 20.91 % Favored : 77.54 % 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: 0.67 (0.26), residues: 1080 helix: 1.85 (0.23), residues: 505 sheet: -0.59 (0.40), residues: 177 loop : -0.86 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 412 TYR 0.019 0.001 TYR C 445 PHE 0.014 0.001 PHE B 109 TRP 0.012 0.001 TRP B 118 HIS 0.004 0.001 HIS B 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 9240) covalent geometry : angle 0.54204 / 0.29 (12532) SS BOND : bond 0.00374 / 0.19 ( 2) SS BOND : angle 1.29766 / 0.97 ( 4) hydrogen bonds : bond 0.04246 / 2.91 ( 458) hydrogen bonds : angle 4.06924 / 3.05 ( 1332) Misc. bond : bond 0.00049 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4542.08 seconds wall clock time: 77 minutes 45.66 seconds (4665.66 seconds total)