Starting phenix.real_space_refine on Sun Jul 27 05:35:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yvu_34138/07_2025/7yvu_34138.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yvu_34138/07_2025/7yvu_34138.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yvu_34138/07_2025/7yvu_34138.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yvu_34138/07_2025/7yvu_34138.map" model { file = "/net/cci-nas-00/data/ceres_data/7yvu_34138/07_2025/7yvu_34138.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yvu_34138/07_2025/7yvu_34138.cif" } resolution = 3.2 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= 0.001 sd= 0.018 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 3164 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 37 5.16 5 C 4124 2.51 5 N 1081 2.21 5 O 1213 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 6456 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4856 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "B" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1557 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.49, per 1000 atoms: 1.01 Number of scatterers: 6456 At special positions: 0 Unit cell: (81.07, 90.45, 114.57, 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 37 16.00 O 1213 8.00 N 1081 7.00 C 4124 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=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 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 Links applied NAG-ASN " NAG A 701 " - " ASN A 53 " " NAG A 702 " - " ASN A 546 " " NAG B 601 " - " ASN B 343 " Time building additional restraints: 1.66 Conformation dependent library (CDL) restraints added in 981.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 703 " pdb="ZN ZN A 703 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 703 " - pdb=" NE2 HIS A 378 " 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: 1492 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 4 sheets defined 57.3% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 20 through 52 removed outlier: 4.352A pdb=" N ASN A 24 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.571A pdb=" N GLN A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TRP A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 Processing helix chain 'A' and resid 90 through 102 Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 147 through 155 removed outlier: 3.597A pdb=" N SER A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.842A pdb=" N ALA A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYS A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.741A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 221 through 232 removed outlier: 3.713A pdb=" N GLU A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.656A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP A 250 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 256 removed outlier: 4.397A pdb=" N ILE A 256 " --> pdb=" O PRO A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 253 through 256' 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 283 Proline residue: A 280 - end of helix removed outlier: 4.109A pdb=" N VAL A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 301 Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.580A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.591A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) 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 399 through 411 removed outlier: 3.521A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.839A pdb=" N ILE A 436 " --> pdb=" O SER A 432 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 465 Processing helix chain 'A' and resid 472 through 478 Processing helix chain 'A' and resid 498 through 502 removed outlier: 3.549A pdb=" N ALA A 501 " --> pdb=" O CYS A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 508 removed outlier: 3.571A pdb=" N ASN A 508 " --> pdb=" O PHE A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.594A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 4.078A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN A 552 " --> pdb=" O THR A 548 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.810A pdb=" N ALA A 569 " --> pdb=" O PRO A 565 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 570 " --> pdb=" O TRP A 566 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU A 571 " --> pdb=" O THR A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.608A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.629A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.711A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 4.041A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.681A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.277A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.059A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.774A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 452 through 454 284 hydrogen bonds defined for protein. 