Starting phenix.real_space_refine on Tue Mar 11 15:08:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d32_46512/03_2025/9d32_46512.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d32_46512/03_2025/9d32_46512.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d32_46512/03_2025/9d32_46512.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d32_46512/03_2025/9d32_46512.map" model { file = "/net/cci-nas-00/data/ceres_data/9d32_46512/03_2025/9d32_46512.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d32_46512/03_2025/9d32_46512.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.063 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 41 5.16 5 C 3969 2.51 5 N 1029 2.21 5 O 1090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6130 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4570 Classifications: {'peptide': 584} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 26, 'TRANS': 557} Unresolved non-hydrogen bonds: 227 Unresolved non-hydrogen angles: 283 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 19, 'HIS:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 15} Unresolved non-hydrogen planarities: 146 Chain: "B" Number of atoms: 1423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1423 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 13, 'TRANS': 180} Chain breaks: 1 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 37 Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: "A" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 85 Unusual residues: {' ZN': 1, 'NAG': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" 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 Time building chain proxies: 4.47, per 1000 atoms: 0.73 Number of scatterers: 6130 At special positions: 0 Unit cell: (76, 84, 116, 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 41 16.00 O 1090 8.00 N 1029 7.00 C 3969 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 343 " - pdb=" SG CYS A 360 " distance=2.03 Simple disulfide: pdb=" SG CYS A 529 " - pdb=" SG CYS A 541 " distance=2.03 Simple disulfide: pdb=" SG CYS B 392 " - pdb=" SG CYS B 416 " distance=2.03 Simple disulfide: pdb=" SG CYS B 434 " - pdb=" SG CYS B 487 " distance=2.03 Simple disulfide: pdb=" SG CYS B 446 " - pdb=" SG CYS B 584 " distance=2.03 Simple disulfide: pdb=" SG CYS B 512 " - pdb=" SG CYS B 533 " 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 BETA1-6 " NAG C 1 " - " FUC C 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 801 " - " ASN A 53 " " NAG A 802 " - " ASN A 279 " " NAG A 803 " - " ASN A 431 " " NAG A 804 " - " ASN A 545 " " NAG A 805 " - " ASN A 103 " " NAG A 806 " - " ASN A 215 " " NAG B 701 " - " ASN B 419 " " NAG B 702 " - " ASN B 496 " " NAG C 1 " - " ASN A 386 " Time building additional restraints: 1.60 Conformation dependent library (CDL) restraints added in 878.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 807 " pdb="ZN ZN A 807 " - pdb=" NE2 HIS A 377 " pdb="ZN ZN A 807 " - pdb=" NE2 HIS A 373 " 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1470 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 5 sheets defined 58.2% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 20 through 52 removed outlier: 3.626A pdb=" N GLU A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N HIS A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.812A pdb=" N ILE A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 83 No H-bonds generated for 'chain 'A' and resid 82 through 83' Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.536A pdb=" N GLU A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 101 removed outlier: 3.523A pdb=" N ILE A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.738A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 129 Processing helix chain 'A' and resid 144 through 152 Processing helix chain 'A' and resid 156 through 171 removed outlier: 3.684A pdb=" N VAL A 163 " --> pdb=" O GLU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 193 removed outlier: 3.601A pdb=" N GLU A 181 " --> pdb=" O PRO A 177 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 204 Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 220 through 251 Proline residue: A 234 - end of helix removed outlier: 3.804A pdb=" N LYS A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 266 No H-bonds generated for 'chain 'A' and resid 264 through 266' Processing helix chain 'A' and resid 274 through 276 No H-bonds generated for 'chain 'A' and resid 274 through 276' Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 292 through 299 Processing helix chain 'A' and resid 302 