Starting phenix.real_space_refine on Thu Jun 5 11:58:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d32_46512/06_2025/9d32_46512.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d32_46512/06_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_46512/06_2025/9d32_46512.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d32_46512/06_2025/9d32_46512.map" model { file = "/net/cci-nas-00/data/ceres_data/9d32_46512/06_2025/9d32_46512.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d32_46512/06_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-5710/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: 4.58, per 1000 atoms: 0.75 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: 1.67 Conformation dependent library (CDL) restraints added in 983.9 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: 0.63 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: 2.10 Time building geometry restraints manager: 1.95 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: 4.270 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 20.350 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.700 ------------------------------------------------------------------------------- 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 6316 Z= 0.174 Angle : 0.596 6.603 8613 Z= 0.332 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00178 ( 9) link_NAG-ASN : angle 1.75779 ( 27) hydrogen bonds : bond 0.17337 ( 311) hydrogen bonds : angle 6.59485 ( 870) link_BETA1-6 : bond 0.01215 ( 1) link_BETA1-6 : angle 1.22720 ( 3) metal coordination : bond 0.00244 ( 2) SS BOND : bond 0.00263 ( 7) SS BOND : angle 1.33592 ( 14) covalent geometry : bond 0.00391 ( 6297) covalent geometry : angle 0.58589 ( 8569) *********************** 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 : 0.630 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: 0.2146 time to fit residues: 27.3962 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 : 0.636 ------------------------------------------------------------------------------- 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: 0.0870 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: 1.9990 chunk 44 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.3445 r_free = 0.3445 target = 0.138472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.113057 restraints weight = 6081.398| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.55 r_work: 0.3050 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6316 Z= 0.148 Angle : 0.538 5.983 8613 Z= 0.272 Chirality : 0.041 0.142 949 Planarity : 0.004 0.044 1084 Dihedral : 6.273 52.502 1070 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.31 % Allowed : 9.25 % Favored : 88.43 % 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: 0.98 (0.30), residues: 772 helix: 0.78 (0.26), residues: 385 sheet: 1.83 (0.65), residues: 60 loop : 0.46 (0.36), residues: 327 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 0.009 0.001 PHE A 307 TYR 0.013 0.001 TYR A 182 ARG 0.003 0.000 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00185 ( 9) link_NAG-ASN : angle 1.91843 ( 27) hydrogen bonds : bond 0.05326 ( 311) hydrogen bonds : angle 4.52011 ( 870) link_BETA1-6 : bond 0.01272 ( 1) link_BETA1-6 : angle 1.19624 ( 3) metal coordination : bond 0.00238 ( 2) SS BOND : bond 0.00244 ( 7) SS BOND : angle 1.17977 ( 14) covalent geometry : bond 0.00343 ( 6297) covalent geometry : angle 0.52614 ( 8569) *********************** 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: 13 poor density : 78 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8134 (mmtp) cc_final: 0.7734 (mmtt) REVERT: A 269 MET cc_start: 0.8683 (mmt) cc_final: 0.8333 (tpp) REVERT: A 375 MET cc_start: 0.7999 (mtt) cc_final: 0.7799 (mtt) REVERT: A 381 ASP cc_start: 0.8493 (m-30) cc_final: 0.8273 (m-30) REVERT: A 400 HIS cc_start: 0.8639 (OUTLIER) cc_final: 0.7000 (t-90) REVERT: A 407 MET cc_start: 0.7132 (mmt) cc_final: 0.6854 (mmt) REVERT: A 473 MET cc_start: 0.8351 (mmp) cc_final: 0.7936 (mmp) REVERT: B 409 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8126 (tttm) REVERT: B 479 LYS cc_start: 0.8718 (tttm) cc_final: 0.8004 (ttmt) outliers start: 13 outliers final: 8 residues processed: 84 average time/residue: 0.2436 time to fit residues: 26.3279 Evaluate side-chains 83 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 