792 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: 1.69 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2080 1.35 - 1.48: 1820 1.48 - 1.61: 2680 1.61 - 1.73: 0 1.73 - 1.86: 58 Bond restraints: 6638 Sorted by residual: bond pdb=" CA ASN A 49 " pdb=" C ASN A 49 " ideal model delta sigma weight residual 1.523 1.484 0.039 1.35e-02 5.49e+03 8.43e+00 bond pdb=" N GLU A 402 " pdb=" CA GLU A 402 " ideal model delta sigma weight residual 1.459 1.486 -0.026 1.19e-02 7.06e+03 4.96e+00 bond pdb=" CB PRO B 521 " pdb=" CG PRO B 521 " ideal model delta sigma weight residual 1.492 1.570 -0.078 5.00e-02 4.00e+02 2.41e+00 bond pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " ideal model delta sigma weight residual 1.808 1.859 -0.051 3.30e-02 9.18e+02 2.36e+00 bond pdb=" C1 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.27e+00 ... (remaining 6633 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 8831 1.97 - 3.94: 158 3.94 - 5.91: 23 5.91 - 7.88: 5 7.88 - 9.84: 1 Bond angle restraints: 9018 Sorted by residual: angle pdb=" N ILE B 468 " pdb=" CA ILE B 468 " pdb=" C ILE B 468 " ideal model delta sigma weight residual 113.20 108.38 4.82 9.60e-01 1.09e+00 2.52e+01 angle pdb=" C ASP A 509 " pdb=" CA ASP A 509 " pdb=" CB ASP A 509 " ideal model delta sigma weight residual 116.34 110.19 6.15 1.40e+00 5.10e-01 1.93e+01 angle pdb=" C LEU A 144 " pdb=" N GLU A 145 " pdb=" CA GLU A 145 " ideal model delta sigma weight residual 121.80 131.64 -9.84 2.44e+00 1.68e-01 1.63e+01 angle pdb=" N CYS B 432 " pdb=" CA CYS B 432 " pdb=" C CYS B 432 " ideal model delta sigma weight residual 108.14 114.18 -6.04 1.52e+00 4.33e-01 1.58e+01 angle pdb=" CA CYS B 432 " pdb=" CB CYS B 432 " pdb=" SG CYS B 432 " ideal model delta sigma weight residual 114.40 121.85 -7.45 2.30e+00 1.89e-01 1.05e+01 ... (remaining 9013 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 3518 17.49 - 34.98: 355 34.98 - 52.46: 66 52.46 - 69.95: 16 69.95 - 87.44: 10 Dihedral angle restraints: 3965 sinusoidal: 1640 harmonic: 2325 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 93.00 152.96 -59.96 1 1.00e+01 1.00e-02 4.79e+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 93.00 42.17 50.83 1 1.00e+01 1.00e-02 3.54e+01 dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 129.29 -36.29 1 1.00e+01 1.00e-02 1.86e+01 ... (remaining 3962 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 609 0.037 - 0.073: 235 0.073 - 0.110: 73 0.110 - 0.147: 23 0.147 - 0.183: 3 Chirality restraints: 943 Sorted by residual: chirality pdb=" CA PRO B 521 " pdb=" N PRO B 521 " pdb=" C PRO B 521 " pdb=" CB PRO B 521 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.40e-01 chirality pdb=" C2 NAG A 701 " pdb=" C1 NAG A 701 " pdb=" C3 NAG A 701 " pdb=" N2 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.49 -2.32 -0.17 2.00e-01 2.50e+01 7.50e-01 chirality pdb=" CA CYS B 432 " pdb=" N CYS B 432 " pdb=" C CYS B 432 " pdb=" CB CYS B 432 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.27e-01 ... (remaining 940 not shown) Planarity restraints: 1172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 520 " 0.078 5.00e-02 4.00e+02 1.17e-01 2.19e+01 pdb=" N PRO B 521 " -0.202 5.00e-02 4.00e+02 pdb=" CA PRO B 521 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO B 521 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 145 " 0.070 5.00e-02 4.00e+02 1.06e-01 1.78e+01 pdb=" N PRO A 146 " -0.183 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 252 " 0.038 5.00e-02 4.00e+02 5.86e-02 5.50e+00 pdb=" N PRO A 253 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 253 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 253 " 0.032 5.00e-02 4.00e+02 ... (remaining 1169 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 77 2.66 - 3.22: 6007 3.22 - 3.78: 9260 3.78 - 4.34: 12549 4.34 - 4.90: 21450 Nonbonded interactions: 49343 Sorted by model distance: nonbonded pdb=" OE1 GLU A 402 " pdb="ZN ZN A 703 " model vdw 2.103 2.230 nonbonded pdb=" O PHE A 327 " pdb=" OG SER A 331 " model vdw 2.153 3.040 nonbonded pdb=" NH1 ARG B 457 " pdb=" OD2 ASP B 467 " model vdw 2.215 3.120 nonbonded pdb=" NH1 ARG A 177 " pdb=" O GLU A 495 " model vdw 2.253 3.120 nonbonded pdb=" O PRO B 384 " pdb=" OG1 THR B 385 " model vdw 2.292 3.040 ... (remaining 49338 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: 46.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 22.580 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:3.