through 317 removed outlier: 3.765A pdb=" N VAL A 317 " --> pdb=" O PHE A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 330 removed outlier: 3.547A pdb=" N TRP A 327 " --> pdb=" O THR A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 384 removed outlier: 3.668A pdb=" N HIS A 372 " --> pdb=" O PHE A 368 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR A 384 " --> pdb=" O TYR A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 392 removed outlier: 3.578A pdb=" N ARG A 392 " --> pdb=" O TYR A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 412 removed outlier: 3.778A pdb=" N MET A 407 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER A 410 " --> pdb=" O VAL A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 421 Processing helix chain 'A' and resid 430 through 446 Processing helix chain 'A' and resid 448 through 465 Processing helix chain 'A' and resid 468 through 470 No H-bonds generated for 'chain 'A' and resid 468 through 470' Processing helix chain 'A' and resid 471 through 483 Processing helix chain 'A' and resid 498 through 501 Processing helix chain 'A' and resid 502 through 507 Processing helix chain 'A' and resid 512 through 532 removed outlier: 4.018A pdb=" N THR A 518 " --> pdb=" O TYR A 514 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A 519 " --> pdb=" O PHE A 515 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A 523 " --> pdb=" O ILE A 519 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA A 527 " --> pdb=" O GLN A 523 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 541 Processing helix chain 'A' and resid 546 through 558 removed outlier: 3.535A pdb=" N GLY A 550 " --> pdb=" O SER A 546 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET A 556 " --> pdb=" O LYS A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 574 removed outlier: 3.766A pdb=" N ILE A 572 " --> pdb=" O ALA A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 587 Processing helix chain 'A' and resid 587 through 599 removed outlier: 3.544A pdb=" N GLU A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 Processing helix chain 'B' and resid 423 through 427 Processing helix chain 'B' and resid 438 through 443 removed outlier: 4.179A pdb=" N ALA B 443 " --> pdb=" O PRO B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 465 removed outlier: 4.652A pdb=" N SER B 463 " --> pdb=" O ASP B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 477 Processing helix chain 'B' and resid 533 through 538 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 261 through 262 removed outlier: 6.008A pdb=" N LEU A 261 " --> pdb=" O VAL A 487 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 346 through 349 Processing sheet with id=AA4, first strand: chain 'B' and resid 409 through 413 removed outlier: 6.863A pdb=" N THR B 486 " --> pdb=" O CYS B 434 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N CYS B 434 " --> pdb=" O THR B 486 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ARG B 488 " --> pdb=" O PHE B 432 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE B 432 " --> pdb=" O ARG B 488 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU B 490 " --> pdb=" O SER B 430 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 519 through 522 removed outlier: 6.530A pdb=" N THR B 556 " --> pdb=" O THR B 510 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N CYS B 512 " --> pdb=" O THR B 554 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR B 554 " --> pdb=" O CYS B 512 " (cutoff:3.500A) 311 hydrogen bonds defined for protein. 870 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: 1.90 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1905 1.34 - 1.46: 1444 1.46 - 1.58: 2882 1.58 - 1.70: 0 1.70 - 1.82: 66 Bond restraints: 6297 Sorted by residual: bond pdb=" CA VAL B 493 " pdb=" CB VAL B 493 " ideal model delta sigma weight residual 1.537 1.523 0.014 1.29e-02 6.01e+03 1.25e+00 bond pdb=" N VAL A 363 " pdb=" CA VAL A 363 " ideal model delta sigma weight residual 1.474 1.458 0.017 1.57e-02 4.06e+03 1.12e+00 bond pdb=" CA ASN A 53 " pdb=" C ASN A 53 " ideal model delta sigma weight residual 1.530 1.521 0.009 1.08e-02 8.57e+03 6.89e-01 bond pdb=" C GLU A 35 " pdb=" O GLU A 35 " ideal model delta sigma weight residual 1.236 1.247 -0.011 1.29e-02 6.01e+03 6.84e-01 bond pdb=" C1 FUC C 2 " pdb=" O5 FUC C 2 " ideal model delta sigma weight residual 1.400 1.416 -0.016 2.00e-02 2.50e+03 6.68e-01 ... (remaining 6292 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 8277 1.32 - 2.64: 223 2.64 - 3.96: 57 3.96 - 5.28: 10 5.28 - 6.60: 2 Bond angle restraints: 8569 