Starting phenix.real_space_refine on Tue Jun 10 02:24:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wse_32755/06_2025/7wse_32755.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wse_32755/06_2025/7wse_32755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wse_32755/06_2025/7wse_32755.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wse_32755/06_2025/7wse_32755.map" model { file = "/net/cci-nas-00/data/ceres_data/7wse_32755/06_2025/7wse_32755.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wse_32755/06_2025/7wse_32755.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.063 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 5923 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 35 5.16 5 C 4115 2.51 5 N 1069 2.21 5 O 1211 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 6431 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4887 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 566} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.80, per 1000 atoms: 0.75 Number of scatterers: 6431 At special positions: 0 Unit cell: (72.921, 82.287, 117.744, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 35 16.00 O 1211 8.00 N 1069 7.00 C 4115 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 360 " distance=2.03 Simple disulfide: pdb=" SG CYS A 529 " - pdb=" SG CYS A 541 " 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 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " 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 Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 934.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 373 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 377 " 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 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: 36 helices and 5 sheets defined 52.8% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.672A pdb=" N PHE A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N TYR A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASN A 49 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.624A pdb=" N VAL A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN A 60 " --> pdb=" O ASP A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 83 No H-bonds generated for 'chain 'A' and resid 82 through 83' Processing helix chain 'A' and resid 84 through 88 Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.529A pdb=" N ARG A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 removed outlier: 3.768A pdb=" N SER A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER A 128 " --> pdb=" O SER A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 154 Processing helix chain 'A' and resid 156 through 193 removed outlier: 3.794A pdb=" N LYS A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) Proline residue: A 177 - end of helix removed outlier: 3.616A pdb=" N GLU A 181 " --> pdb=" O PRO A 177 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 202 Processing helix chain 'A' and resid 203 through 207 Processing helix chain 'A' and resid 219 through 251 removed outlier: 3.824A pdb=" N ALA A 223 " --> pdb=" O ASN A 219 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLU A 231 " --> pdb=" O ARG A 227 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 232 " --> pdb=" O THR A 228 " (cutoff:3.500A) Proline residue: A 234 - end of helix removed outlier: 3.709A pdb=" N GLN A 238 " --> pdb=" O PRO A 234 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 266 No H-bonds generated for 'chain 'A' and resid 264 through 266' Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 292 through 299 removed outlier: 3.594A pdb=" N GLN A 297 " --> pdb=" O THR A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 317 Processing helix chain 'A' and resid 323 through 330 removed outlier: 3.770A pdb=" N TRP A 327 " --> pdb=" O THR A 323 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL A 328 " --> pdb=" O GLN A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 373 through 384 removed outlier: 3.760A pdb=" N GLN A 379 " --> pdb=" O MET A 375 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR A 384 " --> pdb=" O TYR A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 387 No H-bonds generated for 'chain 'A' and resid 385 through 387' Processing