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 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 : 0.005 0.167 6650 Z= 0.209 Angle : 0.641 9.844 9041 Z= 0.343 Chirality : 0.045 0.183 943 Planarity : 0.007 0.117 1169 Dihedral : 14.813 87.438 2452 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.46 % Favored : 94.03 % Rotamer: Outliers : 0.29 % Allowed : 0.44 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.60 (0.30), residues: 787 helix: 0.61 (0.28), residues: 388 sheet: 0.04 (0.71), residues: 50 loop : -1.64 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 594 HIS 0.006 0.001 HIS A 378 PHE 0.023 0.001 PHE A 308 TYR 0.017 0.001 TYR A 381 ARG 0.006 0.000 ARG A 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00293 ( 3) link_NAG-ASN : angle 1.96507 ( 9) hydrogen bonds : bond 0.17931 ( 284) hydrogen bonds : angle 6.07070 ( 792) metal coordination : bond 0.16530 ( 2) SS BOND : bond 0.00558 ( 7) SS BOND : angle 1.58627 ( 14) covalent geometry : bond 0.00419 ( 6638) covalent geometry : angle 0.63556 ( 9018) *********************** 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 207 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 205 time to evaluate : 0.723 Fit side-chains REVERT: A 78 LYS cc_start: 0.8354 (tptm) cc_final: 0.8014 (tptm) REVERT: A 216 ASN cc_start: 0.7667 (m-40) cc_final: 0.7430 (m-40) REVERT: A 402 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.6352 (mm-30) REVERT: A 421 ILE cc_start: 0.8013 (tp) cc_final: 0.7812 (tp) REVERT: A 455 MET cc_start: 0.7398 (tmm) cc_final: 0.6952 (tmm) REVERT: A 479 GLU cc_start: 0.7463 (tm-30) cc_final: 0.7153 (tm-30) REVERT: A 508 ASN cc_start: 0.7589 (m-40) cc_final: 0.7296 (t0) REVERT: B 357 ARG cc_start: 0.8157 (ttp80) cc_final: 0.7901 (ttp80) REVERT: B 438 SER cc_start: 0.7762 (t) cc_final: 0.7441 (t) REVERT: B 443 SER cc_start: 0.8240 (m) cc_final: 0.7986 (m) outliers start: 2 outliers final: 0 residues processed: 206 average time/residue: 0.2097 time to fit residues: 57.2078 Evaluate side-chains 191 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 31 optimal weight: 0.3980 chunk 61 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS A 374 HIS A 601 ASN B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.115678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.103612 restraints weight = 9693.515| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.15 r_work: 0.3184 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.164 6650 Z= 0.213 Angle : 0.640 10.257 9041 Z= 0.324 Chirality : 0.047 0.258 943 Planarity : 0.007 0.118 1169 Dihedral : 6.261 59.379 932 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.84 % Favored : 93.65 % Rotamer: Outliers : 1.75 % Allowed : 10.77 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.35 (0.30), residues: 787 helix: 0.85 (0.27), residues: 391 sheet: -0.21 (0.67), residues: 53 loop : -1.53 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 477 HIS 0.006 0.001 HIS A 378 PHE 0.013 0.001 PHE A 308 TYR 0.021 0.001 TYR A 385 ARG 0.004 0.000 ARG A 465 Details of bonding type rmsd link_NAG-ASN : bond 0.00327 ( 3) link_NAG-ASN : angle 2.09548 ( 9) hydrogen bonds : bond 0.05972 ( 284) hydrogen bonds : angle 4.41602 ( 792) metal coordination : bond 0.11631 ( 2) SS BOND : bond 0.00550 ( 7) SS BOND : angle 1.50867 ( 14) covalent geometry : bond 0.00483 ( 6638) covalent geometry : angle 0.63496 ( 9018) *********************** 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 203 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 191 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: A 54 ILE cc_start: 0.7992 (mt) cc_final: 0.7768 (tt) REVERT: A 75 GLU cc_start: 0.8448 (tp30) cc_final: 0.8149 (tp30) REVERT: A 78 LYS cc_start: 0.8615 (tptm) cc_final: 0.8279 (tptm) REVERT: A 84 SER cc_start: 0.8665 (t) cc_final: 0.8451 (m) REVERT: A 87 GLU cc_start: 0.7394 (tm-30) cc_final: 0.7087 (tm-30) REVERT: A 111 ASP cc_start: 0.8280 (m-30) cc_final: 0.8034 (t70) REVERT: A 149 ASP cc_start: 0.8080 (t70) cc_final: 0.7862 (t70) REVERT: A 421 ILE cc_start: 0.8750 (tp) cc_final: 0.8514 (tp) REVERT: A 455 MET cc_start: 0.8469 (tmm) cc_final: 0.8091 (tmm) REVERT: A 470 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8522 (tttp) REVERT: A 479 GLU cc_start: 0.8314 (tm-30) cc_final: 0.7974 (tm-30) REVERT: A 508 ASN cc_start: 0.8122 (m-40) cc_final: 0.7659 (t0) REVERT: A 556 LYS cc_start: 0.8615 (ttmm) cc_final: 0.8274 (mtpp) REVERT: B 438 SER cc_start: 0.8077 (t) cc_final: 0.7829 (t) REVERT: B 443 SER cc_start: 0.8507 (m) cc_final: 0.8268 (m) outliers start: 12 outliers final: 8 residues processed: 195 average time/residue: 0.2149 time to fit residues: 55.4631 Evaluate side-chains 198 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 189 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 469 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 42 optimal weight: 