Starting phenix.real_space_refine on Wed Feb 12 01:25:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jje_36345/02_2025/8jje_36345.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jje_36345/02_2025/8jje_36345.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jje_36345/02_2025/8jje_36345.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jje_36345/02_2025/8jje_36345.map" model { file = "/net/cci-nas-00/data/ceres_data/8jje_36345/02_2025/8jje_36345.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jje_36345/02_2025/8jje_36345.cif" } resolution = 3.4 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= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 40 5.16 5 C 4245 2.51 5 N 1079 2.21 5 O 1305 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6670 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4881 Classifications: {'peptide': 598} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 570} Chain: "B" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1551 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' ZN': 1, 'NAG': 1, 'SO4': 1} Classifications: {'undetermined': 3, 'water': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.70, per 1000 atoms: 0.70 Number of scatterers: 6670 At special positions: 0 Unit cell: (93.84, 82.11, 119.646, 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 40 16.00 O 1305 8.00 N 1079 7.00 C 4245 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.04 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.06 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.00 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.11 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " MAN E 4 " - " MAN E 5 " " BMA H 3 " - " MAN H 4 " ALPHA1-6 " BMA E 3 " - " MAN E 4 " " BMA H 3 " - " MAN H 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " NAG-ASN " NAG A1001 " - " ASN A 432 " Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 888.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A1002 " - pdb=" NE2 HIS A 374 " 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1494 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 7 sheets defined 59.3% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 19 through 53 removed outlier: 4.418A pdb=" N VAL A 25 " --> pdb=" O ILE A 21 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU A 39 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.744A pdb=" N ASN A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 4.277A pdb=" N LEU A 100 " --> pdb=" O GLN A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 4.052A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 146 through 155 removed outlier: 3.554A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.737A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 194 removed outlier: 3.865A pdb=" N ARG A 177 " --> pdb=" O GLY A 173 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 220 through 232 removed outlier: 3.668A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 252 removed outlier: 4.804A pdb=" N ASN A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.621A pdb=" N PHE A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.691A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 397 through 405 removed outlier: 4.491A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 413 removed outlier: 3.534A pdb=" N SER A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 433 through 447 removed outlier: 3.682A pdb=" N LYS A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 466 removed outlier: 4.595A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.802A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 4.407A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 564 removed outlier: 4.627A pdb=" N GLU A 564 " --> pdb=" O GLY A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.848A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix removed outlier: 3.966A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.621A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.988A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.881A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.142A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.720A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.248A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 332 through 334 removed outlier: 6.281A pdb=" N MET A 332 " --> pdb=" O MET A 360 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N THR A 362 " --> pdb=" O MET A 332 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N THR A 334 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA5, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.012A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA7, first strand: chain 'B' and resid 473 through 474 298 hydrogen bonds defined for protein. 