Starting phenix.real_space_refine on Wed Feb 4 11:58:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iu1_60886/02_2026/9iu1_60886.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iu1_60886/02_2026/9iu1_60886.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9iu1_60886/02_2026/9iu1_60886.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iu1_60886/02_2026/9iu1_60886.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9iu1_60886/02_2026/9iu1_60886.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iu1_60886/02_2026/9iu1_60886.map" } resolution = 4.3 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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4904 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4222 2.51 5 N 1076 2.21 5 O 1268 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6603 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "B" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1557 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 12, 'TRANS': 181} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.31, per 1000 atoms: 0.20 Number of scatterers: 6603 At special positions: 0 Unit cell: (87.435, 86.43, 116.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1268 8.00 N 1076 7.00 C 4222 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 524 " 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=0, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG A 701 " - " ASN A 322 " " NAG B1300 " - " ASN B 343 " " NAG C 1 " - " ASN A 53 " " NAG D 1 " - " ASN A 546 " " NAG E 1 " - " ASN A 90 " " NAG F 1 " - " ASN A 103 " Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 203.5 milliseconds 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1490 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 6 sheets defined 52.4% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.697A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 92 through 103 Processing helix chain 'A' and resid 109 through 130 removed outlier: 3.822A pdb=" N THR A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 152 Processing helix chain 'A' and resid 157 through 174 removed outlier: 4.598A pdb=" N GLU A 171 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N VAL A 172 " --> pdb=" O TRP A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 194 removed outlier: 3.791A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 221 through 249 Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 276 through 283 removed outlier: 3.814A pdb=" N SER A 280 " --> pdb=" O ASN A 277 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU A 281 " --> pdb=" O LEU A 278 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR A 282 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL A 283 " --> pdb=" O SER A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 removed outlier: 3.734A pdb=" N VAL A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 removed outlier: 3.859A pdb=" N PHE A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.602A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 411 removed outlier: 4.283A pdb=" N HIS A 401 " --> pdb=" O ASN A 397 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLU A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 431 through 466 removed outlier: 4.049A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 469 through 485 removed outlier: 4.463A pdb=" N MET A 474 " --> pdb=" O LYS A 470 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N LYS A 475 " --> pdb=" O ASP A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 534 removed outlier: 4.544A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 removed outlier: 3.990A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG A 559 " --> pdb=" O PHE A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.266A pdb=" N LYS B 386 " --> pdb=" O SER B 383 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.299A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 134 removed outlier: 3.780A pdb=" N VAL A 132 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 142 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLU A 140 " --> pdb=" O ASN A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.839A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 349 Processing sheet with id=AA4, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.640A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS B 432 " --> pdb=" O LEU B 512 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474 281 hydrogen bonds defined for protein. 