Starting phenix.real_space_refine on Tue Feb 3 14:36:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dkk_46960/02_2026/9dkk_46960.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dkk_46960/02_2026/9dkk_46960.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dkk_46960/02_2026/9dkk_46960.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dkk_46960/02_2026/9dkk_46960.map" model { file = "/net/cci-nas-00/data/ceres_data/9dkk_46960/02_2026/9dkk_46960.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dkk_46960/02_2026/9dkk_46960.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.041 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: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 2461 2.51 5 N 622 2.21 5 O 677 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3782 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1492 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 14, 'TRANS': 190} Chain breaks: 1 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "D" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 309 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'TRANS': 48} Chain breaks: 2 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 15, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 101 Chain: "A" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1498 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 14, 'TRANS': 190} Chain breaks: 1 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 2, 'ARG:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 30 Chain: "C" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 399 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 1, 'TRANS': 54} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 13, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 70 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.11, per 1000 atoms: 0.29 Number of scatterers: 3782 At special positions: 0 Unit cell: (86, 106, 102, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 677 8.00 N 622 7.00 C 2461 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS B 407 " distance=2.03 Simple disulfide: pdb=" SG CYS B 425 " - pdb=" SG CYS B 478 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 585 " distance=2.03 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 526 " distance=2.03 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 407 " distance=2.03 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS A 478 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 585 " distance=2.03 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 526 " 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 BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1401 " - " ASN A 487 " " NAG B1401 " - " ASN B 487 " " NAG E 1 " - " ASN A 410 " " NAG F 1 " - " ASN B 410 " Time building additional restraints: 0.34 Conformation dependent library (CDL) restraints added in 154.3 milliseconds 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 992 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 6 sheets defined 33.4% alpha, 29.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.633A pdb=" N SER B 390 " --> pdb=" O PRO B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 399 removed outlier: 3.664A pdb=" N PHE B 399 " --> pdb=" O VAL B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 416 removed outlier: 3.635A pdb=" N LEU B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 453 Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 524 through 529 removed outlier: 4.202A pdb=" N SER B 528 " --> pdb=" O PRO B 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 22 removed outlier: 3.554A pdb=" N GLU D 19 " --> pdb=" O GLU D 15 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA D 20 " --> pdb=" O GLU D 16 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR D 21 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU D 22 " --> pdb=" O GLU D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 43 Processing helix chain 'D' and resid 47 through 57 removed outlier: 3.751A pdb=" N LYS D 57 " --> pdb=" O ARG D 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'A' and resid 395 through 399 removed outlier: 3.625A pdb=" N PHE A 399 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 415 removed outlier: 3.510A pdb=" N LEU A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 453 Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 524 through 529 removed outlier: 4.140A pdb=" N SER A 528 " --> pdb=" O PRO A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 550 Processing helix chain 'C' and resid 6 through 24 removed