helix chain 'A' and resid 399 through 413 removed outlier: 4.085A pdb=" N GLY A 404 " --> pdb=" O HIS A 400 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU A 405 " --> pdb=" O GLU A 401 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N MET A 407 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 421 Processing helix chain 'A' and resid 430 through 443 Processing helix chain 'A' and resid 448 through 465 Processing helix chain 'A' and resid 468 through 470 No H-bonds generated for 'chain 'A' and resid 468 through 470' Processing helix chain 'A' and resid 471 through 483 removed outlier: 3.912A pdb=" N TRP A 477 " --> pdb=" O MET A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 501 Processing helix chain 'A' and resid 502 through 507 Processing helix chain 'A' and resid 512 through 532 removed outlier: 3.965A pdb=" N THR A 518 " --> pdb=" O TYR A 514 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE A 522 " --> pdb=" O THR A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 558 Processing helix chain 'A' and resid 564 through 573 removed outlier: 3.700A pdb=" N ILE A 572 " --> pdb=" O ALA A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 587 Processing helix chain 'A' and resid 587 through 598 Processing helix chain 'A' and resid 610 through 614 removed outlier: 3.960A pdb=" N ASP A 614 " --> pdb=" O PRO A 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.685A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.793A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing sheet with id=AA1, first strand: chain 'A' and resid 261 through 262 removed outlier: 6.081A pdb=" N LEU A 261 " --> pdb=" O VAL A 487 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 331 through 333 removed outlier: 8.336A pdb=" N LEU A 332 " --> pdb=" O THR A 361 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASP A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.525A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'B' and resid 473 through 474 272 hydrogen bonds defined for protein. 777 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.70 Time building geometry restraints manager: 1.78 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: 2071 1.34 - 1.46: 1664 1.46 - 1.58: 2822 1.58 - 1.70: 0 1.70 - 1.81: 55 Bond restraints: 6612 Sorted by residual: bond pdb=" CG PRO A 145 " pdb=" CD PRO A 145 " ideal model delta sigma weight residual 1.512 1.491 0.021 2.70e-02 1.37e+03 6.19e-01 bond pdb=" C ILE A 467 " pdb=" O ILE A 467 " ideal model delta sigma weight residual 1.240 1.231 0.008 1.26e-02 6.30e+03 4.54e-01 bond pdb=" C TYR A 278 " pdb=" N PRO A 279 " ideal model delta sigma weight residual 1.335 1.344 -0.008 1.36e-02 5.41e+03 3.72e-01 bond pdb=" CA ILE B 410 " pdb=" CB ILE B 410 " ideal model delta sigma weight residual 1.528 1.535 -0.007 1.34e-02 5.57e+03 2.99e-01 bond pdb=" N ILE A 467 " pdb=" CA ILE A 467 " ideal model delta sigma weight residual 1.461 1.455 0.006 1.23e-02 6.61e+03 2.48e-01 ... (remaining 6607 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 8925 2.26 - 4.52: 54 4.52 - 6.78: 4 6.78 - 9.04: 0 9.04 - 11.30: 1 Bond angle restraints: 8984 Sorted by residual: angle pdb=" C GLN B 409 " pdb=" N ILE B 410 " pdb=" CA ILE B 410 " ideal model delta sigma weight residual 122.59 120.26 2.33 1.10e+00 8.26e-01 4.48e+00 angle pdb=" C THR A 361 " pdb=" N LYS A 362 " pdb=" CA LYS A 362 " ideal model delta sigma weight residual 121.54 125.54 -4.00 1.91e+00 2.74e-01 4.38e+00 angle pdb=" N ILE B 410 " pdb=" CA ILE B 410 " pdb=" C ILE B 410 " ideal model delta sigma weight residual 106.32 109.60 -3.28 1.61e+00 3.86e-01 4.15e+00 angle pdb=" C LEU A 133 " pdb=" N ASP A 134 " pdb=" CA ASP A 134 " ideal model delta sigma weight residual 121.41 132.71 -11.30 5.58e+00 3.21e-02 4.10e+00 angle pdb=" C VAL A 363 " pdb=" N THR A 364 " pdb=" CA THR A 364 " ideal model delta sigma weight residual 121.63 125.28 -3.65 1.92e+00 2.71e-01 3.62e+00 ... (remaining 8979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.42: 3684 16.42 - 32.83: 188 32.83 - 49.25: 37 49.25 - 65.66: 4 65.66 - 82.08: 2 Dihedral angle restraints: 3915 sinusoidal: 1589 harmonic: 2326 Sorted by residual: dihedral pdb=" CA LYS A 362 " pdb=" C LYS A 362 " pdb=" N VAL A 363 " pdb=" CA VAL