834 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: 1.56 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1349 1.33 - 1.46: 2208 1.46 - 1.59: 3231 1.59 - 1.72: 0 1.72 - 1.84: 60 Bond restraints: 6848 Sorted by residual: bond pdb=" CD GLU A 375 " pdb=" OE2 GLU A 375 " ideal model delta sigma weight residual 1.249 1.469 -0.220 1.90e-02 2.77e+03 1.34e+02 bond pdb=" O3 SO4 A1003 " pdb=" S SO4 A1003 " ideal model delta sigma weight residual 1.499 1.396 0.103 2.00e-02 2.50e+03 2.63e+01 bond pdb=" O1 SO4 A1003 " pdb=" S SO4 A1003 " ideal model delta sigma weight residual 1.498 1.403 0.095 2.00e-02 2.50e+03 2.27e+01 bond pdb=" CG HIS A 374 " pdb=" CD2 HIS A 374 " ideal model delta sigma weight residual 1.354 1.310 0.044 1.10e-02 8.26e+03 1.57e+01 bond pdb=" CG HIS A 378 " pdb=" CD2 HIS A 378 " ideal model delta sigma weight residual 1.354 1.314 0.040 1.10e-02 8.26e+03 1.34e+01 ... (remaining 6843 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 8656 2.80 - 5.60: 633 5.60 - 8.40: 16 8.40 - 11.21: 3 11.21 - 14.01: 1 Bond angle restraints: 9309 Sorted by residual: angle pdb=" CA VAL A 172 " pdb=" CB VAL A 172 " pdb=" CG1 VAL A 172 " ideal model delta sigma weight residual 110.40 121.14 -10.74 1.70e+00 3.46e-01 3.99e+01 angle pdb=" CA PHE A 400 " pdb=" CB PHE A 400 " pdb=" CG PHE A 400 " ideal model delta sigma weight residual 113.80 119.12 -5.32 1.00e+00 1.00e+00 2.83e+01 angle pdb=" CA ASP A 216 " pdb=" CB ASP A 216 " pdb=" CG ASP A 216 " ideal model delta sigma weight residual 112.60 117.70 -5.10 1.00e+00 1.00e+00 2.60e+01 angle pdb=" CA ASN B 501 " pdb=" CB ASN B 501 " pdb=" CG ASN B 501 " ideal model delta sigma weight residual 112.60 117.62 -5.02 1.00e+00 1.00e+00 2.52e+01 angle pdb=" CA ASN A 394 " pdb=" CB ASN A 394 " pdb=" CG ASN A 394 " ideal model delta sigma weight residual 112.60 117.47 -4.87 1.00e+00 1.00e+00 2.38e+01 ... (remaining 9304 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.28: 3956 21.28 - 42.56: 231 42.56 - 63.84: 42 63.84 - 85.13: 27 85.13 - 106.41: 13 Dihedral angle restraints: 4269 sinusoidal: 1940 harmonic: 2329 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual -86.00 -175.43 89.43 1 1.00e+01 1.00e-02 9.51e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual -86.00 -140.68 54.68 1 1.00e+01 1.00e-02 4.05e+01 dihedral pdb=" CA ILE A 544 " pdb=" C ILE A 544 " pdb=" N SER A 545 " pdb=" CA SER A 545 " ideal model delta harmonic sigma weight residual -180.00 -152.02 -27.98 0 5.00e+00 4.00e-02 3.13e+01 ... (remaining 4266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.189: 990 0.189 - 0.377: 31 0.377 - 0.566: 2 0.566 - 0.755: 0 0.755 - 0.944: 1 Chirality restraints: 1024 Sorted by residual: chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-02 2.50e+03 4.37e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.36e+01 chirality pdb=" C1 NAG A1001 " pdb=" ND2 ASN A 432 " pdb=" C2 NAG A1001 " pdb=" O5 NAG A1001 " both_signs ideal model delta sigma weight residual False -2.40 -1.46 -0.94 2.00e-01 2.50e+01 2.23e+01 ... (remaining 1021 not shown) Planarity restraints: 1181 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 477 " 0.083 2.00e-02 2.50e+03 3.94e-02 3.88e+01 pdb=" CG TRP A 477 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP A 477 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP A 477 " -0.037 2.00e-02 2.50e+03 pdb=" NE1 TRP A 477 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP A 477 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 477 " -0.048 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 477 " 0.034 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 477 " -0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP A 477 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 207 " -0.080 2.00e-02 2.50e+03 4.16e-02 