outlier: 3.828A pdb=" N GLU C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 43 Processing helix chain 'C' and resid 45 through 59 Processing sheet with id=AA1, first strand: chain 'B' and resid 400 through 404 removed outlier: 7.912A pdb=" N SER B 440 " --> pdb=" O ASN B 582 " (cutoff:3.500A) removed outlier: 9.590A pdb=" N ASN B 582 " --> pdb=" O SER B 440 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 400 through 404 removed outlier: 6.675A pdb=" N THR B 483 " --> pdb=" O VAL B 420 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N VAL B 420 " --> pdb=" O THR B 483 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 512 through 515 removed outlier: 5.288A pdb=" N SER B 498 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL B 561 " --> pdb=" O SER B 498 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ILE B 500 " --> pdb=" O SER B 559 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N SER B 559 " --> pdb=" O ILE B 500 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS B 502 " --> pdb=" O SER B 557 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 400 through 404 removed outlier: 8.079A pdb=" N SER A 440 " --> pdb=" O ASN A 582 " (cutoff:3.500A) removed outlier: 9.683A pdb=" N ASN A 582 " --> pdb=" O SER A 440 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 400 through 404 Processing sheet with id=AA6, first strand: chain 'A' and resid 513 through 515 removed outlier: 6.393A pdb=" N SER A 557 " --> pdb=" O ASN A 501 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N CYS A 503 " --> pdb=" O VAL A 555 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL A 555 " --> pdb=" O CYS A 503 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ARG A 505 " --> pdb=" O TRP A 553 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N TRP A 553 " --> pdb=" O ARG A 505 " (cutoff:3.500A) 188 hydrogen bonds defined for protein. 477 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: 0.52 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 614 1.32 - 1.44: 1036 1.44 - 1.57: 2191 1.57 - 1.70: 0 1.70 - 1.82: 28 Bond restraints: 3869 Sorted by residual: bond pdb=" C PRO A 485 " pdb=" O PRO A 485 " ideal model delta sigma weight residual 1.233 1.191 0.042 1.19e-02 7.06e+03 1.22e+01 bond pdb=" N LEU A 507 " pdb=" CA LEU A 507 " ideal model delta sigma weight residual 1.453 1.489 -0.037 1.31e-02 5.83e+03 7.86e+00 bond pdb=" N THR A 490 " pdb=" CA THR A 490 " ideal model delta sigma weight residual 1.458 1.483 -0.025 9.00e-03 1.23e+04 7.51e+00 bond pdb=" N ILE B 500 " pdb=" CA ILE B 500 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.24e-02 6.50e+03 7.37e+00 bond pdb=" N SER B 459 " pdb=" CA SER B 459 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.12e-02 7.97e+03 6.83e+00 ... (remaining 3864 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 5049 1.69 - 3.39: 228 3.39 - 5.08: 23 5.08 - 6.78: 5 6.78 - 8.47: 2 Bond angle restraints: 5307 Sorted by residual: angle pdb=" N THR A 490 " pdb=" CA THR A 490 " pdb=" C THR A 490 " ideal model delta sigma weight residual 113.50 105.03 8.47 1.65e+00 3.67e-01 2.64e+01 angle pdb=" N GLU A 549 " pdb=" CA GLU A 549 " pdb=" C GLU A 549 " ideal model delta sigma weight residual 113.19 108.90 4.29 1.19e+00 7.06e-01 1.30e+01 angle pdb=" N ILE A 491 " pdb=" CA ILE A 491 " pdb=" C ILE A 491 " ideal model delta sigma weight residual 109.34 101.84 7.50 2.08e+00 2.31e-01 1.30e+01 angle pdb=" CA TYR B 499 " pdb=" CB TYR B 499 " pdb=" CG TYR B 499 " ideal model delta sigma weight residual 113.90 120.04 -6.14 1.80e+00 3.09e-01 1.16e+01 angle pdb=" CA ARG A 511 " pdb=" C ARG A 511 " pdb=" O ARG A 511 " ideal model delta sigma weight residual 122.03 118.07 3.96 1.17e+00 7.31e-01 1.15e+01 ... (remaining 5302 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 2280 17.58 - 35.17: 85 35.17 - 52.75: 8 52.75 - 70.33: 4 70.33 - 87.92: 2 Dihedral angle restraints: 2379 sinusoidal: 855 harmonic: 1524 Sorted by residual: dihedral pdb=" SG CYS A 437 " pdb=" CB CYS A 585 " pdb=" SG CYS A 585 " pdb=" CA CYS A 585 " ideal model delta sinusoidal sigma weight residual 79.00 12.62 66.38 1 2.00e+01 2.50e-03 1.44e+01 dihedral pdb=" N VAL B 458 " pdb=" CA VAL B 458 " pdb=" CB VAL B 458 " pdb=" CG1 VAL B 458 " ideal model delta sinusoidal sigma weight residual -60.00 -116.87 56.87 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" N LEU A 507 " pdb=" CA LEU A 507 " pdb=" CB LEU A 507 " pdb=" CG LEU A 507 " ideal model delta sinusoidal sigma weight residual -60.00 -108.49 48.49 3 1.50e+01 4.44e-03 8.65e+00 ... (remaining 2376 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 