810 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: 0.91 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2077 1.34 - 1.46: 1507 1.46 - 1.58: 3149 1.58 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 6791 Sorted by residual: bond pdb=" C1 MAN F 4 " pdb=" C2 MAN F 4 " ideal model delta sigma weight residual 1.526 1.570 -0.044 2.00e-02 2.50e+03 4.82e+00 bond pdb=" C1 BMA E 3 " pdb=" C2 BMA E 3 " ideal model delta sigma weight residual 1.519 1.555 -0.036 2.00e-02 2.50e+03 3.20e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.55e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.49e+00 bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.37e+00 ... (remaining 6786 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 8859 1.31 - 2.61: 285 2.61 - 3.92: 54 3.92 - 5.23: 22 5.23 - 6.53: 10 Bond angle restraints: 9230 Sorted by residual: angle pdb=" C ASN B 417 " pdb=" N ILE B 418 " pdb=" CA ILE B 418 " ideal model delta sigma weight residual 120.60 124.24 -3.64 1.29e+00 6.01e-01 7.97e+00 angle pdb=" N THR B 522 " pdb=" CA THR B 522 " pdb=" C THR B 522 " ideal model delta sigma weight residual 110.80 116.40 -5.60 2.13e+00 2.20e-01 6.90e+00 angle pdb=" CA ILE A 468 " pdb=" C ILE A 468 " pdb=" N PRO A 469 " ideal model delta sigma weight residual 116.57 118.99 -2.42 9.80e-01 1.04e+00 6.12e+00 angle pdb=" N LEU A 450 " pdb=" CA LEU A 450 " pdb=" C LEU A 450 " ideal model delta sigma weight residual 109.81 114.92 -5.11 2.21e+00 2.05e-01 5.34e+00 angle pdb=" C ASP B 420 " pdb=" N TYR B 421 " pdb=" CA TYR B 421 " ideal model delta sigma weight residual 121.98 118.71 3.27 1.53e+00 4.27e-01 4.57e+00 ... (remaining 9225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.08: 3782 22.08 - 44.17: 317 44.17 - 66.25: 47 66.25 - 88.34: 22 88.34 - 110.42: 10 Dihedral angle restraints: 4178 sinusoidal: 1857 harmonic: 2321 Sorted by residual: dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual -86.00 -161.61 75.61 1 1.00e+01 1.00e-02 7.21e+01 dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 524 " pdb=" CB CYS B 524 " ideal model delta sinusoidal sigma weight residual 93.00 138.37 -45.37 1 1.00e+01 1.00e-02 2.86e+01 dihedral pdb=" CA ALA B 521 " pdb=" C ALA B 521 " pdb=" N THR B 522 " pdb=" CA THR B 522 " ideal model delta harmonic sigma weight residual 180.00 158.66 21.34 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 4175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 863 0.061 - 0.121: 125 0.121 - 0.182: 11 0.182 - 0.242: 1 0.242 - 0.303: 3 Chirality restraints: 1003 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 546 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 1000 not shown) Planarity restraints: 1179 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 199 " 0.014 2.00e-02 2.50e+03 1.51e-02 4.57e+00 pdb=" CG TYR A 199 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR A 199 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR A 199 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 199 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 199 " 0.015 2.00e-02 2.50e+03 pdb=" CZ TYR A 199 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 199 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 477 " -0.013 2.00e-02 2.50e+03 1.32e-02 4.35e+00 pdb=" CG TRP A 477 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP A 477 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 477 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 477 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 477 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 477 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 477 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 477 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 477 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 414 " -0.024 5.00e-02 4.00e+02 3.70e-02 2.20e+00 pdb=" N PRO A 415 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 415 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 415 " -0.021 5.00e-02 4.00e+02 ... (remaining 1176 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1303 2.77 - 3.30: 6581 3.30 - 3.84: 11079 3.84 - 4.37: 11746 4.37 - 4.90: 19875 Nonbonded interactions: 50584 Sorted by model distance: nonbonded pdb=" OG1 THR B 393 " pdb=" OD1 ASN B 394 " model vdw 2.241 3.040 nonbonded pdb=" OG1 THR B 356 " pdb=" O ALA B 397 " model vdw 2.253 3.040 nonbonded pdb=" OG SER A 411 " pdb=" OE1 GLN A 526 " model vdw 2.271 3.040 nonbonded pdb=" OG1 THR A 365 " pdb=" OD1 ASP A 367 " model vdw 2.290 3.040 nonbonded pdb=" NH2 ARG A 482 " pdb=" O THR A 608 " model vdw 2.303 3.120 ... (remaining 50579 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 '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 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: 3.