Starting phenix.real_space_refine on Sun Dec 29 19:24:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wse_32755/12_2024/7wse_32755.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wse_32755/12_2024/7wse_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_32755/12_2024/7wse_32755.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wse_32755/12_2024/7wse_32755.map" model { file = "/net/cci-nas-00/data/ceres_data/7wse_32755/12_2024/7wse_32755.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wse_32755/12_2024/7wse_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-5532/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: 4.41, per 1000 atoms: 0.69 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: 1.48 Conformation dependent library (CDL) restraints added in 861.9 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: 0.65 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: 1.65 Time building geometry restraints manager: 1.73 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: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.120 Find NCS groups from input model: 0.060 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:12.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.070 ------------------------------------------------------------------------------- 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 6612 Z= 0.110 Angle : 0.445 11.304 8984 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 *********************** 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 : 0.636 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: 1.1777 time to fit residues: 172.2694 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 : 0.733 ------------------------------------------------------------------------------- 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: 0.8980 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 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: 1.3964 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6612 Z= 0.276 Angle : 0.583 8.492 8984 Z= 0.304 Chirality : 0.044 0.168 935 Planarity : 0.005 0.052 1164 Dihedral : 5.016 54.424 873 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.03 % Allowed : 11.69 % 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: -0.21 (0.30), residues: 787 helix: -0.05 (0.26), residues: 394 sheet: 1.10 (0.81), residues: 49 loop : -0.26 (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 0.016 0.001 PHE B 374 TYR 0.015 0.002 TYR A 384 ARG 0.010 0.001 ARG A 599 *********************** 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 127 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7740 (tt) REVERT: A 535 GLU cc_start: 0.6038 (OUTLIER) cc_final: 0.5646 (mt-10) REVERT: B 454 ARG cc_start: 0.7785 (ttm-80) cc_final: 0.7497 (ttm-80) outliers start: 21 outliers final: 7 residues processed: 120 average time/residue: 1.1023 time to fit residues: 139.7244 Evaluate side-chains 91 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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 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 39 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6612 Z= 0.201 Angle : 0.551 8.136 8984 Z= 0.279 Chirality : 0.042 0.146 935 Planarity : 0.005 0.059 1164 Dihedral : 5.022 59.943 873 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.61 % Allowed : 13.71 % Favored : 82.68 % 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: -0.07 (0.30), residues: 787 helix: 0.14 (0.26), residues: 394 sheet: 0.90 (0.79), 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 0.003 0.001 HIS A 377 PHE 0.011 0.001 PHE A 522 TYR 0.012 0.001 TYR A 384 ARG 0.011 0.001 ARG A 599 *********************** 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 123 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ILE cc_start: 0.8864 (mm) cc_final: 0.8472 (mp) REVERT: A 102 GLN cc_start: 0.6494 (OUTLIER) cc_final: 0.6179 (mt0) REVERT: A 151 MET cc_start: 0.8575 (mmm) cc_final: 0.7940 (mmt) REVERT: A 535 GLU cc_start: 0.5996 (OUTLIER) cc_final: 0.5615 (mt-10) REVERT: B 454 ARG cc_start: 0.7805 (ttm-80) cc_final: 0.7496 (ttm-80) REVERT: B 455 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8661 (tt) outliers start: 25 outliers final: 9 residues processed: 114 average time/residue: 1.1321 time to fit residues: 136.5252 Evaluate side-chains 100 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLN 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 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 455 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 523 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 67 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 62 optimal weight: 0.0060 chunk 42 optimal weight: 1.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6612 Z= 0.167 Angle : 0.536 8.524 8984 Z= 0.270 Chirality : 0.041 0.144 935 Planarity : 0.004 0.058 1164 Dihedral : 4.895 57.116 873 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.03 % Allowed : 14.57 % Favored : 82.40 % 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: 0.09 (0.30), residues: 787 helix: 0.33 (0.27), residues: 393 sheet: 1.03 (0.79), residues: 49 loop : -0.26 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 164 HIS 0.003 0.001 HIS A 377 PHE 0.012 0.001 PHE A 522 TYR 0.015 0.001 TYR A 50 ARG 0.011 0.001 ARG A 599 *********************** 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 117 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ILE cc_start: 0.8820 (mm) cc_final: 0.8576 (mp) REVERT: A 102 GLN cc_start: 0.6471 (OUTLIER) cc_final: 0.6144 (mt0) REVERT: A 151 MET cc_start: 0.8525 (mmm) cc_final: 0.7759 (mmt) REVERT: A 407 MET cc_start: 0.8656 (mmt) cc_final: 0.7825 (mmt) REVERT: A 535 GLU cc_start: 0.6017 (OUTLIER) cc_final: 0.5626 (mt-10) REVERT: B 454 ARG cc_start: 0.7830 (ttm-80) cc_final: 0.7528 (ttm-80) REVERT: B 455 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8705 (tt) outliers start: 21 outliers final: 7 residues processed: 108 average time/residue: 1.1300 time to fit residues: 129.1628 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 : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 360 CYS 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 432 CYS Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 478 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 0.4980 chunk 64 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6612 Z= 0.179 Angle : 0.542 8.497 8984 Z= 0.269 Chirality : 0.042 0.142 935 Planarity : 0.004 0.061 1164 Dihedral : 4.848 56.348 873 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.46 % Allowed : 15.01 % Favored : 81.53 % 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: 0.13 (0.30), residues: 787 helix: 0.33 (0.26), residues: 399 sheet: 1.20 (0.78), residues: 48 loop : -0.21 (0.33), residues: 340 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 0.013 0.001 PHE A 522 TYR 0.012 0.001 TYR A 50 ARG 0.015 0.001 ARG A 599 *********************** 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 118 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 GLN cc_start: 0.6451 (OUTLIER) cc_final: 0.6138 (mt0) REVERT: A 151 MET cc_start: 0.8512 (mmm) cc_final: 0.7752 (mmt) REVERT: A 407 MET cc_start: 0.8675 (mmt) cc_final: 0.7846 (mmt) REVERT: B 454 ARG cc_start: 0.7818 (ttm-80) cc_final: 0.7497 (ttm-80) REVERT: B 455 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8706 (tt) outliers start: 24 outliers final: 11 residues processed: 110 average time/residue: 1.1527 time to fit residues: 134.1169 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 : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 369 LEU 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 455 LEU 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 44 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 75 optimal weight: 0.1980 chunk 62 optimal weight: 0.5980 chunk 34 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 72 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6612 Z= 0.169 Angle : 0.548 8.704 8984 Z= 0.271 Chirality : 0.041 0.142 935 Planarity : 0.004 0.059 1164 Dihedral : 4.814 55.997 873 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.04 % Allowed : 15.73 % Favored : 80.23 % 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: 0.28 (0.30), residues: 787 helix: 0.48 (0.26), residues: 400 sheet: 1.19 (0.76), residues: 48 loop : -0.18 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 69 HIS 0.002 0.001 HIS A 525 PHE 0.012 0.001 PHE A 522 TYR 0.022 0.001 TYR A 201 ARG 0.013 0.001 ARG A 599 *********************** 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 116 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 88 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ILE cc_start: 0.8849 (mm) cc_final: 0.8456 (mp) REVERT: A 151 MET cc_start: 0.8453 (mmm) cc_final: 0.7746 (mmt) REVERT: A 280 LEU cc_start: 0.8207 (mp) cc_final: 0.7937 (mt) REVERT: A 535 GLU cc_start: 0.5992 (OUTLIER) cc_final: 0.5519 (mt-10) REVERT: B 454 ARG cc_start: 0.7832 (ttm-80) cc_final: 0.7526 (ttm-80) REVERT: B 455 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8705 (tt) outliers start: 28 outliers final: 12 residues processed: 106 average time/residue: 1.1736 time to fit residues: 131.2826 Evaluate side-chains 96 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 248 MET 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 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 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 55 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 ASN A 585 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6612 Z= 0.202 Angle : 0.562 8.582 8984 Z= 0.278 Chirality : 0.042 0.140 935 Planarity : 0.004 0.046 1164 Dihedral : 4.804 55.696 873 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.46 % Allowed : 17.46 % 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: 0.34 (0.30), residues: 787 helix: 0.54 (0.26), residues: 400 sheet: 1.21 (0.75), residues: 48 loop : -0.15 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 69 HIS 0.003 0.001 HIS A 377 PHE 0.013 0.001 PHE A 522 TYR 0.019 0.001 TYR A 50 ARG 0.011 0.001 ARG A 599 *********************** 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 113 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ILE cc_start: 0.8824 (mm) cc_final: 0.8525 (mp) REVERT: A 151 MET cc_start: 0.8469 (mmm) cc_final: 0.7701 (mmt) REVERT: A 407 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.7739 (mmt) REVERT: A 535 GLU cc_start: 0.6032 (OUTLIER) cc_final: 0.5550 (mt-10) REVERT: B 454 ARG cc_start: 0.7789 (ttm-80) cc_final: 0.7520 (ttm-80) REVERT: B 455 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8702 (tt) outliers start: 24 outliers final: 15 residues processed: 107 average time/residue: 1.1653 time to fit residues: 131.7269 Evaluate side-chains 103 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 446 VAL 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 455 LEU 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 14 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 59 optimal weight: 0.0570 chunk 68 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 ASN A 597 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6612 Z= 0.182 Angle : 0.560 8.699 8984 Z= 0.277 Chirality : 0.041 0.141 935 Planarity : 0.004 0.053 1164 Dihedral : 4.792 55.443 873 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.17 % Allowed : 18.04 % Favored : 78.79 % 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: 0.44 (0.30), residues: 787 helix: 0.62 (0.26), residues: 401 sheet: 1.27 (0.75), residues: 48 loop : -0.11 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 69 HIS 0.002 0.001 HIS A 377 PHE 0.012 