3.45e+01 pdb=" CG TYR A 207 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR A 207 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TYR A 207 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR A 207 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR A 207 " 0.021 2.00e-02 2.50e+03 pdb=" CZ TYR A 207 " -0.012 2.00e-02 2.50e+03 pdb=" OH TYR A 207 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 374 " -0.054 2.00e-02 2.50e+03 4.65e-02 3.24e+01 pdb=" CG HIS A 374 " 0.039 2.00e-02 2.50e+03 pdb=" ND1 HIS A 374 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 HIS A 374 " 0.061 2.00e-02 2.50e+03 pdb=" CE1 HIS A 374 " -0.007 2.00e-02 2.50e+03 pdb=" NE2 HIS A 374 " -0.064 2.00e-02 2.50e+03 ... (remaining 1178 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 5 2.44 - 3.06: 4056 3.06 - 3.67: 9575 3.67 - 4.29: 15004 4.29 - 4.90: 24595 Nonbonded interactions: 53235 Sorted by model distance: nonbonded pdb="ZN ZN A1002 " pdb=" O HOH A1101 " model vdw 1.829 2.230 nonbonded pdb="ZN ZN A1002 " pdb=" O1 SO4 A1003 " model vdw 1.965 2.230 nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A1002 " model vdw 2.178 2.230 nonbonded pdb=" OE1 GLU A 402 " pdb="ZN ZN A1002 " model vdw 2.180 2.230 nonbonded pdb=" OE2 GLU A 375 " pdb=" O HOH A1101 " model vdw 2.356 3.040 ... (remaining 53230 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' } 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: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.400 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 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 : 0.011 0.220 6848 Z= 0.707 Angle : 1.507 14.008 9309 Z= 0.979 Chirality : 0.093 0.944 1024 Planarity : 0.014 0.225 1180 Dihedral : 16.243 106.406 2754 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 0.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.86 % Allowed : 5.44 % Favored : 92.69 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.00 (0.26), residues: 790 helix: -1.73 (0.20), residues: 393 sheet: 1.63 (0.86), residues: 35 loop : -0.99 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.012 TRP A 477 HIS 0.035 0.006 HIS A 374 PHE 0.065 0.010 PHE A 400 TYR 0.080 0.013 TYR A 207 ARG 0.023 0.003 ARG A 559 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 0.804 Fit side-chains revert: symmetry clash REVERT: A 42 GLN cc_start: 0.8611 (tp40) cc_final: 0.8243 (mm110) REVERT: A 54 ILE cc_start: 0.7943 (mt) cc_final: 0.7718 (mt) REVERT: A 131 LYS cc_start: 0.6917 (ptpt) cc_final: 0.6580 (mtpt) REVERT: A 152 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8258 (mmm) REVERT: A 171 GLU cc_start: 0.7739 (tp30) cc_final: 0.7131 (tm-30) REVERT: A 207 TYR cc_start: 0.8687 (m-80) cc_final: 0.8153 (m-80) REVERT: A 331 SER cc_start: 0.9128 (m) cc_final: 0.8907 (p) REVERT: A 343 CYS cc_start: 0.8237 (m) cc_final: 0.7752 (t) REVERT: A 360 MET cc_start: 0.9072 (ttt) cc_final: 0.8854 (ttt) REVERT: A 428 PHE cc_start: 0.7962 (t80) cc_final: 0.7730 (t80) REVERT: A 475 LYS cc_start: 0.8365 (tttt) cc_final: 0.8147 (tmmt) REVERT: B 346 ARG cc_start: 0.8452 (ttm110) cc_final: 0.8163 (ptm-80) REVERT: B 382 VAL cc_start: 0.7925 (t) cc_final: 0.7545 (t) REVERT: B 408 ARG cc_start: 0.9037 (ptm160) cc_final: 0.8330 (ppt170) REVERT: B 428 ASP cc_start: 0.8683 (t0) cc_final: 0.8406 (p0) REVERT: B 484 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8405 (mt-10) outliers start: 13 outliers final: 8 residues processed: 140 average time/residue: 0.2188 time to fit residues: 39.7608 Evaluate side-chains 86 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain B residue 518 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 chunk 37 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 HIS B 501 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.163580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.129178 restraints weight = 9603.655| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.59 r_work: 0.3482 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6848 Z= 0.211 Angle : 0.668 6.707 9309 Z= 0.340 Chirality : 0.046 0.406 1024 Planarity : 0.004 0.038 1180 Dihedral : 11.999 77.301 1245 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.58 % Allowed : 9.46 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.39 (0.29), residues: 790 helix: -0.06 (0.26), residues: 404 sheet: 1.04 (0.79), residues: 44 loop : -0.52 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 168 HIS 0.005 0.001 HIS A 378 PHE 0.030 0.002 PHE B 486 TYR 0.016 0.002 TYR B 396 ARG 0.003 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 ASN cc_start: 0.8208 (m-40) cc_final: 0.7557 (t0) REVERT: A 207 TYR cc_start: 0.8310 (m-80) cc_final: 0.7700 (m-80) REVERT: A 475 LYS cc_start: 0.8395 (tttt) cc_final: 0.8181 (tmmt) REVERT: B 408 ARG cc_start: 0.8659 (ptm160) cc_final: 0.7931 (ppt170) REVERT: B 439 ASN cc_start: 0.8880 (t0) cc_final: 0.8651 (t0) REVERT: B 486 PHE cc_start: 0.7407 (t80) cc_final: 0.7172 (t80) outliers start: 25 outliers final: 19 residues processed: 104 average time/residue: 0.1995 time to fit residues: 28.0016 Evaluate side-chains 84 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 518 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 31 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 96 GLN A 277 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.163654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.129645 restraints weight = 9851.562| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.59 r_work: 0.3450 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6848 Z= 0.217 Angle : 0.608 6.562 9309 Z= 0.302 Chirality : 0.045 0.320 1024 Planarity : 0.004 0.057 1180 Dihedral : 9.822 62.586 1242 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.15 % Allowed : 11.60 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 (0.29), residues: 790 helix: 0.40 (0.26), residues: 401 sheet: 0.73 (0.80), residues: 44 loop : -0.57 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 477 HIS 0.004 0.001 HIS A 378 PHE 0.034 0.002 PHE B 486 TYR 0.016 0.002 TYR A 385 ARG 0.002 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 TYR cc_start: 0.8291 (m-80) cc_final: 0.7681 (m-80) REVERT: A 440 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8223 (tp) REVERT: A 469 PRO cc_start: 0.8648 (Cg_exo) cc_final: 0.8322 (Cg_endo) REVERT: A 475 LYS cc_start: 0.8465 (tttt) cc_final: 0.8264 (ttpt) REVERT: B 408 ARG cc_start: 0.8659 (ptm160) cc_final: 0.7934 (ppt170) REVERT: B 439 ASN cc_start: 0.8889 (t0) cc_final: 0.8638 (t0) REVERT: B 484 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7772 (mt-10) outliers start: 22 outliers final: 14 residues processed: 92 average time/residue: 0.1863 time to fit residues: 23.3383 Evaluate side-chains 80 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 518 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 56 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 52 optimal weight: 0.3980 chunk 1 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.151070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.117311 restraints weight = 9666.557| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.49 r_work: 0.3463 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6848 Z= 0.194 Angle : 0.572 5.345 9309 Z= 0.281 Chirality : 0.044 0.303 1024 Planarity : 0.004 0.039 1180 Dihedral : 8.499 59.774 1242 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.58 % Allowed : 12.46 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 (0.29), residues: 790 helix: 0.52 (0.26), residues: 401 sheet: 0.56 (0.80), residues: 44 loop : -0.57 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 477 HIS 0.003 0.001 HIS A 378 PHE 0.022 0.001 PHE A 369 TYR 0.013 0.001 TYR A 252 ARG 0.002 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 SER cc_start: 0.8897 (p) cc_final: 0.8522 (m) REVERT: A 207 TYR cc_start: 0.8211 (m-80) cc_final: 0.7680 (m-80) REVERT: A 334 THR cc_start: 0.8956 (m) cc_final: 0.8731 (m) REVERT: A 440 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8225 (tp) REVERT: A 475 LYS cc_start: 0.8473 (tttt) cc_final: 0.8263 (ttpt) REVERT: B 408 ARG cc_start: 0.8659 (ptm160) cc_final: 0.8169 (ppt170) REVERT: B 439 ASN cc_start: 0.8875 (t0) cc_final: 0.8630 (t0) REVERT: B 484 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7627 (mt-10) outliers start: 25 outliers final: 18 residues processed: 93 average time/residue: 0.1876 time to fit residues: 23.9700 Evaluate side-chains 82 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 518 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 15 optimal weight: 0.4980 chunk 