Sorted by residual: angle pdb=" N VAL A 292 " pdb=" CA VAL A 292 " pdb=" C VAL A 292 " ideal model delta sigma weight residual 112.43 110.06 2.37 9.20e-01 1.18e+00 6.62e+00 angle pdb=" N VAL A 363 " pdb=" CA VAL A 363 " pdb=" C VAL A 363 " ideal model delta sigma weight residual 106.21 108.95 -2.74 1.07e+00 8.73e-01 6.56e+00 angle pdb=" CA CYS B 487 " pdb=" CB CYS B 487 " pdb=" SG CYS B 487 " ideal model delta sigma weight residual 114.40 119.61 -5.21 2.30e+00 1.89e-01 5.14e+00 angle pdb=" N GLY B 557 " pdb=" CA GLY B 557 " pdb=" C GLY B 557 " ideal model delta sigma weight residual 111.19 114.91 -3.72 1.75e+00 3.27e-01 4.52e+00 angle pdb=" CA TRP A 162 " pdb=" CB TRP A 162 " pdb=" CG TRP A 162 " ideal model delta sigma weight residual 113.60 117.51 -3.91 1.90e+00 2.77e-01 4.23e+00 ... (remaining 8564 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 3627 17.52 - 35.04: 173 35.04 - 52.55: 43 52.55 - 70.07: 9 70.07 - 87.59: 1 Dihedral angle restraints: 3853 sinusoidal: 1563 harmonic: 2290 Sorted by residual: dihedral pdb=" CB CYS A 343 " pdb=" SG CYS A 343 " pdb=" SG CYS A 360 " pdb=" CB CYS A 360 " ideal model delta sinusoidal sigma weight residual 93.00 143.47 -50.47 1 1.00e+01 1.00e-02 3.49e+01 dihedral pdb=" CB CYS B 434 " pdb=" SG CYS B 434 " pdb=" SG CYS B 487 " pdb=" CB CYS B 487 " ideal model delta sinusoidal sigma weight residual -86.00 -52.74 -33.26 1 1.00e+01 1.00e-02 1.57e+01 dihedral pdb=" CA ASN B 505 " pdb=" C ASN B 505 " pdb=" N TYR B 506 " pdb=" CA TYR B 506 " ideal model delta harmonic sigma weight residual 180.00 162.54 17.46 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 3850 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 534 0.029 - 0.058: 273 0.058 - 0.087: 90 0.087 - 0.116: 43 0.116 - 0.145: 9 Chirality restraints: 949 Sorted by residual: chirality pdb=" C1 NAG B 702 " pdb=" ND2 ASN B 496 " pdb=" C2 NAG B 702 " pdb=" O5 NAG B 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" C1 NAG A 805 " pdb=" ND2 ASN A 103 " pdb=" C2 NAG A 805 " pdb=" O5 NAG A 805 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA ILE B 571 " pdb=" N ILE B 571 " pdb=" C ILE B 571 " pdb=" CB ILE B 571 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 ... (remaining 946 not shown) Planarity restraints: 1093 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 233 " 0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO A 234 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 234 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 234 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 395 " 0.025 5.00e-02 4.00e+02 3.81e-02 2.33e+00 pdb=" N PRO B 396 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 396 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 396 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 581 " -0.021 5.00e-02 4.00e+02 3.17e-02 1.60e+00 pdb=" N PRO A 582 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 582 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 582 " -0.018 5.00e-02 4.00e+02 ... (remaining 1090 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 25 2.59 - 3.17: 4897 3.17 - 3.74: 9077 3.74 - 4.32: 12984 4.32 - 4.90: 22356 Nonbonded interactions: 49339 Sorted by model distance: nonbonded pdb=" OE2 GLU A 401 " pdb="ZN ZN A 807 " model vdw 2.012 2.230 nonbonded pdb=" OG SER A 315 " pdb=" OD1 ASN A 321 " model vdw 2.271 3.040 nonbonded pdb=" OG SER A 410 " pdb=" OD1 ASP A 542 " model vdw 2.318 3.040 nonbonded pdb=" NH2 ARG B 410 " pdb=" O GLY B 528 " model vdw 2.328 3.120 nonbonded pdb=" OE1 GLU A 464 " pdb=" NZ LYS A 466 " model vdw 2.378 3.120 ... (remaining 49334 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.560 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 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 : 0.004 0.034 6297 Z= 0.251 Angle : 0.586 6.603 8569 Z= 0.330 Chirality : 0.041 0.145 949 Planarity : 0.004 0.043 1084 Dihedral : 11.073 87.590 2362 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.02 % Allowed : 5.16 % Favored : 91.81 % 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: 0.80 (0.30), residues: 772 helix: 0.46 (0.27), residues: 383 sheet: 1.58 (0.60), residues: 70 loop : 0.62 (0.36), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 162 HIS 0.006 0.001 HIS A 240 PHE 0.010 0.002 PHE A 307 TYR 0.014 0.001 TYR A 182 ARG 0.003 0.000 ARG A 392 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.731 Fit side-chains revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8093 (mmtp) cc_final: 0.7733 (mmtt) REVERT: A 159 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7240 (tt0) REVERT: A 269 