A 363 " ideal model delta harmonic sigma weight residual -180.00 -145.98 -34.02 0 5.00e+00 4.00e-02 4.63e+01 dihedral pdb=" CB CYS A 343 " pdb=" SG CYS A 343 " pdb=" SG CYS A 360 " pdb=" CB CYS A 360 " ideal model delta sinusoidal sigma weight residual 93.00 148.62 -55.62 1 1.00e+01 1.00e-02 4.18e+01 dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual -86.00 -124.50 38.50 1 1.00e+01 1.00e-02 2.09e+01 ... (remaining 3912 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 519 0.025 - 0.050: 268 0.050 - 0.076: 86 0.076 - 0.101: 43 0.101 - 0.126: 19 Chirality restraints: 935 Sorted by residual: chirality pdb=" CA VAL B 362 " pdb=" N VAL B 362 " pdb=" C VAL B 362 " pdb=" CB VAL B 362 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.98e-01 chirality pdb=" CA VAL A 282 " pdb=" N VAL A 282 " pdb=" C VAL A 282 " pdb=" CB VAL A 282 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CA ILE A 357 " pdb=" N ILE A 357 " pdb=" C ILE A 357 " pdb=" CB ILE A 357 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 ... (remaining 932 not shown) Planarity restraints: 1164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS B 336 " 0.022 5.00e-02 4.00e+02 3.39e-02 1.83e+00 pdb=" N PRO B 337 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 337 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 337 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 134 " -0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO A 135 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 135 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 135 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 462 " -0.020 5.00e-02 4.00e+02 2.96e-02 1.40e+00 pdb=" N PRO B 463 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO B 463 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 463 " -0.016 5.00e-02 4.00e+02 ... (remaining 1161 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 333 2.73 - 3.28: 6510 3.28 - 3.82: 10557 3.82 - 4.36: 13505 4.36 - 4.90: 22692 Nonbonded interactions: 53597 Sorted by model distance: nonbonded pdb=" OH TYR A 182 " pdb=" OD1 ASP A 508 " model vdw 2.193 3.040 nonbonded pdb=" OE1 GLU A 401 " pdb="ZN ZN A 801 " model vdw 2.253 2.230 nonbonded pdb=" OD1 ASP A 381 " pdb=" OH TYR A 384 " model vdw 2.263 3.040 nonbonded pdb=" NZ LYS A 81 " pdb=" O GLN A 101 " model vdw 2.319 3.120 nonbonded pdb=" OD1 ASP A 38 " pdb=" OH TYR B 449 " model vdw 2.334 3.040 ... (remaining 53592 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.650 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 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 : 0.002 0.023 6620 Z= 0.082 Angle : 0.445 11.304 8996 Z= 0.227 Chirality : 0.038 0.126 935 Planarity : 0.004 0.034 1164 Dihedral : 10.168 82.077 2407 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.01 % Allowed : 3.75 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.30), residues: 787 helix: -0.57 (0.27), residues: 376 sheet: 1.53 (0.82), residues: 47 loop : -0.41 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 477 HIS 0.002 0.000 HIS A 558 PHE 0.006 0.001 PHE A 522 TYR 0.012 0.001 TYR A 384 ARG 0.001 0.000 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.27180 ( 272) hydrogen bonds : angle 8.86304 ( 777) metal coordination : bond 0.00103 ( 2) SS BOND : bond 0.00135 ( 6) SS BOND : angle 0.58667 ( 12) covalent geometry : bond 0.00169 ( 6612) covalent geometry : angle 0.44496 ( 8984) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 134 time to evaluate : 0.717 Fit side-chains revert: symmetry clash REVERT: A 407 MET cc_start: 0.8455 (mmt) cc_final: 0.7970 (mmt) REVERT: B 454 ARG cc_start: 0.7683 (ttm-80) cc_final: 0.7361 (ttm-80) outliers start: 7 outliers final: 2 residues processed: 139 average time/residue: 1.1167 time to fit residues: 163.5321 Evaluate side-chains 99 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain B residue 432 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 0.0870 chunk 70 optimal weight: 4.