0.0170 chunk 68 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 45 optimal weight: 0.0670 chunk 18 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS A 601 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.116688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.104581 restraints weight = 9756.090| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.16 r_work: 0.3197 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 6650 Z= 0.156 Angle : 0.601 10.328 9041 Z= 0.301 Chirality : 0.044 0.264 943 Planarity : 0.006 0.118 1169 Dihedral : 5.885 59.447 929 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.08 % Favored : 94.41 % Rotamer: Outliers : 1.75 % Allowed : 13.97 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.29 (0.30), residues: 787 helix: 0.89 (0.27), residues: 391 sheet: -0.15 (0.65), residues: 53 loop : -1.48 (0.33), residues: 343 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 0.011 0.001 PHE A 308 TYR 0.018 0.001 TYR A 385 ARG 0.003 0.000 ARG A 465 Details of bonding type rmsd link_NAG-ASN : bond 0.00263 ( 3) link_NAG-ASN : angle 1.98940 ( 9) hydrogen bonds : bond 0.05256 ( 284) hydrogen bonds : angle 4.27786 ( 792) metal coordination : bond 0.00148 ( 2) SS BOND : bond 0.00440 ( 7) SS BOND : angle 1.32948 ( 14) covalent geometry : bond 0.00375 ( 6638) covalent geometry : angle 0.59570 ( 9018) *********************** 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 197 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 185 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: A 54 ILE cc_start: 0.7929 (mt) cc_final: 0.7715 (tt) REVERT: A 75 GLU cc_start: 0.8442 (tp30) cc_final: 0.8161 (tp30) REVERT: A 78 LYS cc_start: 0.8615 (tptm) cc_final: 0.8278 (tptm) REVERT: A 84 SER cc_start: 0.8572 (t) cc_final: 0.8264 (m) REVERT: A 87 GLU cc_start: 0.7393 (tm-30) cc_final: 0.7063 (tm-30) REVERT: A 111 ASP cc_start: 0.8323 (m-30) cc_final: 0.8060 (t70) REVERT: A 149 ASP cc_start: 0.8086 (t70) cc_final: 0.7872 (t70) REVERT: A 287 GLN cc_start: 0.8287 (mm-40) cc_final: 0.8034 (mm-40) REVERT: A 421 ILE cc_start: 0.8693 (tp) cc_final: 0.8435 (tp) REVERT: A 455 MET cc_start: 0.8459 (tmm) cc_final: 0.8096 (tmm) REVERT: A 470 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8462 (tttp) REVERT: A 471 GLU cc_start: 0.7701 (pm20) cc_final: 0.7467 (pm20) REVERT: A 479 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7958 (tm-30) REVERT: A 508 ASN cc_start: 0.8056 (m-40) cc_final: 0.7650 (t0) REVERT: A 556 LYS cc_start: 0.8581 (ttmm) cc_final: 0.8248 (mtpp) REVERT: B 347 PHE cc_start: 0.8412 (m-10) cc_final: 0.8117 (m-10) REVERT: B 438 SER cc_start: 0.8103 (t) cc_final: 0.7846 (t) REVERT: B 443 SER cc_start: 0.8505 (m) cc_final: 0.8264 (m) outliers start: 12 outliers final: 6 residues processed: 191 average time/residue: 0.1781 time to fit residues: 44.7602 Evaluate side-chains 188 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 181 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 469 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 16 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 40 optimal weight: 0.0870 chunk 21 optimal weight: 0.2980 chunk 73 optimal weight: 0.0010 chunk 15 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 overall best weight: 0.3164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS A 601 ASN B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.118006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.105613 restraints weight = 9925.705| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.23 r_work: 0.3212 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 6650 Z= 0.128 Angle : 0.576 10.375 9041 Z= 0.288 Chirality : 0.043 0.259 943 Planarity : 0.006 0.117 1169 Dihedral : 5.754 59.093 929 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.96 % Favored : 94.54 % Rotamer: Outliers : 1.46 % Allowed : 15.87 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.16 (0.30), residues: 787 helix: 1.07 (0.27), residues: 385 sheet: 0.27 (0.67), residues: 50 loop : -1.55 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 477 HIS 0.004 0.001 HIS A 378 PHE 0.009 0.001 PHE A 308 TYR 0.017 0.001 TYR A 535 ARG 0.003 0.000 ARG A 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00267 ( 3) link_NAG-ASN : angle 1.83411 ( 9) hydrogen bonds : bond 0.04489 ( 284) hydrogen bonds : angle 4.12069 ( 792) metal coordination : bond 0.00088 ( 2) SS BOND : bond 0.00411 ( 7) SS BOND : angle 1.35433 ( 14) covalent geometry : bond 0.00310 ( 6638) covalent geometry : angle 0.57165 ( 9018) *********************** 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 184 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 174 time to evaluate : 0.788 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8456 (tp30) cc_final: 0.8168 (tp30) REVERT: A 78 LYS cc_start: 0.8575 (tptm) cc_final: 0.8227 (tptm) REVERT: A 84 SER cc_start: 0.8531 (t) cc_final: 0.8279 (m) REVERT: A 111 ASP cc_start: 0.8349 (m-30) cc_final: 0.8057 (t70) REVERT: A 287 GLN cc_start: 0.8283 (mm-40) cc_final: 0.8054 (mm-40) REVERT: A 455 MET cc_start: 0.8470 (tmm) cc_final: 0.8121 (tmm) REVERT: A 470 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8451 (tttp) REVERT: A 479 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7928 (tm-30) REVERT: A 508 ASN cc_start: 0.8018 (m-40) cc_final: 0.7662 (t0) REVERT: A 556 LYS cc_start: 0.8579 (ttmm) cc_final: 0.8246 (mtpp) REVERT: B 347 PHE cc_start: 0.8438 (m-10) cc_final: 0.8111 (m-10) REVERT: B 438 SER cc_start: 0.8135 (t) cc_final: 0.7840 (t) REVERT: B 443 SER cc_start: 0.8450 (m) cc_final: 0.8198 (m) outliers start: 10 outliers final: 4 residues processed: 181 average time/residue: 0.2074 time to fit residues: 50.6755 Evaluate side-chains 181 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 176 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 574 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 38 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 55 optimal weight: 0.0980 chunk 5 optimal weight: 0.0970 chunk 28 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 61 optimal weight: 0.2980 chunk 47 optimal weight: 0.3980 chunk 57 optimal weight: 0.5980 chunk 50 optimal weight: 0.3980 overall best weight: 0.2578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS A 601 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.118660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.106230 restraints weight = 9905.378| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.23 r_work: 0.3226 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 6650 Z= 0.120 Angle : 0.587 10.377 9041 Z= 0.292 Chirality : 0.043 0.264 943 Planarity : 0.006 0.117 1169 Dihedral : 5.660 58.590 929 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.45 % Favored : 95.04 % Rotamer: Outliers : 1.60 % Allowed : 17.47 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.06 (0.30), residues: 787 helix: 1.14 (0.27), residues: 385 sheet: 0.09 (0.67), residues: 53 loop : -1.45 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.004 0.001 HIS A 378 PHE 0.009 0.001 PHE A 308 TYR 0.017 0.001 TYR A 385 ARG 0.003 0.000 ARG A 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00283 ( 3) link_NAG-ASN : angle 1.83141 ( 9) hydrogen bonds : bond 0.04153 ( 284) hydrogen bonds : angle 4.06527 ( 792) metal coordination : bond 0.00056 ( 2) SS BOND : bond 0.00444 ( 7) SS BOND : angle 1.14708 ( 14) covalent geometry : bond 0.00288 ( 6638) covalent geometry : angle 0.58360 ( 9018) *********************** 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 190 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 179 time to evaluate : 0.765 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8448 (tp30) cc_final: 0.8163 (tp30) REVERT: A 78 LYS cc_start: 0.8565 (tptm) cc_final: 0.8233 (tptm) REVERT: A 84 SER cc_start: 0.8502 (t) cc_final: 0.8295 (m) REVERT: A 111 ASP cc_start: 0.8302 (m-30) cc_final: 0.8053 (t70) REVERT: A 114 LYS cc_start: 0.8003 (mmtt) cc_final: 0.7770 (mmtt) REVERT: A 270 MET cc_start: 0.8825 (tpt) cc_final: 0.8354 (tpt) REVERT: A 455 MET cc_start: 0.8449 (tmm) cc_final: 0.8105 (tmm) REVERT: A 470 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8450 (tttp) REVERT: A 479 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7892 (tm-30) REVERT: A 489 GLU cc_start: 0.7911 (pm20) cc_final: 0.7696 (pm20) REVERT: A 508 ASN cc_start: 0.8029 (m-40) cc_final: 0.7695 (t0) REVERT: A 556 LYS cc_start: 0.8600 (ttmm) cc_final: 0.8276 (mtpp) REVERT: B 438 SER cc_start: 0.8106 (t) cc_final: 0.7867 (t) REVERT: B 443 SER cc_start: 0.8417 (m) cc_final: 0.8165 (m) outliers start: 11 outliers final: 7 residues processed: 185 average time/residue: 0.2972 time to fit residues: 73.1242 Evaluate side-chains 196 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 188 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 362 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 48 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 24 optimal weight: 0.0050 chunk 19 optimal weight: 0.0020 chunk 70 optimal weight: 1.9990 chunk 34 optimal weight: 0.0050 chunk 8 optimal weight: 0.9990 overall best weight: 0.2016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS A 601 ASN B 394 ASN B 422 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.119747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.107450 restraints weight = 9678.705| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.16 r_work: 0.3253 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 6650 Z= 0.113 Angle : 