32 optimal weight: 0.0020 chunk 49 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 52 optimal weight: 0.0020 chunk 27 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 chunk 25 optimal weight: 0.0070 chunk 17 optimal weight: 3.9990 overall best weight: 0.2214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 373 HIS B 487 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.168542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.134768 restraints weight = 9755.092| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.59 r_work: 0.3510 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6848 Z= 0.131 Angle : 0.517 5.202 9309 Z= 0.254 Chirality : 0.041 0.262 1024 Planarity : 0.004 0.046 1180 Dihedral : 7.412 58.783 1242 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.58 % Allowed : 13.18 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.31 (0.30), residues: 790 helix: 0.80 (0.27), residues: 406 sheet: 0.44 (0.81), residues: 44 loop : -0.46 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 168 HIS 0.002 0.001 HIS A 345 PHE 0.015 0.001 PHE A 369 TYR 0.009 0.001 TYR A 158 ARG 0.001 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: A 73 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8491 (tt) REVERT: A 198 ASP cc_start: 0.8175 (p0) cc_final: 0.7912 (p0) REVERT: A 207 TYR cc_start: 0.8173 (m-80) cc_final: 0.7646 (m-80) REVERT: A 347 THR cc_start: 0.8233 (OUTLIER) cc_final: 0.7898 (p) REVERT: A 435 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6924 (tt0) REVERT: A 440 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8129 (tp) REVERT: A 469 PRO cc_start: 0.8414 (Cg_exo) cc_final: 0.8190 (Cg_endo) REVERT: A 475 LYS cc_start: 0.8424 (tttt) cc_final: 0.8207 (ttpt) REVERT: B 387 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8125 (mt) REVERT: B 408 ARG cc_start: 0.8632 (ptm160) cc_final: 0.8140 (ppt170) outliers start: 25 outliers final: 19 residues processed: 104 average time/residue: 0.1715 time to fit residues: 25.0334 Evaluate side-chains 103 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 518 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 24 optimal weight: 0.1980 chunk 20 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.165980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.132104 restraints weight = 9802.284| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.58 r_work: 0.3502 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6848 Z= 0.184 Angle : 0.555 12.106 9309 Z= 0.273 Chirality : 0.043 0.266 1024 Planarity : 0.004 0.046 1180 Dihedral : 7.136 54.812 1242 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.44 % Allowed : 13.47 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.39 (0.30), residues: 790 helix: 0.88 (0.27), residues: 406 sheet: 0.49 (0.80), residues: 44 loop : -0.44 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 477 HIS 0.004 0.001 HIS A 378 PHE 0.017 0.001 PHE A 369 TYR 0.009 0.001 TYR A 243 ARG 0.002 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.625 Fit side-chains revert: symmetry clash REVERT: A 73 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8550 (tt) REVERT: A 207 TYR cc_start: 0.8111 (m-80) cc_final: 0.7550 (m-80) REVERT: A 347 THR cc_start: 0.8366 (OUTLIER) cc_final: 0.8009 (p) REVERT: A 429 GLN cc_start: 0.7490 (tp-100) cc_final: 0.7278 (tp40) REVERT: A 440 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8220 (tp) REVERT: A 475 LYS cc_start: 0.8446 (tttt) cc_final: 0.8230 (ttpt) REVERT: B 387 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8067 (mt) REVERT: B 408 ARG cc_start: 0.8623 (ptm160) cc_final: 0.8150 (ppt170) REVERT: B 484 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7439 (mt-10) outliers start: 24 outliers final: 17 residues processed: 98 average time/residue: 0.1645 time to fit residues: 22.5524 Evaluate side-chains 89 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 518 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 4 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 58 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.155261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.121206 restraints weight = 9858.671| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.61 r_work: 0.3376 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6848 