MET cc_start: 0.8748 (mmt) cc_final: 0.8500 (tpp) REVERT: A 381 ASP cc_start: 0.8519 (m-30) cc_final: 0.8295 (m-30) REVERT: A 400 HIS cc_start: 0.8579 (OUTLIER) cc_final: 0.7030 (t-90) REVERT: A 407 MET cc_start: 0.7186 (mmt) cc_final: 0.6951 (mmt) REVERT: A 473 MET cc_start: 0.8475 (mmp) cc_final: 0.8031 (mmp) REVERT: B 479 LYS cc_start: 0.8692 (tttm) cc_final: 0.7938 (ttmt) REVERT: B 525 ASN cc_start: 0.7800 (m-40) cc_final: 0.7568 (m-40) outliers start: 17 outliers final: 7 residues processed: 100 average time/residue: 0.2141 time to fit residues: 27.5019 Evaluate side-chains 85 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 562 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 0.4980 chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 372 HIS B 436 GLN B 565 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.137135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.111739 restraints weight = 6104.688| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.55 r_work: 0.3033 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6297 Z= 0.269 Angle : 0.553 6.227 8569 Z= 0.283 Chirality : 0.042 0.152 949 Planarity : 0.005 0.049 1084 Dihedral : 6.368 52.705 1070 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.67 % Allowed : 9.25 % Favored : 88.08 % 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: 0.85 (0.30), residues: 772 helix: 0.66 (0.26), residues: 385 sheet: 1.72 (0.65), residues: 60 loop : 0.43 (0.36), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 162 HIS 0.007 0.001 HIS A 240 PHE 0.010 0.001 PHE A 307 TYR 0.014 0.002 TYR A 182 ARG 0.004 0.001 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8128 (mmtp) cc_final: 0.7727 (mmtt) REVERT: A 159 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7220 (tt0) REVERT: A 269 MET cc_start: 0.8685 (mmt) cc_final: 0.8318 (tpp) REVERT: A 381 ASP cc_start: 0.8490 (m-30) cc_final: 0.8281 (m-30) REVERT: A 400 HIS cc_start: 0.8665 (OUTLIER) cc_final: 0.7126 (t-90) REVERT: A 407 MET cc_start: 0.7131 (mmt) cc_final: 0.6858 (mmt) REVERT: A 473 MET cc_start: 0.8341 (mmp) cc_final: 0.7723 (mmp) REVERT: B 479 LYS cc_start: 0.8723 (tttm) cc_final: 0.7995 (ttmt) outliers start: 15 outliers final: 10 residues processed: 84 average time/residue: 0.2174 time to fit residues: 23.4288 Evaluate side-chains 82 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 487 CYS Chi-restraints excluded: chain B residue 562 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 29 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 47 optimal weight: 0.0770 chunk 43 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 72 optimal weight: 0.0670 chunk 39 optimal weight: 0.7980 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 565 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.139733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.114310 restraints weight = 6134.215| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.54 r_work: 0.3071 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6297 Z= 0.161 Angle : 0.477 5.444 8569 Z= 0.242 Chirality : 0.040 0.144 949 Planarity : 0.004 0.039 1084 Dihedral : 5.677 52.132 1065 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.20 % Allowed : 8.90 % Favored : 87.90 % 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: 1.10 (0.30), residues: 772 helix: 1.00 (0.26), residues: 385 sheet: 1.68 (0.66), residues: 60 loop : 0.40 (0.36), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 162 HIS 0.004 0.001 HIS A 240 PHE 0.007 0.001 PHE A 307 TYR 0.012 0.001 TYR A 182 ARG 0.002 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 381 ASP cc_start: 0.8460 (m-30) cc_final: 0.8258 (m-30) REVERT: A 400 HIS cc_start: 0.8504 (OUTLIER) cc_final: 0.6775 (t-90) REVERT: A 407 MET cc_start: 0.7096 (mmt) cc_final: 0.6731 (mmt) REVERT: A 473 MET cc_start: 0.8339 (mmp) cc_final: 0.7916 (mmp) REVERT: B 472 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7820 (pm20) REVERT: B 479 LYS cc_start: 0.8705 (tttm) cc_final: 0.7999 (ttmt) REVERT: B 525 ASN cc_start: 0.7802 (m-40) cc_final: 0.7518 (m-40) outliers start: 18 outliers final: 9 residues processed: 88 average time/residue: 0.2258 time to fit residues: 25.3640 Evaluate side-chains 86 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 513 ARG Chi-restraints excluded: chain B residue 409 LYS Chi-restraints excluded: chain B residue 472 GLU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 487 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 18 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 62 optimal weight: 0.0980 chunk 40 optimal weight: 