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 585 ASN B 414 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.172240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.126887 restraints weight = 7508.108| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.65 r_work: 0.3358 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6620 Z= 0.161 Angle : 0.563 8.541 8996 Z= 0.293 Chirality : 0.043 0.183 935 Planarity : 0.005 0.053 1164 Dihedral : 4.945 54.225 873 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.74 % Allowed : 11.98 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.30), residues: 787 helix: -0.03 (0.26), residues: 394 sheet: 1.10 (0.81), residues: 49 loop : -0.24 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 164 HIS 0.004 0.001 HIS A 377 PHE 0.017 0.001 PHE B 374 TYR 0.014 0.001 TYR A 384 ARG 0.009 0.001 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.05827 ( 272) hydrogen bonds : angle 5.19642 ( 777) metal coordination : bond 0.00350 ( 2) SS BOND : bond 0.00238 ( 6) SS BOND : angle 0.64833 ( 12) covalent geometry : bond 0.00367 ( 6612) covalent geometry : angle 0.56290 ( 8984) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7215 (tt) REVERT: A 69 TRP cc_start: 0.7971 (t-100) cc_final: 0.7672 (t-100) REVERT: A 490 LEU cc_start: 0.7630 (mt) cc_final: 0.7399 (mt) REVERT: A 535 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7180 (mt-10) REVERT: A 596 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7875 (tp30) REVERT: A 599 ARG cc_start: 0.7494 (mtm110) cc_final: 0.7165 (mtm110) REVERT: B 438 SER cc_start: 0.8354 (t) cc_final: 0.8132 (t) REVERT: B 454 ARG cc_start: 0.7089 (ttm-80) cc_final: 0.6834 (ttm-80) REVERT: B 509 ARG cc_start: 0.6171 (mtt180) cc_final: 0.5902 (mtt180) outliers start: 19 outliers final: 7 residues processed: 119 average time/residue: 1.1646 time to fit residues: 146.5617 Evaluate side-chains 102 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 596 GLU Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 63 optimal weight: 8.9990 chunk 50 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 75 optimal weight: 0.0970 chunk 65 optimal weight: 7.9990 chunk 26 optimal weight: 0.0470 chunk 35 optimal weight: 0.5980 chunk 67 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN A 474 GLN A 585 ASN B 414 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.175573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.130598 restraints weight = 7618.014| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.66 r_work: 0.3403 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6620 Z= 0.106 Angle : 0.525 7.863 8996 Z= 0.266 Chirality : 0.041 0.146 935 Planarity : 0.004 0.042 1164 Dihedral : 4.877 58.932 873 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.89 % Allowed : 13.71 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.30), residues: 787 helix: 0.16 (0.26), residues: 401 sheet: 1.10 (0.80), residues: 48 loop : -0.21 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 164 HIS 0.003 0.001 HIS A 34 PHE 0.012 0.001 PHE A 522 TYR 0.012 0.001 TYR A 50 ARG 0.006 0.000 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.04434 ( 272) hydrogen bonds : angle 4.64301 ( 777) metal coordination : bond 0.00216 ( 2) SS BOND : bond 0.00183 ( 6) SS BOND : angle 0.78236 ( 12) covalent geometry : bond 0.00225 ( 6612) covalent geometry : angle 0.52502 ( 8984) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.7869 (t-100) cc_final: 0.7555 (t-100) REVERT: A 79 ILE cc_start: 0.8254 (mm) cc_final: 0.7929 (mp) REVERT: A 348 TRP cc_start: 0.7259 (m100) cc_final: 0.6920 (m100) REVERT: A 407 MET cc_start: 0.7900 (mmt) cc_final: 0.7317 (mmt) REVERT: A 490 LEU cc_start: 0.7605 (mt) cc_final: 0.7302 (mt) REVERT: A 507 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8092 (mt-10) REVERT: A 514 TYR cc_start: 0.8374 (m-80) cc_final: 0.8173 (m-80) REVERT: A 535 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7196 (mt-10) REVERT: A 596 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7912 (tp30) REVERT: B 454 ARG cc_start: 0.7101 (ttm-80) cc_final: 0.6824 (ttm-80) REVERT: B 455 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7847 (tt) outliers start: 20 outliers final: 4 residues processed: 122 average time/residue: 1.5273 time to fit residues: 196.8473 Evaluate side-chains 100 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 596 GLU Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 455 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 13 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 61 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 59 optimal weight: 0.0970 chunk 68 optimal weight: 7.