0.001 PHE A 522 TYR 0.022 0.001 TYR A 201 ARG 0.013 0.001 ARG A 599 *********************** 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 112 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ILE cc_start: 0.8783 (mm) cc_final: 0.8561 (mp) REVERT: A 151 MET cc_start: 0.8442 (mmm) cc_final: 0.7790 (mmt) REVERT: A 226 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8237 (mm-30) REVERT: A 407 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8354 (mmt) REVERT: A 535 GLU cc_start: 0.6021 (OUTLIER) cc_final: 0.5525 (mt-10) REVERT: B 454 ARG cc_start: 0.7790 (ttm-80) cc_final: 0.7525 (ttm-80) REVERT: B 455 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8695 (tt) outliers start: 22 outliers final: 14 residues processed: 104 average time/residue: 1.2226 time to fit residues: 134.0215 Evaluate side-chains 101 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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 248 MET Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 538 LEU 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 455 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 69 optimal weight: 0.0970 chunk 46 optimal weight: 0.2980 chunk 74 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 ASN A 585 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6612 Z= 0.171 Angle : 0.561 8.835 8984 Z= 0.275 Chirality : 0.041 0.141 935 Planarity : 0.004 0.054 1164 Dihedral : 4.729 55.318 873 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.89 % Allowed : 18.90 % Favored : 78.21 % 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: 0.54 (0.30), residues: 787 helix: 0.73 (0.26), residues: 401 sheet: 1.27 (0.75), residues: 48 loop : -0.09 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 69 HIS 0.002 0.001 HIS A 377 PHE 0.012 0.001 PHE A 522 TYR 0.022 0.001 TYR A 50 ARG 0.013 0.001 ARG A 599 *********************** 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 116 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ILE cc_start: 0.8770 (mm) cc_final: 0.8561 (mp) REVERT: A 151 MET cc_start: 0.8404 (mmm) cc_final: 0.7783 (mmt) REVERT: A 226 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8194 (mm-30) REVERT: A 407 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8339 (mmt) REVERT: A 535 GLU cc_start: 0.5989 (OUTLIER) cc_final: 0.5493 (mt-10) REVERT: B 454 ARG cc_start: 0.7768 (ttm-80) cc_final: 0.7503 (ttm-80) outliers start: 20 outliers final: 14 residues processed: 108 average time/residue: 1.1298 time to fit residues: 129.4740 Evaluate side-chains 103 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.798 ------------------------------------------------------------------------------- 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 248 MET Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 538 LEU 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 503 VAL 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 77 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 6 optimal weight: 0.0070 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 ASN A 585 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6612 Z= 0.185 Angle : 0.572 8.969 8984 Z= 0.280 Chirality : 0.042 0.140 935 Planarity : 0.005 0.059 1164 Dihedral : 4.746 55.293 873 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.89 % Allowed : 19.05 % Favored : 78.07 % 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: 0.64 (0.30), residues: 787 helix: 0.81 (0.27), residues: 396 sheet: 1.26 (0.75), residues: 48 loop : -0.01 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 69 HIS 0.003 0.001 HIS A 377 PHE 0.013 0.001 PHE A 522 TYR 0.027 0.001 TYR A 50 ARG 0.014 0.001 ARG A 599 ********************** 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 108 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ILE cc_start: 0.8775 (mm) cc_final: 0.8562 (mp) REVERT: A 151 MET cc_start: 0.8425 (mmm) cc_final: 0.7722 (mmt) REVERT: A 226 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8209 (mm-30) REVERT: A 322 MET cc_start: 0.7511 (mmt) cc_final: 0.7053 (mmt) REVERT: A 407 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8352 (mmt) REVERT: B 454 ARG cc_start: 0.7780 (ttm-80) cc_final: 0.7509 (ttm-80) outliers start: 20 outliers final: 14 residues processed: 101 average time/residue: 1.0829 time to fit residues: 115.9128 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 : 0.723 ------------------------------------------------------------------------------- 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 248 MET Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 538 LEU 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 503 VAL 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 17 optimal weight: 0.7980 chunk 61 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 0.0670 chunk 54 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 44 optimal weight: 0.2980 chunk 70 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.175201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.129656 restraints weight = 7516.833| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.59 r_work: 0.3355 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6612 Z= 0.169 Angle : 0.556 9.035 8984 Z= 0.274 Chirality : 0.041 0.140 935 Planarity : 0.005 0.068 1164 Dihedral : 4.719 55.279 873 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.03 % Allowed : 19.19 % Favored : 77.78 % 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: 0.72 (0.30), residues: 787 helix: 0.86 (0.27), residues: 399 sheet: 1.26 (0.75), residues: 48 loop : 0.05 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 69 HIS 0.003 0.001 HIS A 377 PHE 0.012 0.001 PHE A 522 TYR 0.026 0.001 TYR A 50 ARG 0.014 0.001 ARG A 599 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2856.47 seconds wall clock time: 52 minutes 24.22 seconds (3144.22 seconds total)