0.573 10.359 9041 Z= 0.285 Chirality : 0.042 0.258 943 Planarity : 0.006 0.116 1169 Dihedral : 5.593 58.552 929 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.83 % Favored : 94.66 % Rotamer: Outliers : 1.89 % Allowed : 17.90 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.02 (0.30), residues: 787 helix: 1.23 (0.27), residues: 384 sheet: 0.43 (0.69), residues: 50 loop : -1.47 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 477 HIS 0.003 0.001 HIS A 378 PHE 0.008 0.001 PHE A 308 TYR 0.017 0.001 TYR A 385 ARG 0.003 0.000 ARG A 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00285 ( 3) link_NAG-ASN : angle 1.62646 ( 9) hydrogen bonds : bond 0.03841 ( 284) hydrogen bonds : angle 3.99665 ( 792) metal coordination : bond 0.00075 ( 2) SS BOND : bond 0.00369 ( 7) SS BOND : angle 1.17702 ( 14) covalent geometry : bond 0.00273 ( 6638) covalent geometry : angle 0.56993 ( 9018) *********************** 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 197 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 184 time to evaluate : 0.843 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8468 (tp30) cc_final: 0.8202 (tp30) REVERT: A 78 LYS cc_start: 0.8558 (tptm) cc_final: 0.8253 (tptm) REVERT: A 114 LYS cc_start: 0.7997 (mmtt) cc_final: 0.7765 (mmtt) REVERT: A 270 MET cc_start: 0.8798 (tpt) cc_final: 0.8522 (tpt) REVERT: A 287 GLN cc_start: 0.8358 (mm-40) cc_final: 0.8105 (mm-40) REVERT: A 402 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7169 (mm-30) REVERT: A 455 MET cc_start: 0.8352 (tmm) cc_final: 0.8001 (tmm) REVERT: A 470 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8470 (tttp) REVERT: A 479 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7748 (tm-30) REVERT: A 489 GLU cc_start: 0.7881 (pm20) cc_final: 0.7659 (pm20) REVERT: A 508 ASN cc_start: 0.7962 (m-40) cc_final: 0.7756 (t0) REVERT: A 556 LYS cc_start: 0.8602 (ttmm) cc_final: 0.8285 (mtpp) REVERT: B 438 SER cc_start: 0.8052 (t) cc_final: 0.7799 (t) REVERT: B 443 SER cc_start: 0.8394 (m) cc_final: 0.8134 (m) outliers start: 13 outliers final: 10 residues processed: 190 average time/residue: 0.2321 time to fit residues: 59.4215 Evaluate side-chains 185 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 174 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 422 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 9 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 54 optimal weight: 0.0980 chunk 48 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS A 601 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.116130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.103896 restraints weight = 9667.563| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.16 r_work: 0.3192 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 6650 Z= 0.180 Angle : 0.638 10.150 9041 Z= 0.321 Chirality : 0.045 0.255 943 Planarity : 0.006 0.117 1169 Dihedral : 5.760 57.902 929 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.10 % Favored : 93.39 % Rotamer: Outliers : 1.75 % Allowed : 18.05 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.06 (0.30), residues: 787 helix: 1.09 (0.27), residues: 391 sheet: 0.06 (0.65), residues: 53 loop : -1.42 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 477 HIS 0.006 0.001 HIS A 378 PHE 0.013 0.001 PHE A 308 TYR 0.019 0.001 TYR A 385 ARG 0.003 0.000 ARG A 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00292 ( 3) link_NAG-ASN : angle 1.78922 ( 9) hydrogen bonds : bond 0.05228 ( 284) hydrogen bonds : angle 4.13402 ( 792) metal coordination : bond 0.00093 ( 2) SS BOND : bond 0.00493 ( 7) SS BOND : angle 1.56956 ( 14) covalent geometry : bond 0.00430 ( 6638) covalent geometry : angle 0.63345 ( 9018) *********************** 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 198 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 186 time to evaluate : 0.767 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8454 (tp30) cc_final: 0.8161 (tp30) REVERT: A 114 LYS cc_start: 0.8009 (mmtt) cc_final: 0.7757 (mmtt) REVERT: A 402 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7191 (mm-30) REVERT: A 455 MET cc_start: 0.8430 (tmm) cc_final: 0.8067 (tmm) REVERT: A 470 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8473 (tttp) REVERT: A 479 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7801 (tm-30) REVERT: A 508 ASN cc_start: 0.7950 (m-40) cc_final: 0.7717 (t0) REVERT: A 556 LYS cc_start: 0.8607 (ttmm) cc_final: 0.8283 (mtpp) REVERT: B 438 SER cc_start: 0.8124 (t) cc_final: 0.7832 (t) REVERT: B 443 SER cc_start: 0.8488 (m) cc_final: 0.8239 (m) outliers start: 12 outliers final: 8 residues processed: 193 average time/residue: 0.1833 time to fit residues: 47.1351 Evaluate side-chains 192 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 