0.3980 chunk 49 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 565 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.139825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.115423 restraints weight = 6239.511| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.56 r_work: 0.3083 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6297 Z= 0.164 Angle : 0.477 5.305 8569 Z= 0.242 Chirality : 0.040 0.146 949 Planarity : 0.004 0.035 1084 Dihedral : 5.615 52.898 1064 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.02 % Allowed : 10.14 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.19 (0.30), residues: 772 helix: 1.13 (0.26), residues: 385 sheet: 1.48 (0.66), residues: 61 loop : 0.40 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 162 HIS 0.005 0.001 HIS A 240 PHE 0.008 0.001 PHE A 307 TYR 0.013 0.001 TYR A 182 ARG 0.004 0.000 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 400 HIS cc_start: 0.8550 (OUTLIER) cc_final: 0.6953 (t-90) REVERT: A 473 MET cc_start: 0.8407 (mmp) cc_final: 0.7991 (mmp) REVERT: B 472 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7838 (pm20) REVERT: B 479 LYS cc_start: 0.8740 (tttm) cc_final: 0.8054 (ttmt) outliers start: 17 outliers final: 9 residues processed: 87 average time/residue: 0.2323 time to fit residues: 26.0281 Evaluate side-chains 86 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 513 ARG Chi-restraints excluded: chain B residue 409 LYS Chi-restraints excluded: chain B residue 472 GLU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 487 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 31 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 chunk 47 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 585 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.136842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.111353 restraints weight = 6181.409| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.56 r_work: 0.3026 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6297 Z= 0.256 Angle : 0.528 5.853 8569 Z= 0.268 Chirality : 0.042 0.157 949 Planarity : 0.004 0.038 1084 Dihedral : 5.636 53.520 1061 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.38 % Allowed : 9.79 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.04 (0.30), residues: 772 helix: 0.99 (0.26), residues: 385 sheet: 1.29 (0.67), residues: 61 loop : 0.38 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 162 HIS 0.007 0.001 HIS A 240 PHE 0.010 0.001 PHE A 522 TYR 0.013 0.001 TYR A 182 ARG 0.003 0.001 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7210 (tt0) REVERT: A 400 HIS cc_start: 0.8554 (OUTLIER) cc_final: 0.6944 (t-90) REVERT: A 473 MET cc_start: 0.8399 (mmp) cc_final: 0.7752 (mmp) REVERT: B 479 LYS cc_start: 0.8704 (tttm) cc_final: 0.7930 (ttmt) outliers start: 19 outliers final: 13 residues processed: 85 average time/residue: 0.2058 time to fit residues: 22.7303 Evaluate side-chains 87 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 513 ARG Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain B residue 409 LYS Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 487 CYS Chi-restraints excluded: chain B residue 562 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 25 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 0.5980 chunk 76 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 48 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3444 r_free = 0.3444 target = 0.138366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.113043 restraints weight = 6125.381| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.56 r_work: 0.3051 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6297 Z= 0.190 Angle : 0.492 5.572 8569 Z= 0.249 Chirality : 0.040 0.153 949 Planarity : 0.004 0.035 1084 Dihedral : 5.492 53.486 1061 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.49 % Allowed : 11.03 % Favored : 86.48 % 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: 1.15 (0.30), residues: 772 helix: 1.11 (0.26), residues: 385 sheet: 1.27 (0.67), residues: 61 loop : 0.41 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 162 HIS 0.006 0.001 HIS A 240 PHE 0.008 0.001 PHE A 522 TYR 0.013 0.001 TYR A 182 ARG 0.002 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8168 (mmtp) cc_final: 0.7719 (mmtt) REVERT: A 400 HIS cc_start: 0.8527 (OUTLIER) cc_final: 0.6931 (t-90) REVERT: A 473 MET cc_start: 0.8387 (mmp) cc_final: 0.7948 (mmp) REVERT: B 479 LYS cc_start: 0.8754 (tttm) cc_final: 0.8018 (ttmt) outliers start: 14 outliers final: 13 residues processed: 86 average time/residue: 0.2118 time to fit residues: 23.8089 