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.390 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 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 0.044 6811 Z= 0.159 Angle : 0.625 11.220 9284 Z= 0.299 Chirality : 0.045 0.303 1003 Planarity : 0.003 0.037 1173 Dihedral : 17.138 110.421 2670 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: 0.02 (0.31), residues: 786 helix: 1.93 (0.29), residues: 361 sheet: 2.25 (1.21), residues: 22 loop : -2.08 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 460 TYR 0.034 0.001 TYR A 199 PHE 0.010 0.001 PHE A 523 TRP 0.036 0.002 TRP A 477 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 6791) covalent geometry : angle 0.60041 ( 9230) SS BOND : bond 0.00178 ( 6) SS BOND : angle 0.56046 ( 12) hydrogen bonds : bond 0.09981 ( 281) hydrogen bonds : angle 5.14367 ( 810) link_ALPHA1-3 : bond 0.00481 ( 1) link_ALPHA1-3 : angle 1.68575 ( 3) link_ALPHA1-6 : bond 0.00538 ( 1) link_ALPHA1-6 : angle 1.50007 ( 3) link_BETA1-4 : bond 0.00438 ( 6) link_BETA1-4 : angle 1.33185 ( 18) link_NAG-ASN : bond 0.01011 ( 6) link_NAG-ASN : angle 3.69641 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.8630 (m) cc_final: 0.7945 (t) REVERT: A 72 PHE cc_start: 0.8554 (t80) cc_final: 0.8227 (t80) REVERT: A 83 TYR cc_start: 0.6486 (m-80) cc_final: 0.4755 (m-80) REVERT: A 97 LEU cc_start: 0.8731 (tp) cc_final: 0.8522 (tp) REVERT: A 189 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8309 (mm-30) REVERT: A 207 TYR cc_start: 0.7867 (m-80) cc_final: 0.7535 (m-80) REVERT: A 232 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7868 (mm-30) REVERT: A 265 HIS cc_start: 0.7868 (p90) cc_final: 0.7667 (p90) REVERT: A 279 TYR cc_start: 0.7245 (t80) cc_final: 0.6939 (t80) REVERT: A 483 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7087 (mt-10) REVERT: A 518 ARG cc_start: 0.6955 (ppt170) cc_final: 0.6306 (ppt170) REVERT: A 557 MET cc_start: 0.8294 (tmm) cc_final: 0.8034 (ppp) REVERT: B 347 PHE cc_start: 0.6553 (m-10) cc_final: 0.4936 (m-80) REVERT: B 351 TYR cc_start: 0.6728 (t80) cc_final: 0.6397 (t80) REVERT: B 353 TRP cc_start: 0.7597 (p-90) cc_final: 0.7167 (p-90) REVERT: B 355 ARG cc_start: 0.7832 (tpp80) cc_final: 0.7363 (mmm-85) REVERT: B 442 ASP cc_start: 0.7890 (t70) cc_final: 0.7039 (p0) REVERT: B 444 LYS cc_start: 0.8176 (mtpt) cc_final: 0.7870 (mmtt) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.0752 time to fit residues: 18.2709 Evaluate side-chains 118 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 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 = 0.4044 r_free = 0.4044 target = 0.149880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.128617 restraints weight = 18364.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.132360 restraints weight = 13430.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.133480 restraints weight = 8656.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.134137 restraints weight = 6931.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.135502 restraints weight = 6244.320| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6811 Z= 0.147 Angle : 0.650 11.373 9284 Z= 0.324 Chirality : 0.045 0.265 1003 Planarity : 0.005 0.041 1173 Dihedral : 11.325 75.633 1143 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 0.14 % Allowed : 3.17 % Favored : 96.69 % 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: -0.16 (0.31), residues: 786 helix: 1.68 (0.28), residues: 366 sheet: 0.46 (0.91), residues: 32 loop : -2.06 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 346 TYR 0.015 0.002 TYR B 453 PHE 0.021 0.001 PHE B 464 TRP 0.016 0.001 TRP A 461 HIS 0.010 0.002 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 6791) covalent geometry : angle 0.61561 ( 9230) SS BOND : bond 0.00472 ( 6) SS BOND : angle 2.20781 ( 12) hydrogen bonds : bond 0.04344 ( 281) hydrogen bonds : angle 4.92049 ( 810) link_ALPHA1-3 : bond 0.01213 ( 1) link_ALPHA1-3 : angle 3.22826 ( 3) link_ALPHA1-6 : bond 0.00441 ( 1) link_ALPHA1-6 : angle 2.11753 ( 3) link_BETA1-4 : bond 0.00712 ( 6) link_BETA1-4 : angle 1.84609 ( 18) link_NAG-ASN : bond 0.01068 ( 6) link_NAG-ASN : angle 3.78361 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.8752 (m) cc_final: 0.7854 (t) REVERT: A 72 PHE cc_start: 0.8427 (t80) cc_final: 0.8078 (t80) REVERT: A 207 TYR cc_start: 0.7808 (m-80) cc_final: 0.7546 (m-80) REVERT: A 232 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7934 (mm-30) REVERT: A 265 HIS cc_start: 0.7869 (p90) cc_final: 0.7001 (p90) REVERT: A 474 MET cc_start: 0.8067 (mmm) cc_final: 0.7807 (mmm) REVERT: A 483 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7294 (mt-10) REVERT: B 351 TYR cc_start: 0.7056 (t80) cc_final: 0.6588 (t80) REVERT: B 353 TRP cc_start: 0.7560 (p-90) cc_final: 0.6943 (p-90) REVERT: B 442 ASP cc_start: 0.7978 (t70) cc_final: 0.7117 (p0) REVERT: B 444 LYS cc_start: 0.8012 (mtpt) cc_final: 0.7811 (mmtt) REVERT: B 457 ARG cc_start: 0.7741 (tmt-80) cc_final: 0.7094 (tmt-80) outliers start: 1 outliers final: 0 residues processed: 143 average time/residue: 0.0615 time to fit residues: 12.0056 Evaluate side-chains 106 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 12 optimal weight: 0.6980 chunk 58 optimal weight: 0.0980 chunk 18 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 71 optimal weight: 0.0770 chunk 4 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.150047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.129357 restraints weight = 18367.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.133132 restraints weight = 13452.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.134230 restraints weight = 8472.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.134999 restraints weight = 6650.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.135621 restraints weight = 6206.774| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 6811 Z= 0.129 Angle : 0.633 12.389 9284 Z= 0.311 Chirality : 0.044 0.259 1003 Planarity : 0.004 0.040 1173 Dihedral : 9.632 65.626 1143 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % 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: -0.20 (0.31), residues: 786 helix: 1.62 (0.28), residues: 366 sheet: 0.29 (0.90), residues: 32 loop : -2.03 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 357 TYR 0.018 0.001 TYR B 453 PHE 0.016 0.001 PHE A 512 TRP 0.016 0.001 TRP A 594 HIS 0.004 0.001 HIS A 535 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 6791) covalent geometry : angle 0.59897 ( 9230) SS BOND : bond 0.01141 ( 6) SS BOND : angle 2.28446 ( 12) hydrogen bonds : bond 0.04280 ( 281) hydrogen bonds : angle 4.77628 ( 810) link_ALPHA1-3 : bond 0.01284 ( 1) link_ALPHA1-3 : angle 2.49520 ( 3) link_ALPHA1-6 : bond 0.00768 ( 1) link_ALPHA1-6 : angle 2.19379 ( 3) link_BETA1-4 : bond 0.00578 ( 6) link_BETA1-4 : angle 1.89206 ( 18) link_NAG-ASN : bond 0.01031 ( 6) link_NAG-ASN : angle 3.72391 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.8609 (m) cc_final: 0.7570 (t) REVERT: A 83 TYR cc_start: 0.6338 (m-80) cc_final: 0.5605 (m-80) REVERT: A 207 TYR cc_start: 0.7741 (m-80) cc_final: 0.7471 (m-80) REVERT: A 232 GLU cc_start: 0.8283 (mm-30) cc_final: 0.8027 (mt-10) REVERT: A 355 ASP cc_start: 0.8001 (t0) cc_final: 0.7656 (p0) REVERT: A 406 GLU cc_start: 0.6144 (mt-10) cc_final: 0.5914 (mt-10) REVERT: A 480 MET cc_start: 0.7854 (ptt) cc_final: 0.7654 (ptt) REVERT: A 483 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7320 (mt-10) REVERT: A 589 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7593 (mt-10) REVERT: B 351 TYR cc_start: 0.6983 (t80) cc_final: 0.6575 (t80) REVERT: B 355 ARG cc_start: 0.7421 (tpp80) cc_final: 0.6681 (mmm-85) REVERT: B 405 ASN cc_start: 0.7120 (p0) cc_final: 0.6813 (p0) REVERT: B 409 GLN cc_start: 0.7528 (mm-40) cc_final: 0.7019 (mt0) REVERT: B 442 ASP cc_start: 0.7488 (t70) cc_final: 0.7181 (p0) REVERT: B 444 LYS cc_start: 0.8066 (mtpt) cc_final: 0.7843 (mmtt) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.0669 time to fit residues: 13.3862 Evaluate side-chains 115 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 54 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 chunk 30 optimal weight: 0.3980 chunk 15 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 59 optimal weight: 0.0870 chunk 16 optimal weight: 6.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.151123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.130343 restraints weight = 18641.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.134083 restraints weight = 13287.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.135114 restraints weight = 8899.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.135872 restraints weight = 7266.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.136582 restraints weight = 6468.506| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 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 0.057 6811 Z= 0.132 Angle : 0.643 11.118 9284 Z= 0.316 Chirality : 0.045 0.261 1003 Planarity : 0.004 0.037 1173 Dihedral : 8.742 59.613 1143 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % 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: -0.31 (0.31), residues: 786 helix: 1.56 (0.28), residues: 368 sheet: -0.09 (0.85), residues: 32 loop : -2.12 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 355 TYR 0.018 0.002 TYR B 453 PHE 0.018 0.001 PHE B 464 TRP 0.014 0.001 TRP A 477 HIS 0.007 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 