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 474 GLN A 585 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.173923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.127668 restraints weight = 7651.148| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.46 r_work: 0.3375 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6620 Z= 0.122 Angle : 0.545 8.454 8996 Z= 0.273 Chirality : 0.042 0.143 935 Planarity : 0.004 0.056 1164 Dihedral : 4.828 56.354 873 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.03 % Allowed : 14.14 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.30), residues: 787 helix: 0.36 (0.27), residues: 393 sheet: 1.06 (0.80), residues: 49 loop : -0.28 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 164 HIS 0.003 0.001 HIS A 377 PHE 0.013 0.001 PHE A 522 TYR 0.015 0.001 TYR A 50 ARG 0.014 0.001 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.04234 ( 272) hydrogen bonds : angle 4.44527 ( 777) metal coordination : bond 0.00177 ( 2) SS BOND : bond 0.00215 ( 6) SS BOND : angle 0.79623 ( 12) covalent geometry : bond 0.00275 ( 6612) covalent geometry : angle 0.54437 ( 8984) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 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: 21 poor density : 102 time to evaluate : 0.654 Fit side-chains revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8423 (t-100) cc_final: 0.8147 (t-100) REVERT: A 151 MET cc_start: 0.8495 (mmm) cc_final: 0.7399 (mmt) REVERT: A 407 MET cc_start: 0.8640 (mmt) cc_final: 0.7968 (mmt) REVERT: A 490 LEU cc_start: 0.8064 (mt) cc_final: 0.7793 (mt) REVERT: A 596 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8190 (tp30) REVERT: A 599 ARG cc_start: 0.7627 (mtm110) cc_final: 0.7270 (mtm110) REVERT: B 454 ARG cc_start: 0.7695 (ttm-80) cc_final: 0.7435 (ttm-80) outliers start: 21 outliers final: 8 residues processed: 114 average time/residue: 1.2450 time to fit residues: 150.0547 Evaluate side-chains 102 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 596 GLU Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 523 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 27 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 474 GLN A 585 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.172483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.125724 restraints weight = 7620.676| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.45 r_work: 0.3353 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6620 Z= 0.139 Angle : 0.550 8.552 8996 Z= 0.275 Chirality : 0.043 0.140 935 Planarity : 0.004 0.046 1164 Dihedral : 4.844 56.476 873 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.17 % Allowed : 15.01 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.30), residues: 787 helix: 0.44 (0.27), residues: 393 sheet: 1.04 (0.78), residues: 49 loop : -0.24 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 164 HIS 0.003 0.001 HIS A 525 PHE 0.014 0.001 PHE B 347 TYR 0.019 0.001 TYR A 50 ARG 0.010 0.001 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.04240 ( 272) hydrogen bonds : angle 4.40379 ( 777) metal coordination : bond 0.00201 ( 2) SS BOND : bond 0.00339 ( 6) SS BOND : angle 0.83758 ( 12) covalent geometry : bond 0.00322 ( 6612) covalent geometry : angle 0.54917 ( 8984) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.747 Fit side-chains revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8377 (t-100) cc_final: 0.8082 (t-100) REVERT: A 79 ILE cc_start: 0.8606 (mm) cc_final: 0.8277 (mp) REVERT: A 151 MET cc_start: 0.8447 (mmm) cc_final: 0.7322 (mmt) REVERT: A 269 MET cc_start: 0.8824 (tpt) cc_final: 0.8540 (tpt) REVERT: A 407 MET cc_start: 0.8620 (mmt) cc_final: 0.7933 (mmt) REVERT: A 473 MET cc_start: 0.8769 (mmt) cc_final: 0.8491 (mmt) REVERT: A 490 LEU cc_start: 0.8010 (mt) cc_final: 0.7736 (mt) REVERT: A 535 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7194 (mt-10) REVERT: A 596 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8230 (tp30) REVERT: A 599 ARG cc_start: 0.7668 (mtm110) cc_final: 0.7370 (mtm110) REVERT: B 454 ARG cc_start: 0.7601 (ttm-80) cc_final: 0.7337 (ttm-80) outliers