Evaluate side-chains 89 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 513 ARG Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain B residue 409 LYS Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 487 CYS Chi-restraints excluded: chain B residue 562 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 71 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 51 optimal weight: 0.0170 chunk 30 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 0.3980 chunk 50 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 overall best weight: 0.4018 ------------------------------------------------------------------------------- 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 = 0.3459 r_free = 0.3459 target = 0.139852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.114433 restraints weight = 6175.056| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.57 r_work: 0.3070 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6297 Z= 0.155 Angle : 0.472 5.138 8569 Z= 0.238 Chirality : 0.039 0.145 949 Planarity : 0.004 0.033 1084 Dihedral : 5.376 53.269 1061 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.85 % Allowed : 11.39 % Favored : 85.77 % 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: 1.31 (0.31), residues: 772 helix: 1.27 (0.26), residues: 385 sheet: 1.32 (0.67), residues: 61 loop : 0.46 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 162 HIS 0.004 0.001 HIS A 240 PHE 0.007 0.001 PHE A 307 TYR 0.012 0.001 TYR A 182 ARG 0.002 0.000 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8175 (mmtp) cc_final: 0.7722 (mmtt) REVERT: A 170 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7366 (mt-10) REVERT: A 400 HIS cc_start: 0.8478 (OUTLIER) cc_final: 0.6884 (t-90) REVERT: A 407 MET cc_start: 0.6971 (mmt) cc_final: 0.6743 (mmt) REVERT: A 473 MET cc_start: 0.8373 (mmp) cc_final: 0.7931 (mmp) REVERT: A 478 GLU cc_start: 0.8318 (tt0) cc_final: 0.7780 (mt-10) REVERT: A 530 ARG cc_start: 0.7318 (ttp-110) cc_final: 0.6950 (ttp80) REVERT: B 479 LYS cc_start: 0.8758 (tttm) cc_final: 0.8027 (ttmt) REVERT: B 525 ASN cc_start: 0.7819 (m-40) cc_final: 0.7617 (m-40) outliers start: 16 outliers final: 12 residues processed: 89 average time/residue: 0.2006 time to fit residues: 23.1873 Evaluate side-chains 91 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 513 ARG Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain B residue 409 LYS Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 487 CYS Chi-restraints excluded: chain B residue 562 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 57 optimal weight: 0.9980 chunk 4 optimal weight: 0.4980 chunk 20 optimal weight: 0.4980 chunk 70 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.138107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.112615 restraints weight = 6137.828| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.56 r_work: 0.3044 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6297 Z= 0.218 Angle : 0.509 5.540 8569 Z= 0.257 Chirality : 0.041 0.153 949 Planarity : 0.004 0.035 1084 Dihedral : 5.555 54.466 1061 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.85 % Allowed : 11.21 % Favored : 85.94 % 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: 1.10 (0.31), residues: 772 helix: 1.07 (0.26), residues: 391 sheet: 1.22 (0.67), residues: 61 loop : 0.39 (0.37), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 162 HIS 0.006 0.001 HIS A 240 PHE 0.010 0.001 PHE A 522 TYR 0.013 0.001 TYR A 182 ARG 0.003 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8158 (mmtp) cc_final: 0.7701 (mmtt) REVERT: A 159 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7219 (tt0) REVERT: A 400 HIS cc_start: 0.8436 (OUTLIER) cc_final: 0.6706 (t-90) REVERT: A 473 MET cc_start: 0.8407 (mmp) cc_final: 0.7932 (mmp) REVERT: A 530 ARG cc_start: 0.7372 (ttp-110) cc_final: 0.6972 (ttp80) REVERT: B 479 LYS cc_start: 0.8736 (tttm) cc_final: 0.7967 (ttmt) outliers start: 16 outliers final: 14 residues processed: 84 average time/residue: 0.2138 time to fit residues: 23.3769 Evaluate side-chains 89 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 513 ARG Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain B residue 409 LYS Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 487 CYS Chi-restraints excluded: chain B residue 562 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 43 optimal weight: 0.4980 chunk 52 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3481 r_free = 0.3481 target = 0.139921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.116710 restraints weight = 