6791) covalent geometry : angle 0.61127 ( 9230) SS BOND : bond 0.01029 ( 6) SS BOND : angle 1.88611 ( 12) hydrogen bonds : bond 0.04232 ( 281) hydrogen bonds : angle 4.75722 ( 810) link_ALPHA1-3 : bond 0.01247 ( 1) link_ALPHA1-3 : angle 2.71834 ( 3) link_ALPHA1-6 : bond 0.00911 ( 1) link_ALPHA1-6 : angle 2.33289 ( 3) link_BETA1-4 : bond 0.00558 ( 6) link_BETA1-4 : angle 1.87539 ( 18) link_NAG-ASN : bond 0.01009 ( 6) link_NAG-ASN : angle 3.69525 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.8690 (m) cc_final: 0.7598 (t) REVERT: A 72 PHE cc_start: 0.8489 (t80) cc_final: 0.8079 (t80) REVERT: A 207 TYR cc_start: 0.7734 (m-80) cc_final: 0.7502 (m-80) REVERT: A 222 LEU cc_start: 0.9315 (mt) cc_final: 0.9031 (mt) REVERT: A 355 ASP cc_start: 0.7988 (t0) cc_final: 0.7715 (p0) REVERT: A 480 MET cc_start: 0.8035 (ptt) cc_final: 0.7779 (ptt) REVERT: A 483 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7303 (mt-10) REVERT: A 589 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7619 (mt-10) REVERT: B 351 TYR cc_start: 0.7233 (t80) cc_final: 0.6924 (t80) REVERT: B 353 TRP cc_start: 0.7347 (p-90) cc_final: 0.7039 (p-90) REVERT: B 387 LEU cc_start: 0.8791 (tp) cc_final: 0.8585 (tp) REVERT: B 442 ASP cc_start: 0.7616 (t70) cc_final: 0.7206 (p0) REVERT: B 457 ARG cc_start: 0.7754 (tmt-80) cc_final: 0.7054 (tmt-80) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.0655 time to fit residues: 13.3754 Evaluate side-chains 111 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 12 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 23 optimal weight: 0.5980 chunk 10 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 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 = 0.4047 r_free = 0.4047 target = 0.150560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.129752 restraints weight = 18534.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.133340 restraints weight = 13187.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.134402 restraints weight = 8763.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.135153 restraints weight = 7045.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.136849 restraints weight = 6351.807| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6811 Z= 0.131 Angle : 0.646 10.977 9284 Z= 0.320 Chirality : 0.044 0.265 1003 Planarity : 0.004 0.038 1173 Dihedral : 8.261 53.044 1143 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % 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: -0.42 (0.31), residues: 786 helix: 1.46 (0.28), residues: 367 sheet: -0.20 (0.86), residues: 32 loop : -2.14 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 355 TYR 0.025 0.002 TYR A 83 PHE 0.020 0.001 PHE B 377 TRP 0.031 0.001 TRP A 477 HIS 0.006 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 6791) covalent geometry : angle 0.61602 ( 9230) SS BOND : bond 0.00764 ( 6) SS BOND : angle 1.48415 ( 12) hydrogen bonds : bond 0.04298 ( 281) hydrogen bonds : angle 4.69191 ( 810) link_ALPHA1-3 : bond 0.01436 ( 1) link_ALPHA1-3 : angle 2.53357 ( 3) link_ALPHA1-6 : bond 0.00943 ( 1) link_ALPHA1-6 : angle 2.14746 ( 3) link_BETA1-4 : bond 0.00564 ( 6) link_BETA1-4 : angle 1.93543 ( 18) link_NAG-ASN : bond 0.01098 ( 6) link_NAG-ASN : angle 3.70323 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.8595 (m) cc_final: 0.7567 (t) REVERT: A 72 PHE cc_start: 0.8319 (t80) cc_final: 0.7975 (t80) REVERT: A 181 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7577 (mt-10) REVERT: A 207 TYR cc_start: 0.7670 (m-80) cc_final: 0.7423 (m-80) REVERT: A 222 LEU cc_start: 0.9302 (mt) cc_final: 0.9017 (mt) REVERT: A 355 ASP cc_start: 0.8009 (t0) cc_final: 0.7677 (p0) REVERT: A 477 TRP cc_start: 0.7690 (t-100) cc_final: 0.6829 (t-100) REVERT: A 589 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7594 (mt-10) REVERT: A 592 PHE cc_start: 0.7810 (t80) cc_final: 0.7568 (t80) REVERT: B 351 TYR cc_start: 0.7275 (t80) cc_final: 0.6943 (t80) REVERT: B 353 TRP cc_start: 0.7373 (p-90) cc_final: 0.7103 (p-90) REVERT: B 442 ASP cc_start: 0.7682 (t70) cc_final: 0.7138 (p0) REVERT: B 457 ARG cc_start: 0.7714 (tmt-80) cc_final: 0.7431 (tmt-80) REVERT: B 494 TYR cc_start: 0.6325 (m-80) cc_final: 0.6040 (m-80) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.0642 time to fit residues: 12.7525 Evaluate side-chains 113 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 19 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 54 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 0.0870 chunk 65 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 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 = 0.4027 r_free = 0.4027 target = 0.149211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.128360 restraints weight = 18381.