start: 22 outliers final: 13 residues processed: 114 average time/residue: 1.1181 time to fit residues: 134.7472 Evaluate side-chains 102 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 596 GLU Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 523 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 27 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 585 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.172806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.126164 restraints weight = 7479.028| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.40 r_work: 0.3354 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6620 Z= 0.139 Angle : 0.553 8.501 8996 Z= 0.277 Chirality : 0.042 0.140 935 Planarity : 0.004 0.047 1164 Dihedral : 4.875 56.161 873 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.46 % Allowed : 16.59 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.30), residues: 787 helix: 0.46 (0.27), residues: 395 sheet: 1.05 (0.75), residues: 49 loop : -0.22 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 164 HIS 0.003 0.001 HIS A 377 PHE 0.014 0.001 PHE B 347 TYR 0.024 0.001 TYR A 201 ARG 0.009 0.001 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.04178 ( 272) hydrogen bonds : angle 4.39265 ( 777) metal coordination : bond 0.00184 ( 2) SS BOND : bond 0.00309 ( 6) SS BOND : angle 0.81812 ( 12) covalent geometry : bond 0.00324 ( 6612) covalent geometry : angle 0.55293 ( 8984) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ILE cc_start: 0.8578 (mm) cc_final: 0.8272 (mp) REVERT: A 151 MET cc_start: 0.8433 (mmm) cc_final: 0.8132 (mmt) REVERT: A 269 MET cc_start: 0.8782 (tpt) cc_final: 0.8463 (tpt) REVERT: A 490 LEU cc_start: 0.7995 (mt) cc_final: 0.7715 (mt) REVERT: A 535 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7135 (mt-10) REVERT: A 596 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8230 (tp30) REVERT: A 599 ARG cc_start: 0.7704 (mtm110) cc_final: 0.7436 (mtm110) REVERT: B 414 GLN cc_start: 0.8423 (mm-40) cc_final: 0.8114 (mm-40) REVERT: B 454 ARG cc_start: 0.7609 (ttm-80) cc_final: 0.7375 (ttm-80) outliers start: 24 outliers final: 11 residues processed: 102 average time/residue: 1.0933 time to fit residues: 117.9610 Evaluate side-chains 96 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 596 GLU Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 523 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 59 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 585 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.171016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.124232 restraints weight = 7523.581| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.41 r_work: 0.3328 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6620 Z= 0.166 Angle : 0.570 8.868 8996 Z= 0.285 Chirality : 0.043 0.139 935 Planarity : 0.004 0.053 1164 Dihedral : 4.916 56.076 873 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.03 % Allowed : 16.88 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.30), residues: 787 helix: 0.52 (0.27), residues: 392 sheet: 1.01 (0.75), residues: 49 loop : -0.24 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 164 HIS 0.003 0.001 HIS A 377 PHE 0.012 0.001 PHE A 522 TYR 0.020 0.001 TYR A 50 ARG 0.013 0.001 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.04317 ( 272) hydrogen bonds : angle 4.40657 ( 777) metal coordination : bond 0.00193 ( 2) SS BOND : bond 0.00349 ( 6) SS BOND : angle 0.82114 ( 12) covalent geometry : bond 0.00391 ( 6612) covalent geometry : angle 0.56974 ( 8984) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ILE cc_start: 0.8539 (mm) cc_final: 0.8246 (mp) REVERT: A 151 MET cc_start: 0.8429 (mmm) cc_final: 0.8122 (mmt) REVERT: A 490 LEU cc_start: 0.7944 (mt) cc_final: 0.7680 (mt) REVERT: A 535 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7210 (mt-10) REVERT: A 596 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8216 (tp30) REVERT: A 599 ARG cc_start: 0.7686 (mtm110) cc_final: 0.7434 (mtm110) REVERT: B 414 GLN cc_start: 0.8438 (mm-40) cc_final: 0.8116 (mm-40) REVERT: B 454 ARG cc_start: 0.7606 (ttm-80) cc_final: 0.7362 (ttm-80) outliers start: 21 outliers final: 12 residues processed: 103 average time/residue: 1.1645 time to fit residues: 