Z= 0.198 Angle : 0.554 8.873 9309 Z= 0.273 Chirality : 0.042 0.260 1024 Planarity : 0.004 0.053 1180 Dihedral : 6.891 49.694 1242 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.87 % Allowed : 14.33 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.38 (0.30), residues: 790 helix: 0.89 (0.27), residues: 407 sheet: 0.48 (0.81), residues: 44 loop : -0.47 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 477 HIS 0.003 0.001 HIS A 378 PHE 0.020 0.001 PHE A 369 TYR 0.010 0.001 TYR B 453 ARG 0.002 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 73 time to evaluate : 0.789 Fit side-chains revert: symmetry clash REVERT: A 207 TYR cc_start: 0.8100 (m-80) cc_final: 0.7534 (m-80) REVERT: A 347 THR cc_start: 0.8411 (OUTLIER) cc_final: 0.8045 (p) REVERT: A 435 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6796 (tt0) REVERT: A 440 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8196 (tp) REVERT: A 469 PRO cc_start: 0.8430 (Cg_exo) cc_final: 0.8166 (Cg_endo) REVERT: A 475 LYS cc_start: 0.8391 (tttt) cc_final: 0.8163 (ttpt) REVERT: B 387 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8114 (mt) REVERT: B 408 ARG cc_start: 0.8666 (ptm160) cc_final: 0.8146 (ppt170) REVERT: B 484 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7486 (mt-10) outliers start: 27 outliers final: 17 residues processed: 96 average time/residue: 0.1879 time to fit residues: 24.5955 Evaluate side-chains 92 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 518 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 18 optimal weight: 0.3980 chunk 67 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 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 330 ASN A 429 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.154702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.120374 restraints weight = 9916.462| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.66 r_work: 0.3371 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6848 Z= 0.199 Angle : 0.547 8.776 9309 Z= 0.271 Chirality : 0.042 0.271 1024 Planarity : 0.004 0.053 1180 Dihedral : 6.620 47.903 1241 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.72 % Allowed : 14.04 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.39 (0.30), residues: 790 helix: 0.94 (0.27), residues: 407 sheet: 0.46 (0.81), residues: 44 loop : -0.54 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 477 HIS 0.003 0.001 HIS A 378 PHE 0.020 0.001 PHE A 369 TYR 0.010 0.001 TYR B 453 ARG 0.002 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 0.695 Fit side-chains REVERT: A 198 ASP cc_start: 0.8062 (p0) cc_final: 0.7720 (p0) REVERT: A 207 TYR cc_start: 0.8101 (m-80) cc_final: 0.7558 (m-80) REVERT: A 435 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6844 (tt0) REVERT: A 440 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8356 (tp) REVERT: A 469 PRO cc_start: 0.8416 (Cg_exo) cc_final: 0.8108 (Cg_endo) REVERT: A 475 LYS cc_start: 0.8405 (tttt) cc_final: 0.8171 (ttpt) REVERT: B 387 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8167 (mt) REVERT: B 408 ARG cc_start: 0.8628 (ptm160) cc_final: 0.8139 (ppt170) REVERT: B 484 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7477 (mt-10) outliers start: 26 outliers final: 20 residues processed: 93 average time/residue: 0.1767 time to fit residues: 22.6323 Evaluate side-chains 94 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 518 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 63 optimal weight: 2.9990 chunk 8 optimal weight: 0.0170 chunk 18 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 6 optimal weight: 0.0470 chunk 17 optimal weight: 0.9990 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.156888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.122653 restraints weight = 9979.598| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.67 r_work: 0.3403 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6848 Z= 0.154 Angle : 0.525 7.683 9309 Z= 0.259 Chirality : 0.041 0.229 1024 Planarity : 0.004 0.055 1180 Dihedral : 6.374 47.385 1241 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.58 % Allowed : 14.47 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.51 (0.30), residues: 790 helix: 1.07 (0.27), residues: 407 sheet: 0.43 (0.80), residues: 44 loop : -0.49 