183 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 362 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 16 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 35 optimal weight: 0.3980 chunk 64 optimal weight: 0.6980 chunk 20 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN A 345 HIS A 601 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.115662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.103551 restraints weight = 9873.649| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.19 r_work: 0.3182 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 6650 Z= 0.182 Angle : 0.644 10.126 9041 Z= 0.321 Chirality : 0.045 0.258 943 Planarity : 0.006 0.118 1169 Dihedral : 5.803 58.137 929 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.59 % Favored : 93.90 % Rotamer: Outliers : 1.60 % Allowed : 18.63 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.11 (0.30), residues: 787 helix: 1.03 (0.27), residues: 392 sheet: 0.10 (0.65), residues: 53 loop : -1.43 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 477 HIS 0.005 0.001 HIS A 378 PHE 0.013 0.001 PHE A 308 TYR 0.019 0.001 TYR A 385 ARG 0.008 0.000 ARG A 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00303 ( 3) link_NAG-ASN : angle 1.81534 ( 9) hydrogen bonds : bond 0.05223 ( 284) hydrogen bonds : angle 4.19614 ( 792) metal coordination : bond 0.00089 ( 2) SS BOND : bond 0.00463 ( 7) SS BOND : angle 1.60932 ( 14) covalent geometry : bond 0.00437 ( 6638) covalent geometry : angle 0.63917 ( 9018) *********************** 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 191 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 180 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8459 (tp30) cc_final: 0.8159 (tp30) REVERT: A 78 LYS cc_start: 0.8627 (tptm) cc_final: 0.8262 (tptm) REVERT: A 402 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7392 (mm-30) REVERT: A 455 MET cc_start: 0.8486 (tmm) cc_final: 0.8143 (tmm) REVERT: A 470 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8468 (tttp) REVERT: A 479 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7850 (tm-30) REVERT: A 508 ASN cc_start: 0.7972 (m-40) cc_final: 0.7731 (t0) REVERT: A 556 LYS cc_start: 0.8617 (ttmm) cc_final: 0.8281 (mtpp) REVERT: B 347 PHE cc_start: 0.8454 (m-10) cc_final: 0.8096 (m-80) REVERT: B 438 SER cc_start: 0.8131 (t) cc_final: 0.7895 (t) REVERT: B 443 SER cc_start: 0.8491 (m) cc_final: 0.8245 (m) outliers start: 11 outliers final: 8 residues processed: 186 average time/residue: 0.1816 time to fit residues: 45.1985 Evaluate side-chains 190 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 181 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 469 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 41 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 61 optimal weight: 0.0980 chunk 39 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 40 optimal weight: 0.3980 chunk 69 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS A 601 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.116033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.103846 restraints weight = 9972.062| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.22 r_work: 0.3184 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 6650 Z= 0.166 Angle : 0.639 10.071 9041 Z= 0.320 Chirality : 0.045 0.257 943 Planarity : 0.006 0.119 1169 Dihedral : 5.809 58.131 929 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.10 % Favored : 93.39 % Rotamer: Outliers : 2.04 % Allowed : 18.78 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.09 (0.30), residues: 787 helix: 1.03 (0.27), residues: 392 sheet: 0.14 (0.65), residues: 53 loop : -1.41 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 477 HIS 0.005 0.001 HIS A 378 PHE 0.012 0.001 PHE A 308 TYR 0.019 0.001 TYR A 385 ARG 0.007 0.000 ARG A 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00288 ( 3) link_NAG-ASN : angle 1.76601 ( 9) hydrogen bonds : bond 0.05027 ( 284) hydrogen bonds : angle 4.17907 ( 792) metal coordination : bond 0.00077 ( 2) SS BOND : bond 0.00452 ( 7) SS BOND : angle 1.62209 ( 14) covalent geometry : bond 0.00400 ( 6638) covalent geometry : angle 0.63401 ( 9018) *********************** 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 189 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 175 time to evaluate : 0.843 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8464 (tp30) cc_final: 0.8171 (tp30) REVERT: A 78 LYS cc_start: 0.8630 (tptm) cc_final: 0.8261 (tptm) REVERT: A 287 GLN cc_start: 0.8310 (mm-40) cc_final: 0.7922 (mm-40) REVERT: A 402 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7398 (mm-30) REVERT: A 455 MET cc_start: 0.8489 (tmm) cc_final: 0.8152 (tmm) REVERT: A 470 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8461 (tttp) REVERT: A 479 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7840 (tm-30) REVERT: A 508 ASN cc_start: 0.7970 (m-40) cc_final: 0.7752 (t0) REVERT: A 556 LYS cc_start: 0.8610 (ttmm) cc_final: 0.8275 (mtpp) REVERT: B 443 SER cc_start: 0.8482 (m) cc_final: 0.8241 (m) outliers start: 14 outliers final: 11 residues processed: 181 average time/residue: 0.2313 time to fit residues: 56.0189 Evaluate side-chains 187 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 175 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 469 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 54 optimal weight: 0.0270 chunk 32 optimal weight: 0.8980 chunk 24 optimal weight: 0.0980 chunk 45 optimal weight: 0.9990 chunk 34 optimal weight: 0.0770 chunk 46 optimal weight: 0.7980 chunk 17 optimal weight: 0.2980 chunk 8 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 overall best weight: 0.2596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.118153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.105757 restraints weight = 9865.054| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.23 r_work: 0.3218 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 6650 Z= 0.127 Angle : 0.658 14.233 9041 Z= 0.325 Chirality : 0.045 0.360 943 Planarity : 0.006 0.117 1169 Dihedral : 5.739 58.129 929 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.08 % Favored : 94.41 % Rotamer: Outliers : 1.60 % Allowed : 19.21 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.06 (0.30), residues: 787 helix: 1.22 (0.27), residues: 385 sheet: 0.28 (0.67), residues: 53 loop : -1.38 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.003 0.001 HIS A 378 PHE 0.013 0.001 PHE B 486 TYR 0.017 0.001 TYR A 385 ARG 0.007 0.000 ARG A 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00287 ( 3) link_NAG-ASN : angle 1.59937 ( 9) hydrogen bonds : bond 0.04321 ( 284) hydrogen bonds : angle 4.09369 ( 792) metal coordination : bond 0.00048 ( 2) SS BOND : bond 0.00493 ( 7) SS BOND : angle 3.79439 ( 14) covalent geometry : bond 0.00305 ( 6638) covalent geometry : angle 0.64005 ( 9018) ********************** 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 183 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 172 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8480 (tp30) cc_final: 0.8167 (tp30) REVERT: A 78 LYS cc_start: 0.8582 (tptm) cc_final: 0.8247 (tptm) REVERT: A 270 MET cc_start: 0.8882 (tpt) cc_final: 0.8681 (tpt) REVERT: A 287 GLN cc_start: 0.8300 (mm-40) cc_final: 0.7938 (mm-40) REVERT: A 455 MET cc_start: 0.8459 (tmm) cc_final: 0.8090 (tmm) REVERT: A 470 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8457 (tttp) REVERT: A 479 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7779 (tm-30) REVERT: A 556 LYS cc_start: 0.8581 (ttmm) cc_final: 0.8246 (mtpp) REVERT: B 443 SER cc_start: 0.8470 (m) cc_final: 0.8214 (m) outliers start: 11 outliers final: 8 residues processed: 176 average time/residue: 0.1729 time to fit residues: 41.2914 Evaluate side-chains 180 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 171 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 469 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 41 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 43 optimal weight: 0.1980 chunk 61 optimal weight: 0.0060 chunk 42 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 13 optimal weight: 0.2980 chunk 2 optimal weight: 0.5980 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.117703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.105251 restraints weight = 9990.170| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.24 r_work: 0.3211 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 6650 Z= 0.138 Angle : 0.672 14.485 9041 Z= 0.336 Chirality : 0.045 0.348 943 Planarity : 0.006 0.117 1169 Dihedral : 5.727 57.791 929 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.46 % Favored : 94.03 % Rotamer: Outliers : 1.46 % Allowed : 20.09 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.12 (0.30), residues: 787 helix: 1.25 (0.27), residues: 385 sheet: 0.50 (0.68), residues: 53 loop : -1.36 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.004 0.001 HIS A 378 PHE 0.011 0.001 PHE A 308 TYR 0.018 0.001 TYR A 385 ARG 0.007 0.000 ARG A 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00294 ( 3) link_NAG-ASN : angle 1.61824 ( 9) hydrogen bonds : bond 0.04520 ( 284) hydrogen bonds : angle 4.07967 ( 792) metal coordination : bond 0.00048 ( 2) SS BOND : bond 0.00563 ( 7) SS BOND : angle 3.75578 ( 14) covalent geometry : bond 0.00332 ( 6638) covalent geometry : angle 0.65414 ( 9018) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5322.42 seconds wall clock time: 97 minutes 47.96 seconds (5867.96 seconds total)