126.6489 Evaluate side-chains 98 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 596 GLU Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 523 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 41 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 7 optimal weight: 0.0870 chunk 11 optimal weight: 0.0870 chunk 4 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.174796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.128677 restraints weight = 7504.230| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.42 r_work: 0.3386 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6620 Z= 0.108 Angle : 0.544 8.842 8996 Z= 0.269 Chirality : 0.041 0.142 935 Planarity : 0.004 0.047 1164 Dihedral : 4.778 55.280 873 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.74 % Allowed : 18.18 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.30), residues: 787 helix: 0.66 (0.27), residues: 398 sheet: 1.07 (0.74), residues: 49 loop : -0.11 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 164 HIS 0.002 0.001 HIS A 377 PHE 0.012 0.001 PHE A 522 TYR 0.021 0.001 TYR A 201 ARG 0.011 0.001 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.03865 ( 272) hydrogen bonds : angle 4.26523 ( 777) metal coordination : bond 0.00207 ( 2) SS BOND : bond 0.00255 ( 6) SS BOND : angle 0.80505 ( 12) covalent geometry : bond 0.00242 ( 6612) covalent geometry : angle 0.54388 ( 8984) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ILE cc_start: 0.8612 (mm) cc_final: 0.8325 (mp) REVERT: A 151 MET cc_start: 0.8437 (mmm) cc_final: 0.8148 (mmt) REVERT: A 226 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8215 (mm-30) REVERT: A 471 GLN cc_start: 0.8078 (mt0) cc_final: 0.7751 (mt0) REVERT: A 490 LEU cc_start: 0.8004 (mt) cc_final: 0.7739 (mt) REVERT: A 535 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7138 (mt-10) REVERT: A 599 ARG cc_start: 0.7755 (mtm110) cc_final: 0.7545 (mtm110) REVERT: B 414 GLN cc_start: 0.8395 (mm-40) cc_final: 0.8103 (mm-40) REVERT: B 454 ARG cc_start: 0.7675 (ttm-80) cc_final: 0.7434 (ttm-80) outliers start: 19 outliers final: 12 residues processed: 110 average time/residue: 1.2355 time to fit residues: 143.5018 Evaluate side-chains 99 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLN Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 523 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 64 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 11 optimal weight: 0.0370 chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 7 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN A 474 GLN A 585 ASN A 597 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.174519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.128099 restraints weight = 7598.054| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.41 r_work: 0.3376 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6620 Z= 0.119 Angle : 0.555 9.117 8996 Z= 0.276 Chirality : 0.041 0.141 935 Planarity : 0.004 0.052 1164 Dihedral : 4.787 55.162 873 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.03 % Allowed : 18.47 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.30), residues: 787 helix: 0.70 (0.27), residues: 395 sheet: 1.06 (0.74), residues: 49 loop : -0.12 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 164 HIS 0.002 0.001 HIS A 240 PHE 0.013 0.001 PHE A 522 TYR 0.021 0.001 TYR A 50 ARG 0.013 0.001 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.03899 ( 272) hydrogen bonds : angle 4.25310 ( 777) metal coordination : bond 0.00102 ( 2) SS BOND : bond 0.00266 ( 6) SS BOND : angle 0.81296 ( 12) covalent geometry : bond 0.00274 ( 6612) covalent geometry : angle 0.55501 ( 8984) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ILE cc_start: 0.8585 (mm) cc_final: 0.8319 (mp) REVERT: A 226 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8234 (mm-30) REVERT: A 407 MET cc_start: 0.8660 (mmt) cc_final: 0.7995 (mmt) REVERT: A 471 GLN cc_start: 0.8063 (mt0) cc_final: 0.7691 (mt0) REVERT: A 490 LEU cc_start: 0.8007 (mt) cc_final: 0.7737 (mt) REVERT: A 535 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7184 (mt-10) REVERT: B 414 GLN cc_start: 0.8360 (mm-40) cc_final: 0.8079 (mm-40) REVERT: B 454 ARG cc_start: 0.7613 (ttm-80) cc_final: 0.7376 (ttm-80) outliers