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 477 HIS 0.003 0.001 HIS A 378 PHE 0.014 0.001 PHE A 369 TYR 0.008 0.001 TYR A 587 ARG 0.002 0.000 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 0.712 Fit side-chains REVERT: A 198 ASP cc_start: 0.8037 (p0) cc_final: 0.7721 (p0) REVERT: A 207 TYR cc_start: 0.8061 (m-80) cc_final: 0.7541 (m-80) REVERT: A 228 HIS cc_start: 0.7941 (t70) cc_final: 0.7589 (m-70) REVERT: A 435 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6771 (tt0) REVERT: A 440 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8174 (tp) REVERT: A 475 LYS cc_start: 0.8381 (tttt) cc_final: 0.8164 (ttpt) REVERT: B 366 SER cc_start: 0.8586 (t) cc_final: 0.8206 (p) REVERT: B 387 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8133 (mt) REVERT: B 408 ARG cc_start: 0.8613 (ptm160) cc_final: 0.8097 (ppt170) outliers start: 25 outliers final: 19 residues processed: 99 average time/residue: 0.1830 time to fit residues: 24.8772 Evaluate side-chains 95 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 515 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 7 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 46 optimal weight: 0.3980 chunk 66 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 58 optimal weight: 0.0870 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.156275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.122247 restraints weight = 10080.790| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.68 r_work: 0.3398 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6848 Z= 0.172 Angle : 0.539 8.573 9309 Z= 0.263 Chirality : 0.041 0.253 1024 Planarity : 0.004 0.055 1180 Dihedral : 6.091 47.687 1239 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.44 % Allowed : 15.04 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.51 (0.30), residues: 790 helix: 1.07 (0.27), residues: 407 sheet: 0.44 (0.80), residues: 44 loop : -0.50 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 477 HIS 0.004 0.001 HIS B 519 PHE 0.017 0.001 PHE A 369 TYR 0.008 0.001 TYR A 587 ARG 0.002 0.000 ARG B 454 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 0.660 Fit side-chains REVERT: A 207 TYR cc_start: 0.8121 (m-80) cc_final: 0.7536 (m-80) REVERT: A 228 HIS cc_start: 0.7942 (t70) cc_final: 0.7595 (m-70) REVERT: A 435 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6828 (tt0) REVERT: A 440 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8226 (tp) REVERT: A 455 MET cc_start: 0.7868 (tmm) cc_final: 0.7121 (tmm) REVERT: A 474 MET cc_start: 0.7552 (mmm) cc_final: 0.7329 (mmm) REVERT: A 475 LYS cc_start: 0.8400 (tttt) cc_final: 0.8176 (ttpt) REVERT: B 366 SER cc_start: 0.8648 (t) cc_final: 0.8275 (p) REVERT: B 387 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8144 (mt) REVERT: B 408 ARG cc_start: 0.8538 (ptm160) cc_final: 0.8061 (ppt170) REVERT: B 484 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7269 (mt-10) outliers start: 24 outliers final: 19 residues processed: 95 average time/residue: 0.1789 time to fit residues: 23.4101 Evaluate side-chains 94 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 515 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 47 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 70 optimal weight: 0.4980 chunk 5 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 58 optimal weight: 0.0030 chunk 9 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.155747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.121666 restraints weight = 9956.865| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.65 r_work: 0.3395 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6848 Z= 0.170 Angle : 0.542 11.787 9309 Z= 0.263 Chirality : 0.041 0.252 1024 Planarity : 0.004 0.053 1180 Dihedral : 5.987 47.643 1238 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.30 % Allowed : 15.04 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.51 (0.30), residues: 790 helix: 1.04 (0.27), residues: 408 sheet: 0.46 (0.81), residues: 44 loop : -0.46 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 302 HIS 0.004 0.001 HIS A 378 PHE 0.017 0.001 PHE A 369 TYR 0.008 0.001 TYR A 587 ARG 0.002 0.000 ARG A 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3010.11 seconds wall clock time: 54 minutes 42.77 seconds (3282.77 seconds total)