6100.099| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.65 r_work: 0.3036 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 6297 Z= 0.254 Angle : 0.531 5.939 8569 Z= 0.269 Chirality : 0.042 0.154 949 Planarity : 0.004 0.037 1084 Dihedral : 5.695 54.664 1061 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.67 % Allowed : 11.92 % Favored : 85.41 % 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: 0.99 (0.30), residues: 772 helix: 0.95 (0.26), residues: 391 sheet: 1.14 (0.67), residues: 61 loop : 0.37 (0.37), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 162 HIS 0.007 0.001 HIS A 240 PHE 0.010 0.001 PHE A 522 TYR 0.013 0.001 TYR A 182 ARG 0.003 0.000 ARG A 459 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8153 (mmtp) cc_final: 0.7702 (mmtt) REVERT: A 159 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7210 (tt0) REVERT: A 400 HIS cc_start: 0.8478 (OUTLIER) cc_final: 0.6759 (t-90) REVERT: B 479 LYS cc_start: 0.8739 (tttm) cc_final: 0.7966 (ttmt) REVERT: B 525 ASN cc_start: 0.8040 (m-40) cc_final: 0.7725 (m-40) outliers start: 15 outliers final: 14 residues processed: 84 average time/residue: 0.2128 time to fit residues: 23.1399 Evaluate side-chains 89 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 513 ARG Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain B residue 409 LYS Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 487 CYS Chi-restraints excluded: chain B residue 562 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 55 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 32 optimal weight: 0.0670 chunk 17 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.6718 ------------------------------------------------------------------------------- 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 = 0.3487 r_free = 0.3487 target = 0.140534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.117394 restraints weight = 6066.725| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.63 r_work: 0.3047 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 6297 Z= 0.226 Angle : 0.519 5.719 8569 Z= 0.262 Chirality : 0.041 0.150 949 Planarity : 0.004 0.036 1084 Dihedral : 5.664 54.569 1061 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.67 % Allowed : 12.10 % Favored : 85.23 % 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: 1.00 (0.31), residues: 772 helix: 0.98 (0.26), residues: 391 sheet: 1.07 (0.67), residues: 61 loop : 0.35 (0.37), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 162 HIS 0.007 0.001 HIS A 240 PHE 0.010 0.001 PHE A 522 TYR 0.014 0.001 TYR A 314 ARG 0.003 0.000 ARG A 328 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8169 (mmtp) cc_final: 0.7714 (mmtt) REVERT: A 159 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7156 (tt0) REVERT: A 400 HIS cc_start: 0.8472 (OUTLIER) cc_final: 0.6731 (t-90) REVERT: A 473 MET cc_start: 0.8304 (mmp) cc_final: 0.8033 (mmp) REVERT: B 479 LYS cc_start: 0.8736 (tttm) cc_final: 0.7973 (ttmt) REVERT: B 525 ASN cc_start: 0.8035 (m-40) cc_final: 0.7738 (m-40) outliers start: 15 outliers final: 14 residues processed: 84 average time/residue: 0.2081 time to fit residues: 22.6492 Evaluate side-chains 88 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 513 ARG Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain B residue 409 LYS Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 487 CYS Chi-restraints excluded: chain B residue 562 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 11 optimal weight: 0.3980 chunk 29 optimal weight: 0.3980 chunk 31 optimal weight: 0.0770 chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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 = 0.3458 r_free = 0.3458 target = 0.139520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.113854 restraints weight = 6278.036| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.59 r_work: 0.3058 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6297 Z= 0.166 Angle : 0.486 5.387 8569 Z= 0.245 Chirality : 0.040 0.140 949 Planarity : 0.004 0.034 1084 Dihedral : 5.484 53.996 1061 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.67 % Allowed : 11.92 % Favored : 85.41 % 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: 1.17 (0.31), residues: 772 helix: 1.17 (0.26), residues: 390 sheet: 1.15 (0.68), residues: 61 loop : 0.38 (0.37), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 162 HIS 0.005 0.001 HIS A 240 PHE 0.007 0.001 PHE A 307 TYR 0.014 0.001 TYR A 314 ARG 0.002 0.000 ARG A 227 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3657.65 seconds wall clock time: 63 minutes 13.54 seconds (3793.54 seconds total)