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.131745 restraints weight = 13423.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.133160 restraints weight = 8835.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.133997 restraints weight = 6877.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.134959 restraints weight = 6215.082| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6811 Z= 0.140 Angle : 0.652 10.914 9284 Z= 0.328 Chirality : 0.045 0.272 1003 Planarity : 0.004 0.040 1173 Dihedral : 7.850 54.599 1143 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % 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: -0.57 (0.31), residues: 786 helix: 1.30 (0.28), residues: 371 sheet: -0.56 (0.85), residues: 32 loop : -2.18 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 357 TYR 0.021 0.002 TYR A 83 PHE 0.017 0.002 PHE A 512 TRP 0.038 0.001 TRP A 477 HIS 0.004 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 6791) covalent geometry : angle 0.62404 ( 9230) SS BOND : bond 0.00713 ( 6) SS BOND : angle 1.30909 ( 12) hydrogen bonds : bond 0.04494 ( 281) hydrogen bonds : angle 4.82733 ( 810) link_ALPHA1-3 : bond 0.01215 ( 1) link_ALPHA1-3 : angle 2.88990 ( 3) link_ALPHA1-6 : bond 0.00975 ( 1) link_ALPHA1-6 : angle 1.06336 ( 3) link_BETA1-4 : bond 0.00632 ( 6) link_BETA1-4 : angle 1.82446 ( 18) link_NAG-ASN : bond 0.00989 ( 6) link_NAG-ASN : angle 3.69530 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.8719 (m) cc_final: 0.7977 (t) REVERT: A 181 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7637 (mt-10) REVERT: A 207 TYR cc_start: 0.7772 (m-80) cc_final: 0.7491 (m-80) REVERT: A 589 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7595 (mt-10) REVERT: B 351 TYR cc_start: 0.7260 (t80) cc_final: 0.6909 (t80) REVERT: B 353 TRP cc_start: 0.7448 (p-90) cc_final: 0.7177 (p-90) REVERT: B 442 ASP cc_start: 0.7691 (t70) cc_final: 0.7123 (p0) REVERT: B 457 ARG cc_start: 0.7655 (tmt-80) cc_final: 0.7297 (tmt-80) REVERT: B 494 TYR cc_start: 0.6423 (m-80) cc_final: 0.6190 (m-80) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.0653 time to fit residues: 12.2277 Evaluate side-chains 106 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 60 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.150190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.129573 restraints weight = 18125.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.132944 restraints weight = 13233.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.134500 restraints weight = 8698.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.135289 restraints weight = 6717.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.136138 restraints weight = 5950.467| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6811 Z= 0.138 Angle : 0.653 10.835 9284 Z= 0.328 Chirality : 0.044 0.276 1003 Planarity : 0.004 0.040 1173 Dihedral : 7.313 50.484 1143 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % 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 (0.31), residues: 786 helix: 1.32 (0.28), residues: 368 sheet: -0.14 (0.87), residues: 32 loop : -2.15 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 518 TYR 0.020 0.002 TYR B 453 PHE 0.017 0.001 PHE A 592 TRP 0.032 0.001 TRP A 477 HIS 0.011 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 6791) covalent geometry : angle 0.62522 ( 9230) SS BOND : bond 0.00658 ( 6) SS BOND : angle 1.22364 ( 12) hydrogen bonds : bond 0.04493 ( 281) hydrogen bonds : angle 4.82776 ( 810) link_ALPHA1-3 : bond 0.01239 ( 1) link_ALPHA1-3 : angle 3.15482 ( 3) link_ALPHA1-6 : bond 0.01171 ( 1) link_ALPHA1-6 : angle 0.97653 ( 3) link_BETA1-4 : bond 0.00618 ( 6) link_BETA1-4 : angle 1.74935 ( 18) link_NAG-ASN : bond 0.00988 ( 6) link_NAG-ASN : angle 3.67424 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.8645 (m) cc_final: 0.7831 (t) REVERT: A 181 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7679 (mt-10) REVERT: A 207 TYR cc_start: 0.7705 (m-80) cc_final: 0.7462 (m-80) REVERT: A 406 GLU cc_start: 0.6344 (mt-10) cc_final: 0.6007 (mt-10) REVERT: A 589 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7612 (mt-10) REVERT: A 592 PHE cc_start: 0.7863 (t80) cc_final: 0.7596 (t80) REVERT: B 351 TYR cc_start: 0.7281 (t80) cc_final: 0.6867 (t80) REVERT: B 353 TRP cc_start: 0.7439 (p-90) cc_final: 0.7204 (p-90) REVERT: B 442 ASP cc_start: 0.7699 (t70) cc_final: 0.7246 (p0) REVERT: B 457 ARG cc_start: 0.7585 (tmt-80) cc_final: 0.7246 (tmt-80) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.0694 time to fit residues: 12.6713 Evaluate side-chains 105 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 50 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 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 = 0.4036 r_free = 0.4036 target = 0.149974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.129634 restraints weight = 18516.