462 VAL Chi-restraints excluded: chain B residue 409 LYS Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 487 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 29 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 47 optimal weight: 0.0870 chunk 43 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 46 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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 = 0.3451 r_free = 0.3451 target = 0.139240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.113770 restraints weight = 6145.495| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.55 r_work: 0.3062 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6316 Z= 0.124 Angle : 0.494 5.644 8613 Z= 0.248 Chirality : 0.040 0.145 949 Planarity : 0.004 0.039 1084 Dihedral : 5.688 52.447 1064 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.56 % Allowed : 8.19 % Favored : 88.26 % 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: 1.03 (0.26), residues: 385 sheet: 1.74 (0.66), residues: 60 loop : 0.42 (0.36), residues: 327 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 0.002 0.000 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00161 ( 9) link_NAG-ASN : angle 1.79389 ( 27) hydrogen bonds : bond 0.04829 ( 311) hydrogen bonds : angle 4.26308 ( 870) link_BETA1-6 : bond 0.01337 ( 1) link_BETA1-6 : angle 1.26296 ( 3) metal coordination : bond 0.00206 ( 2) SS BOND : bond 0.00197 ( 7) SS BOND : angle 0.82316 ( 14) covalent geometry : bond 0.00280 ( 6297) covalent geometry : angle 0.48359 ( 8569) *********************** 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: 20 poor density : 76 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 400 HIS cc_start: 0.8536 (OUTLIER) cc_final: 0.6925 (t-90) REVERT: A 407 MET cc_start: 0.7119 (mmt) cc_final: 0.6769 (mmt) REVERT: A 473 MET cc_start: 0.8373 (mmp) cc_final: 0.7939 (mmp) REVERT: B 409 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8073 (tttm) REVERT: B 472 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7822 (pm20) REVERT: B 479 LYS cc_start: 0.8729 (tttm) cc_final: 0.8014 (ttmt) REVERT: B 525 ASN cc_start: 0.7799 (m-40) cc_final: 0.7512 (m-40) outliers start: 20 outliers final: 9 residues processed: 88 average time/residue: 0.2276 time to fit residues: 25.7215 Evaluate side-chains 85 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 562 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 18 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 50 optimal weight: 0.4980 chunk 75 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 565 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.138185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.113881 restraints weight = 6265.808| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.54 r_work: 0.3055 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6316 Z= 0.140 Angle : 0.514 5.692 8613 Z= 0.259 Chirality : 0.041 0.151 949 Planarity : 0.004 0.037 1084 Dihedral : 5.751 53.348 1064 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.38 % Allowed : 9.43 % Favored : 87.19 % 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: 1.08 (0.30), residues: 772 helix: 1.03 (0.26), residues: 385 sheet: 1.38 (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 0.006 0.001 HIS A 240 PHE 0.009 0.001 PHE A 307 TYR 0.013 0.001 TYR A 182 ARG 0.004 0.000 ARG A 227 Details of bonding type rmsd link_NAG-ASN : bond 0.00175 ( 9) link_NAG-ASN : angle 1.81129 ( 27) hydrogen bonds : bond 0.05053 ( 311) hydrogen bonds : angle 4.22650 ( 870) link_BETA1-6 : bond 0.01311 ( 1) link_BETA1-6 : angle 1.25981 ( 3) metal coordination : bond 0.00233 ( 2) SS BOND : bond 0.00199 ( 7) SS BOND : angle 1.14910 ( 14) covalent geometry : bond 0.00326 ( 6297) covalent geometry : angle 0.50260 ( 8569) *********************** 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 93 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 MET cc_start: 0.7998 (mtt) cc_final: 0.7781 (mtt) REVERT: A 400 HIS cc_start: 0.8540 (OUTLIER) cc_final: 0.6934 (t-90) REVERT: A 407 MET cc_start: 0.7190 (mmt) cc_final: 0.6820 (mmt) REVERT: A 473 MET cc_start: 0.8387 (mmp) cc_final: 0.7945 (mmp) REVERT: B 409 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8052 (tttm) REVERT: B 472 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7821 (pm20) REVERT: B 479 