start: 21 outliers final: 14 residues processed: 101 average time/residue: 1.1660 time to fit residues: 124.7703 Evaluate side-chains 101 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLN Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 523 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 11 optimal weight: 0.0070 chunk 73 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 28 optimal weight: 0.0980 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 0.0060 chunk 49 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 70 optimal weight: 0.0470 chunk 33 optimal weight: 0.0670 chunk 35 optimal weight: 1.9990 overall best weight: 0.0450 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN A 474 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.177182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.131788 restraints weight = 7563.796| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.41 r_work: 0.3421 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6620 Z= 0.102 Angle : 0.556 9.178 8996 Z= 0.276 Chirality : 0.041 0.153 935 Planarity : 0.005 0.077 1164 Dihedral : 4.725 54.631 873 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.45 % Allowed : 19.62 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.30), residues: 787 helix: 0.85 (0.27), residues: 398 sheet: 1.10 (0.74), residues: 49 loop : -0.08 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 164 HIS 0.002 0.001 HIS A 240 PHE 0.012 0.001 PHE A 522 TYR 0.023 0.001 TYR A 182 ARG 0.017 0.001 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.03651 ( 272) hydrogen bonds : angle 4.20607 ( 777) metal coordination : bond 0.00044 ( 2) SS BOND : bond 0.00193 ( 6) SS BOND : angle 0.86057 ( 12) covalent geometry : bond 0.00217 ( 6612) covalent geometry : angle 0.55526 ( 8984) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.8544 (t70) cc_final: 0.7732 (m-30) REVERT: A 79 ILE cc_start: 0.8590 (mm) cc_final: 0.8339 (mp) REVERT: A 226 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8212 (mm-30) REVERT: A 295 GLU cc_start: 0.7747 (tp30) cc_final: 0.7055 (tm-30) REVERT: A 471 GLN cc_start: 0.7974 (mt0) cc_final: 0.7580 (mt0) REVERT: A 490 LEU cc_start: 0.7982 (mt) cc_final: 0.7726 (mt) REVERT: A 535 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7181 (mt-10) REVERT: B 414 GLN cc_start: 0.8250 (mm-40) cc_final: 0.7988 (mm-40) REVERT: B 454 ARG cc_start: 0.7617 (ttm-80) cc_final: 0.7381 (ttm-80) REVERT: B 455 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8285 (tt) outliers start: 17 outliers final: 11 residues processed: 107 average time/residue: 1.1134 time to fit residues: 126.0880 Evaluate side-chains 99 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLN Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 523 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 28 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 0.2980 chunk 9 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 8 optimal weight: 0.0670 chunk 16 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 31 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.176034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.130460 restraints weight = 7679.014| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.42 r_work: 0.3401 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6620 Z= 0.109 Angle : 0.562 9.135 8996 Z= 0.277 Chirality : 0.041 0.153 935 Planarity : 0.004 0.060 1164 Dihedral : 4.674 55.149 873 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.31 % Allowed : 20.06 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.30), residues: 787 helix: 0.86 (0.27), residues: 400 sheet: 1.01 (0.74), residues: 49 loop : -0.05 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 164 HIS 0.002 0.001 HIS A 240 PHE 0.015 0.001 PHE B 347 TYR 0.024 0.001 TYR A 182 ARG 0.014 0.001 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.03729 ( 272) hydrogen bonds : angle 4.19025 ( 777) metal coordination : bond 0.00088 ( 2) SS BOND : bond 0.00230 ( 6) SS BOND : angle 0.82188 ( 12) covalent geometry : bond 0.00247 ( 6612) covalent geometry : angle 0.56119 ( 8984) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5552.48 seconds wall clock time: 97 minutes 43.52 seconds (5863.52 seconds total)