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.132760 restraints weight = 13092.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.133574 restraints weight = 9208.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.134279 restraints weight = 7455.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.135946 restraints weight = 6667.812| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6811 Z= 0.142 Angle : 0.670 10.790 9284 Z= 0.335 Chirality : 0.045 0.277 1003 Planarity : 0.004 0.042 1173 Dihedral : 7.156 50.988 1143 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % 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: -0.60 (0.30), residues: 786 helix: 1.35 (0.28), residues: 361 sheet: -0.26 (0.86), residues: 32 loop : -2.22 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 357 TYR 0.026 0.002 TYR B 453 PHE 0.016 0.002 PHE A 592 TRP 0.031 0.002 TRP A 477 HIS 0.009 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 6791) covalent geometry : angle 0.64365 ( 9230) SS BOND : bond 0.00619 ( 6) SS BOND : angle 1.16293 ( 12) hydrogen bonds : bond 0.04510 ( 281) hydrogen bonds : angle 4.84196 ( 810) link_ALPHA1-3 : bond 0.01177 ( 1) link_ALPHA1-3 : angle 2.96353 ( 3) link_ALPHA1-6 : bond 0.00991 ( 1) link_ALPHA1-6 : angle 1.01387 ( 3) link_BETA1-4 : bond 0.00615 ( 6) link_BETA1-4 : angle 1.75570 ( 18) link_NAG-ASN : bond 0.00988 ( 6) link_NAG-ASN : angle 3.67926 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.8445 (m) cc_final: 0.7616 (t) REVERT: A 72 PHE cc_start: 0.8465 (t80) cc_final: 0.8231 (t80) REVERT: A 181 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7623 (mt-10) REVERT: A 406 GLU cc_start: 0.6399 (mt-10) cc_final: 0.5993 (mt-10) REVERT: A 455 MET cc_start: 0.8279 (mmt) cc_final: 0.7896 (mmm) REVERT: A 589 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7599 (mt-10) REVERT: B 351 TYR cc_start: 0.7270 (t80) cc_final: 0.6901 (t80) REVERT: B 442 ASP cc_start: 0.7868 (t70) cc_final: 0.7291 (p0) REVERT: B 457 ARG cc_start: 0.7595 (tmt-80) cc_final: 0.7164 (tmt-80) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.0703 time to fit residues: 12.7174 Evaluate side-chains 101 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 44 optimal weight: 0.4980 chunk 66 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 67 optimal weight: 0.0570 overall best weight: 1.0702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 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 = 0.4024 r_free = 0.4024 target = 0.148763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.127930 restraints weight = 18846.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.131283 restraints weight = 13026.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.132517 restraints weight = 8690.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.133069 restraints weight = 7185.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.134048 restraints weight = 6320.771| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6811 Z= 0.140 Angle : 0.659 10.746 9284 Z= 0.330 Chirality : 0.044 0.279 1003 Planarity : 0.004 0.044 1173 Dihedral : 7.012 51.710 1143 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: -0.54 (0.30), residues: 786 helix: 1.46 (0.28), residues: 355 sheet: -0.25 (0.85), residues: 32 loop : -2.20 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 357 TYR 0.024 0.002 TYR B 453 PHE 0.021 0.001 PHE A 32 TRP 0.030 0.002 TRP A 477 HIS 0.010 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 6791) covalent geometry : angle 0.63185 ( 9230) SS BOND : bond 0.00659 ( 6) SS BOND : angle 1.17701 ( 12) hydrogen bonds : bond 0.04519 ( 281) hydrogen bonds : angle 4.82926 ( 810) link_ALPHA1-3 : bond 0.01165 ( 1) link_ALPHA1-3 : angle 2.84250 ( 3) link_ALPHA1-6 : bond 0.01072 ( 1) link_ALPHA1-6 : angle 1.17829 ( 3) link_BETA1-4 : bond 0.00603 ( 6) link_BETA1-4 : angle 1.73867 ( 18) link_NAG-ASN : bond 0.00978 ( 6) link_NAG-ASN : angle 3.67584 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.8442 (m) cc_final: 0.7639 (t) REVERT: A 152 MET cc_start: 0.8339 (mmp) cc_final: 0.7870 (mmm) REVERT: A 181 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7653 (mt-10) REVERT: A 474 MET cc_start: 0.8313 (mmp) cc_final: 0.8066 (mmm) REVERT: A 589 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7663 (mt-10) REVERT: A 592 PHE cc_start: 0.7872 (t80) cc_final: 0.7582 (t80) REVERT: B 351 TYR cc_start: 0.7191 (t80) cc_final: 0.6825 (t80) REVERT: B 387 LEU cc_start: 