LYS cc_start: 0.8734 (tttm) cc_final: 0.7991 (ttmt) outliers start: 19 outliers final: 10 residues processed: 84 average time/residue: 0.2670 time to fit residues: 29.5351 Evaluate side-chains 85 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 1.125 ------------------------------------------------------------------------------- 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 423 LEU 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 Chi-restraints excluded: chain B residue 562 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 31 optimal weight: 0.7980 chunk 28 optimal weight: 0.3980 chunk 73 optimal weight: 0.4980 chunk 10 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 59 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3442 r_free = 0.3442 target = 0.138453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.113147 restraints weight = 6170.651| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.53 r_work: 0.3055 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6316 Z= 0.129 Angle : 0.501 5.614 8613 Z= 0.251 Chirality : 0.040 0.151 949 Planarity : 0.004 0.035 1084 Dihedral : 5.472 53.195 1061 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.20 % Allowed : 10.14 % Favored : 86.65 % 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 (0.30), residues: 772 helix: 1.13 (0.26), residues: 385 sheet: 1.32 (0.67), 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 0.006 0.001 HIS A 240 PHE 0.009 0.001 PHE A 522 TYR 0.013 0.001 TYR A 182 ARG 0.003 0.000 ARG A 227 Details of bonding type rmsd link_NAG-ASN : bond 0.00177 ( 9) link_NAG-ASN : angle 1.77523 ( 27) hydrogen bonds : bond 0.04819 ( 311) hydrogen bonds : angle 4.17745 ( 870) link_BETA1-6 : bond 0.01289 ( 1) link_BETA1-6 : angle 1.26513 ( 3) metal coordination : bond 0.00204 ( 2) SS BOND : bond 0.00202 ( 7) SS BOND : angle 0.87545 ( 14) covalent geometry : bond 0.00295 ( 6297) covalent geometry : angle 0.49000 ( 8569) *********************** 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 93 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 MET cc_start: 0.7942 (mtt) cc_final: 0.7702 (mtt) REVERT: A 400 HIS cc_start: 0.8504 (OUTLIER) cc_final: 0.6902 (t-90) REVERT: A 473 MET cc_start: 0.8382 (mmp) cc_final: 0.7940 (mmp) REVERT: B 409 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8033 (tttm) REVERT: B 472 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7825 (pm20) REVERT: B 479 LYS cc_start: 0.8726 (tttm) cc_final: 0.7964 (ttmt) outliers start: 18 outliers final: 12 residues processed: 87 average time/residue: 0.2172 time to fit residues: 24.7571 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 : 0.581 ------------------------------------------------------------------------------- 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 472 GLU 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: 0.1980 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 71 optimal weight: 0.0070 chunk 54 optimal weight: 0.6980 chunk 48 optimal weight: 0.3980 overall best weight: 0.3798 ------------------------------------------------------------------------------- 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 = 0.3464 r_free = 0.3464 target = 0.140351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.114915 restraints weight = 6110.173| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.56 r_work: 0.3074 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6316 Z= 0.108 Angle : 0.479 5.372 8613 Z= 0.239 Chirality : 0.039 0.146 949 Planarity : 0.004 0.033 1084 Dihedral : 5.335 52.989 1061 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.67 % Allowed : 11.03 % Favored : 86.30 % 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: 1.32 (0.30), residues: 772 helix: 1.29 (0.26), residues: 385 sheet: 1.35 (0.67), residues: 61 loop : 0.43 (0.36), residues: 326 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 0.003 0.000 ARG A 227 Details of bonding type rmsd link_NAG-ASN : bond 0.00178 ( 9) link_NAG-ASN : angle 1.69854 ( 27) hydrogen bonds : bond 0.04334 ( 311) hydrogen bonds : angle 4.10181 ( 870) link_BETA1-6 : bond 0.01276 ( 1) link_BETA1-6 : angle 1.29127 ( 3) metal coordination : bond 0.00138 ( 2) SS BOND : bond 0.00170 ( 7) SS BOND : angle 0.71315 ( 14) covalent geometry : bond 0.00235 ( 6297) covalent geometry : angle 0.46941 ( 8569) *********************** 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 96 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 400 HIS cc_start: 0.8476 (OUTLIER) cc_final: 0.6878 (t-90) REVERT: A 473 MET cc_start: 0.8364 (mmp) cc_final: 0.7931 (mmp) REVERT: A 530 ARG cc_start: 0.7342 (ttp-110) cc_final: 0.6962 (ttp80) REVERT: B 409 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8041 (tttm) REVERT: B 472 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7807 (pm20) REVERT: B 479 LYS cc_start: 0.8750 (tttm) cc_final: 0.8015 (ttmt) REVERT: B 525 ASN cc_start: 0.7766 (m-40) cc_final: 0.7559 (m-40) outliers start: 15 outliers final: 9 residues processed: 90 average time/residue: 0.2936 time to fit residues: 34.1929 Evaluate side-chains 89 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.878 ------------------------------------------------------------------------------- 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 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: 0.0670 chunk 18 optimal weight: 0.5980 chunk 51 optimal weight: 0.0970 chunk 30 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 50 optimal weight: 0.3980 chunk 34 optimal weight: 0.0770 chunk 54 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 38 optimal weight: 0.3980 overall best weight: 0.2074 ------------------------------------------------------------------------------- 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 = 0.3502 r_free = 0.3502 target = 0.143679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.118222 restraints weight = 6156.743| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.57 r_work: 0.3117 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6316 Z= 0.088 Angle : 0.446 4.909 8613 Z= 0.222 Chirality : 0.038 0.136 949 Planarity : 0.003 0.030 1084 Dihedral : 5.133 52.348 1061 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 2.67 % Allowed : 11.57 % 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: 1.55 (0.31), residues: 772 helix: 1.52 (0.26), residues: 384 sheet: 1.43 (0.68), residues: 61 loop : 0.50 (0.36), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 162 HIS 0.002 0.001 HIS A 240 PHE 0.008 0.001 PHE A 326 TYR 0.011 0.001 TYR A 182 ARG 0.004 0.000 ARG A 227 Details of bonding type rmsd link_NAG-ASN : bond 0.00172 ( 9) link_NAG-ASN : angle 1.56491 ( 27) hydrogen bonds : bond 0.03697 ( 311) hydrogen bonds : angle 3.95957 ( 870) link_BETA1-6 : bond 0.01166 ( 1) link_BETA1-6 : angle 1.29527 ( 3) metal coordination : bond 0.00088 ( 2) SS BOND : bond 0.00132 ( 7) SS BOND : angle 0.60346 ( 14) covalent geometry : bond 0.00176 ( 6297) covalent geometry : angle 0.43725 ( 8569) *********************** 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 97 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8151 (mmtp) cc_final: 0.7693 (mmtt) REVERT: A 159 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7058 (tt0) REVERT: A 170 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7347 (mt-10) REVERT: A 235 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7047 (tt) REVERT: A 248 MET cc_start: 0.8023 (mtp) cc_final: 0.7798 (mtm) REVERT: A 400 HIS cc_start: 0.8384 (OUTLIER) cc_final: 0.6710 (t-90) REVERT: A 473 MET cc_start: 0.8336 (mmp) cc_final: 0.7921 (mmp) REVERT: A 478 GLU cc_start: 0.8239 (tt0) cc_final: 0.7771 (mt-10) REVERT: A 530 ARG cc_start: 0.7255 (ttp-110) cc_final: 0.6879 (ttp80) REVERT: A 585 ASN cc_start: 0.7687 (t0) cc_final: 0.7370 (t0) REVERT: B 409 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7942 (tttm) REVERT: B 472 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7859 (pm20) REVERT: B 479 LYS cc_start: 0.8747 (tttm) cc_final: 0.8016 (ttmt) outliers start: 15 outliers final: 7 residues processed: 90 average time/residue: 0.1969 time to fit residues: 23.3005 Evaluate side-chains 92 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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 235 LEU Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 423 LEU 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 472 GLU 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: 0.7980 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 0.3980 chunk 70 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 51 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 