0.8815 (tp) cc_final: 0.8603 (tp) REVERT: B 405 ASN cc_start: 0.7137 (p0) cc_final: 0.6879 (p0) REVERT: B 457 ARG cc_start: 0.7576 (tmt-80) cc_final: 0.7252 (tmt-80) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.0702 time to fit residues: 12.3724 Evaluate side-chains 97 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 53 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 23 optimal weight: 0.0000 chunk 68 optimal weight: 0.7980 chunk 21 optimal weight: 0.0370 chunk 65 optimal weight: 0.2980 chunk 4 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 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 = 0.4067 r_free = 0.4067 target = 0.152225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.131581 restraints weight = 18153.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.135386 restraints weight = 12766.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.136335 restraints weight = 8274.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.136851 restraints weight = 6622.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.137330 restraints weight = 6188.497| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6811 Z= 0.123 Angle : 0.649 10.733 9284 Z= 0.326 Chirality : 0.044 0.282 1003 Planarity : 0.004 0.044 1173 Dihedral : 6.601 52.302 1143 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -0.51 (0.30), residues: 786 helix: 1.50 (0.28), residues: 355 sheet: -0.06 (0.86), residues: 32 loop : -2.21 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 357 TYR 0.018 0.001 TYR A 385 PHE 0.024 0.001 PHE A 32 TRP 0.030 0.001 TRP A 477 HIS 0.010 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 6791) covalent geometry : angle 0.62387 ( 9230) SS BOND : bond 0.00609 ( 6) SS BOND : angle 1.14455 ( 12) hydrogen bonds : bond 0.04368 ( 281) hydrogen bonds : angle 4.68261 ( 810) link_ALPHA1-3 : bond 0.00990 ( 1) link_ALPHA1-3 : angle 2.60372 ( 3) link_ALPHA1-6 : bond 0.01093 ( 1) link_ALPHA1-6 : angle 1.41332 ( 3) link_BETA1-4 : bond 0.00535 ( 6) link_BETA1-4 : angle 1.59990 ( 18) link_NAG-ASN : bond 0.00946 ( 6) link_NAG-ASN : angle 3.56922 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.8596 (m) cc_final: 0.7652 (t) REVERT: A 181 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7892 (mt-10) REVERT: A 355 ASP cc_start: 0.7925 (t0) cc_final: 0.7403 (p0) REVERT: A 474 MET cc_start: 0.8283 (mmp) cc_final: 0.7998 (mmm) REVERT: A 589 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7623 (mt-10) REVERT: A 592 PHE cc_start: 0.7797 (t80) cc_final: 0.7507 (t80) REVERT: B 351 TYR cc_start: 0.7033 (t80) cc_final: 0.6690 (t80) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.0633 time to fit residues: 10.7093 Evaluate side-chains 99 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.0370 chunk 29 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 67 optimal weight: 0.0970 chunk 32 optimal weight: 3.9990 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 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 = 0.4067 r_free = 0.4067 target = 0.152147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.131688 restraints weight = 18490.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.135839 restraints weight = 13675.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.136810 restraints weight = 8367.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.137420 restraints weight = 6800.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.137926 restraints weight = 6073.232| |-----------------------------------------------------------------------------| r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6811 Z= 0.125 Angle : 0.657 10.710 9284 Z= 0.328 Chirality : 0.044 0.284 1003 Planarity : 0.004 0.044 1173 Dihedral : 6.437 50.839 1143 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.49 (0.30), residues: 786 helix: 1.40 (0.28), residues: 363 sheet: 0.01 (0.86), residues: 32 loop : -2.18 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 355 TYR 0.024 0.002 TYR B 453 PHE 0.023 0.001 PHE A 32 TRP 0.031 0.001 TRP A 477 HIS 0.010 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 6791) covalent geometry : angle 0.62889 ( 9230) SS BOND : bond 0.00765 ( 6) SS BOND : angle 2.25578 ( 12) hydrogen bonds : bond 0.04277 ( 281) hydrogen bonds : angle 4.68489 ( 810) link_ALPHA1-3 : bond 0.01090 ( 1) link_ALPHA1-3 : angle 2.55746 ( 3) link_ALPHA1-6 : bond 0.01063 ( 1) link_ALPHA1-6 : angle 1.49049 ( 3) link_BETA1-4 : bond 0.00514 ( 6) link_BETA1-4 : angle 1.61406 ( 18) link_NAG-ASN : bond 0.00934 ( 6) link_NAG-ASN : angle 3.55898 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1023.27 seconds wall clock time: 18 minutes 22.09 seconds (1102.09 seconds total)