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.138542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.112934 restraints weight = 6174.752| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.57 r_work: 0.3047 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6316 Z= 0.145 Angle : 0.519 5.534 8613 Z= 0.260 Chirality : 0.041 0.147 949 Planarity : 0.004 0.034 1084 Dihedral : 5.379 53.228 1060 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.49 % Allowed : 11.92 % Favored : 85.59 % 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: 1.29 (0.31), residues: 772 helix: 1.27 (0.26), residues: 391 sheet: 1.26 (0.67), residues: 61 loop : 0.41 (0.36), residues: 320 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 0.011 0.001 PHE A 522 TYR 0.013 0.001 TYR A 182 ARG 0.003 0.001 ARG A 459 Details of bonding type rmsd link_NAG-ASN : bond 0.00174 ( 9) link_NAG-ASN : angle 1.69774 ( 27) hydrogen bonds : bond 0.04955 ( 311) hydrogen bonds : angle 4.13219 ( 870) link_BETA1-6 : bond 0.01181 ( 1) link_BETA1-6 : angle 1.24592 ( 3) metal coordination : bond 0.00271 ( 2) SS BOND : bond 0.00199 ( 7) SS BOND : angle 1.35178 ( 14) covalent geometry : bond 0.00344 ( 6297) covalent geometry : angle 0.50836 ( 8569) *********************** 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 92 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8165 (mmtp) cc_final: 0.7714 (mmtt) REVERT: A 170 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7407 (mt-10) REVERT: A 400 HIS cc_start: 0.8536 (OUTLIER) cc_final: 0.6917 (t-90) REVERT: A 473 MET cc_start: 0.8426 (mmp) cc_final: 0.7756 (mmp) REVERT: A 478 GLU cc_start: 0.8326 (tt0) cc_final: 0.7808 (mt-10) REVERT: A 530 ARG cc_start: 0.7375 (ttp-110) cc_final: 0.6984 (ttp80) REVERT: B 409 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8082 (tttm) REVERT: B 479 LYS cc_start: 0.8742 (tttm) cc_final: 0.7977 (ttmt) outliers start: 14 outliers final: 11 residues processed: 87 average time/residue: 0.2077 time to fit residues: 23.5133 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 : 0.691 ------------------------------------------------------------------------------- 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 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 B residue 409 LYS Chi-restraints excluded: chain B residue 487 CYS Chi-restraints excluded: chain B residue 553 LEU 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: 0.8980 chunk 52 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.137658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.112125 restraints weight = 6221.824| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.56 r_work: 0.3040 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6316 Z= 0.154 Angle : 0.531 5.721 8613 Z= 0.266 Chirality : 0.041 0.152 949 Planarity : 0.004 0.035 1084 Dihedral : 5.519 53.592 1060 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.49 % Allowed : 12.10 % 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: 1.15 (0.31), residues: 772 helix: 1.13 (0.26), residues: 391 sheet: 1.19 (0.67), residues: 61 loop : 0.38 (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 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00191 ( 9) link_NAG-ASN : angle 1.80558 ( 27) hydrogen bonds : bond 0.05148 ( 311) hydrogen bonds : angle 4.21394 ( 870) link_BETA1-6 : bond 0.01273 ( 1) link_BETA1-6 : angle 1.24837 ( 3) metal coordination : bond 0.00276 ( 2) SS BOND : bond 0.00235 ( 7) SS BOND : angle 1.14321 ( 14) covalent geometry : bond 0.00365 ( 6297) covalent geometry : angle 0.51994 ( 8569) *********************** 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 90 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8154 (mmtp) cc_final: 0.7699 (mmtt) REVERT: A 159 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7159 (tt0) REVERT: A 170 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7389 (mt-10) REVERT: A 375 MET cc_start: 0.8068 (mtt) cc_final: 0.7813 (mtt) REVERT: A 400 HIS cc_start: 0.8530 (OUTLIER) cc_final: 0.6923 (t-90) REVERT: A 473 MET cc_start: 0.8426 (mmp) cc_final: 0.7957 (mmp) REVERT: A 530 ARG cc_start: 0.7351 (ttp-110) cc_final: 0.6958 (ttp80) REVERT: B 409 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8141 (tttm) REVERT: B 479 LYS cc_start: 0.8733 (tttm) cc_final: 0.7980 (ttmt) outliers start: 14 outliers final: 12 residues processed: 86 average time/residue: 0.2150 time to fit residues: 24.0700 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 : 0.675 ------------------------------------------------------------------------------- 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 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: 0.0970 chunk 52 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 17 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 = 0.139527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.116530 restraints weight = 6164.101| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.63 r_work: 0.3067 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6316 Z= 0.118 Angle : 0.494 5.432 8613 Z= 0.247 Chirality : 0.039 0.143 949 Planarity : 0.004 0.033 1084 Dihedral : 5.381 53.290 1060 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.49 % Allowed : 12.28 % 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: 1.29 (0.31), residues: 772 helix: 1.29 (0.26), residues: 390 sheet: 1.22 (0.68), residues: 61 loop : 0.40 (0.37), residues: 321 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 522 TYR 0.012 0.001 TYR A 182 ARG 0.002 0.000 ARG A 227 Details of bonding type rmsd link_NAG-ASN : bond 0.00171 ( 9) link_NAG-ASN : angle 1.75150 ( 27) hydrogen bonds : bond 0.04547 ( 311) hydrogen bonds : angle 4.12884 ( 870) link_BETA1-6 : bond 0.01193 ( 1) link_BETA1-6 : angle 1.25219 ( 3) metal coordination : bond 0.00168 ( 2) SS BOND : bond 0.00189 ( 7) SS BOND : angle 0.98771 ( 14) covalent geometry : bond 0.00264 ( 6297) covalent geometry : angle 0.48329 ( 8569) ********************** 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 94 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8164 (mmtp) cc_final: 0.7708 (mmtt) REVERT: A 170 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7389 (mt-10) REVERT: A 400 HIS cc_start: 0.8474 (OUTLIER) cc_final: 0.6879 (t-90) REVERT: A 473 MET cc_start: 0.8377 (mmp) cc_final: 0.7934 (mmp) REVERT: A 478 GLU cc_start: 0.8304 (tt0) cc_final: 0.7782 (mt-10) REVERT: A 530 ARG cc_start: 0.7329 (ttp-110) cc_final: 0.6941 (ttp80) REVERT: B 409 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8043 (tttm) REVERT: B 479 LYS cc_start: 0.8742 (tttm) cc_final: 0.8014 (ttmt) outliers start: 14 outliers final: 12 residues processed: 89 average time/residue: 0.2001 time to fit residues: 23.1449 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 : 0.632 ------------------------------------------------------------------------------- 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 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: 0.0040 chunk 29 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 17 optimal weight: 0.0870 chunk 65 optimal weight: 0.1980 chunk 32 optimal weight: 0.6980 chunk 7 optimal weight: 0.4980 chunk 3 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 overall best weight: 0.2770 ------------------------------------------------------------------------------- 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 = 0.141953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.116181 restraints weight = 6257.361| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.60 r_work: 0.3088 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6316 Z= 0.096 Angle : 0.462 5.206 8613 Z= 0.230 Chirality : 0.038 0.133 949 Planarity : 0.003 0.032 1084 Dihedral : 5.196 52.655 1060 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.31 % Allowed : 12.46 % 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: 1.48 (0.31), residues: 772 helix: 1.48 (0.26), residues: 390 sheet: 1.29 (0.68), residues: 61 loop : 0.43 (0.37), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 162 HIS 0.003 0.001 HIS A 240 PHE 0.007 0.001 PHE B 570 TYR 0.011 0.001 TYR A 182 ARG 0.003 0.000 ARG A 227 Details of bonding type rmsd link_NAG-ASN : bond 0.00162 ( 9) link_NAG-ASN : angle 1.64430 ( 27) hydrogen bonds : bond 0.03938 ( 311) hydrogen bonds : angle 4.02399 ( 870) link_BETA1-6 : bond 0.01105 ( 1) link_BETA1-6 : angle 1.29192 ( 3) metal coordination : bond 0.00113 ( 2) SS BOND : bond 0.00152 ( 7) SS BOND : angle 0.81651 ( 14) covalent geometry : bond 0.00200 ( 6297) covalent geometry : angle 0.45207 ( 8569) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3738.11 seconds wall clock time: 65 minutes 30.93 seconds (3930.93 seconds total)