486 0.045 - 0.090: 88 0.090 - 0.134: 56 0.134 - 0.179: 5 0.179 - 0.224: 4 Chirality restraints: 639 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.29 -0.11 2.00e-02 2.50e+03 2.97e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 2.04e+01 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN B 410 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 636 not shown) Planarity restraints: 681 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " 0.067 2.00e-02 2.50e+03 5.55e-02 3.85e+01 pdb=" C7 NAG F 1 " -0.020 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " 0.051 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " -0.088 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 505 " 0.377 9.50e-02 1.11e+02 1.69e-01 1.76e+01 pdb=" NE ARG A 505 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG A 505 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 505 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 505 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " 0.039 2.00e-02 2.50e+03 3.21e-02 1.29e+01 pdb=" C7 NAG F 2 " -0.013 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " 0.030 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " -0.050 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " -0.006 2.00e-02 2.50e+03 ... (remaining 678 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 544 2.76 - 3.29: 3398 3.29 - 3.83: 5948 3.83 - 4.36: 6950 4.36 - 4.90: 12543 Nonbonded interactions: 29383 Sorted by model distance: nonbonded pdb=" OG1 THR A 392 " pdb=" OG1 THR A 492 " model vdw 2.222 3.040 nonbonded pdb=" OH TYR A 448 " pdb=" O MET A 452 " model vdw 2.238 3.040 nonbonded pdb=" OD1 ASN B 421 " pdb=" OG1 THR B 483 " model vdw 2.291 3.040 nonbonded pdb=" OH TYR A 409 " pdb=" O ASN A 436 " model vdw 2.310 3.040 nonbonded pdb=" NZ LYS A 496 " pdb=" O TRP A 535 " model vdw 2.317 3.120 ... (remaining 29378 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 381 or (resid 382 and (name N or name CA or name C or name \ O or name CB )) or resid 383 through 391 or (resid 392 and (name N or name CA o \ r name C or name O or name CB )) or resid 393 through 399 or (resid 400 and (nam \ e N or name CA or name C or name O or name CB )) or resid 401 through 412 or (re \ sid 413 and (name N or name CA or name C or name O or name CB )) or resid 414 th \ rough 421 or (resid 422 and (name N or name CA or name C or name O or name CB )) \ or resid 423 through 452 or (resid 453 through 454 and (name N or name CA or na \ me C or name O or name CB )) or resid 455 through 472 or (resid 473 through 474 \ and (name N or name CA or name C or name O or name CB )) or resid 475 through 48 \ 5 or (resid 486 and (name N or name CA or name C or name O or name CB )) or resi \ d 487 through 491 or (resid 492 and (name N or name CA or name C or name O or na \ me CB )) or resid 493 through 494 or (resid 495 and (name N or name CA or name C \ or name O or name CB )) or resid 496 through 503 or (resid 504 and (name N or n \ ame CA or name C or name O or name CB )) or resid 505 through 512 or (resid 513 \ through 514 and (name N or name CA or name C or name O or name CB )) or resid 51 \ 5 through 523 or (resid 524 and (name N or name CA or name C or name O or name C \ B )) or resid 525 through 1401)) selection = (chain 'B' and (resid 381 through 405 or (resid 406 and (name N or name CA or na \ me C or name O or name CB )) or resid 407 through 411 or (resid 412 through 413 \ and (name N or name CA or name C or name O or name CB )) or resid 414 through 41 \ 5 or (resid 416 and (name N or name CA or name C or name O or name CB )) or resi \ d 417 through 446 or (resid 447 and (name N or name CA or name C or name O or na \ me CB )) or resid 448 through 510 or (resid 511 through 514 and (name N or name \ CA or name C or name O or name CB )) or resid 515 through 533 or (resid 534 and \ (name N or name CA or name C or name O or name CB )) or resid 535 through 543 or \ (resid 544 through 546 and (name N or name CA or name C or name O or name CB )) \ or resid 547 or (resid 548 through 549 and (name N or name CA or name C or name \ O or name CB )) or resid 550 through 558 or (resid 559 through 560 and (name N \ or name CA or name C or name O or name CB )) or resid 561 through 563 or (resid \ 564 through 565 and (name N or name CA or name C or name O or name CB )) or resi \ d 566 through 574 or (resid 575 and (name N or name CA or name C or name O or na \ me CB )) or resid 576 through 586 or (resid 587 and (name N or name CA or name C \ or name O or name CB )) or resid 588 through 1401)) } ncs_group { reference = (chain 'C' and (resid 5 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 17 or (resid 18 through 23 and (nam \ e N or name CA or name C or name O or name CB )) or (resid 26 through 28 and (na \ me N or name CA or name C or name O or name CB )) or resid 29 through 36 or (res \ id 37 and (name N or name CA or name C or name O or name CB )) or resid 38 throu \ gh 43 or (resid 46 through 51 and (name N or name CA or name C or name O or name \ CB )) or resid 52 or (resid 53 through 54 and (name N or name CA or name C or n \ ame O or name CB )) or resid 55 or (resid 56 through 57 and (name N or name CA o \ r name C or name O or name CB )))) selection = (chain 'D' and (resid 5 through 30 or (resid 31 and (name N or name CA or name C \ or name O or name CB )) or resid 32 through 57)) } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 9.060 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: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.690 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1760 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 3883 Z= 0.351 Angle : 0.767 12.153 5341 Z= 0.467 Chirality : 0.049 0.224 639 Planarity : 0.008 0.169 677 Dihedral : 9.504 87.916 1363 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.93 % Allowed : 5.26 % Favored : 93.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.38), residues: 499 helix: 0.74 (0.48), residues: 132 sheet: 0.35 (0.45), residues: 150 loop : -1.10 (0.41), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 401 TYR 0.024 0.001 TYR B 499 PHE 0.008 0.001 PHE C 9 TRP 0.009 0.001 TRP A 553 HIS 0.001 0.001 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00521 ( 3869) covalent geometry : angle 0.73080 ( 5307) SS BOND : bond 0.00187 ( 8) SS BOND : angle 1.00702 ( 16) hydrogen bonds : bond 0.17008 ( 176) hydrogen bonds : angle 7.01461 ( 477) link_BETA1-4 : bond 0.04632 ( 2) link_BETA1-4 : angle 6.31279 ( 6) link_NAG-ASN : bond 0.01497 ( 4) link_NAG-ASN : angle 2.13404 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.133 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 50 average time/residue: 0.0743 time to fit residues: 4.6465 Evaluate side-chains 25 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 491 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 0.3980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.3980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.3980 chunk 22 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 427 GLN ** B 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 GLN ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 GLN A 521 ASN A 522 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.189642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.176036 restraints weight = 4882.880| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 1.20 r_work: 0.3762 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3631 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5634 moved from start: 0.7967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.092 3883 Z= 0.364 Angle : 1.268 19.196 5341 Z= 0.620 Chirality : 0.067 0.651 639 Planarity : 0.008 0.092 677 Dihedral : 8.324 57.458 670 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.41 % Allowed : 11.15 % Favored : 85.45 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.37), residues: 499 helix: 1.43 (0.51), residues: 105 sheet: -0.30 (0.43), residues: 150 loop : -0.85 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG A 401 TYR 0.049 0.005 TYR A 448 PHE 0.025 0.004 PHE B 385 TRP 0.052 0.005 TRP D 38 HIS 0.008 0.005 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00759 ( 3869) covalent geometry : angle 1.23544 ( 5307) SS BOND : bond 0.00336 ( 8) SS BOND : angle 2.11093 ( 16) hydrogen bonds : bond 0.05446 ( 176) hydrogen bonds : angle 6.72389 ( 477) link_BETA1-4 : bond 0.00550 ( 2) link_BETA1-4 : angle 2.23995 ( 6) link_NAG-ASN : bond 0.05744 ( 4) link_NAG-ASN : angle 5.70532 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.136 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 3 residues processed: 68 average time/residue: 0.0708 time to fit residues: 6.0171 Evaluate side-chains 42 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 444 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 34 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 28 optimal weight: 0.0030 chunk 41 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 0.0870 chunk 16 optimal weight: 0.7980 overall best weight: 0.4368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 421 ASN B 436 ASN ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 ASN ** A 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.176842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.152345 restraints weight = 4712.251| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.79 r_work: 0.3508 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 1.0432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.151 3883 Z= 0.222 Angle : 0.924 17.855 5341 Z= 0.428 Chirality : 0.050 0.400 639 Planarity : 0.007 0.099 677 Dihedral : 6.701 55.722 668 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.10 % Allowed : 14.55 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.37), residues: 499 helix: 2.32 (0.52), residues: 105 sheet: 0.08 (0.42), residues: 160 loop : -0.86 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG B 505 TYR 0.024 0.003 TYR A 397 PHE 0.020 0.002 PHE C 9 TRP 0.011 0.001 TRP B 553 HIS 0.010 0.006 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00513 ( 3869) covalent geometry : angle 0.83747 ( 5307) SS BOND : bond 0.01078 ( 8) SS BOND : angle 2.84839 ( 16) hydrogen bonds : bond 0.04806 ( 176) hydrogen bonds : angle 5.11482 ( 477) link_BETA1-4 : bond 0.00265 ( 2) link_BETA1-4 : angle 3.74838 ( 6) link_NAG-ASN : bond 0.01712 ( 4) link_NAG-ASN : angle 7.19787 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.139 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 64 average time/residue: 0.0605 time to fit residues: 4.9966 Evaluate side-chains 47 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 507 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 34 optimal weight: 0.3980 chunk 30 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 GLN ** B 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.170359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.146713 restraints weight = 4730.318| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.13 r_work: 0.3370 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 1.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 3883 Z= 0.261 Angle : 0.933 22.577 5341 Z= 0.440 Chirality : 0.052 0.451 639 Planarity : 0.007 0.128 677 Dihedral : 6.457 40.033 668 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.79 % Allowed : 14.55 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.37), residues: 499 helix: 2.20 (0.51), residues: 105 sheet: 0.01 (0.44), residues: 142 loop : -0.86 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG B 505 TYR 0.018 0.002 TYR B 397 PHE 0.016 0.002 PHE C 55 TRP 0.008 0.002 TRP D 38 HIS 0.002 0.002 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00585 ( 3869) covalent geometry : angle 0.83445 ( 5307) SS BOND : bond 0.00273 ( 8) SS BOND : angle 2.19376 ( 16) hydrogen bonds : bond 0.04069 ( 176) hydrogen bonds : angle 5.12121 ( 477) link_BETA1-4 : bond 0.01285 ( 2) link_BETA1-4 : angle 0.80007 ( 6) link_NAG-ASN : bond 0.02654 ( 4) link_NAG-ASN : angle 8.54805 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 502 LYS cc_start: 0.8851 (ptmt) cc_final: 0.8633 (ttpp) REVERT: A 442 ILE cc_start: 0.8806 (mm) cc_final: 0.8579 (mm) outliers start: 9 outliers final: 7 residues processed: 70 average time/residue: 0.0416 time to fit residues: 3.7187 Evaluate side-chains 64 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain A residue 555 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 14 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 18 optimal weight: 0.0670 chunk 10 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 0 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 421 ASN B 468 ASN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.162824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.135810 restraints weight = 4643.119| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.50 r_work: 0.3266 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 1.5568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 3883 Z= 0.187 Angle : 0.761 18.274 5341 Z= 0.362 Chirality : 0.045 0.204 639 Planarity : 0.005 0.042 677 Dihedral : 5.513 27.183 668 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.48 % Allowed : 15.79 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.38), residues: 499 helix: 1.92 (0.51), residues: 117 sheet: 0.17 (0.42), residues: 158 loop : -1.12 (0.38), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 542 TYR 0.013 0.002 TYR A 499 PHE 0.011 0.002 PHE B 399 TRP 0.009 0.001 TRP D 38 HIS 0.003 0.002 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 3869) covalent geometry : angle 0.68159 ( 5307) SS BOND : bond 0.00761 ( 8) SS BOND : angle 2.67187 ( 16) hydrogen bonds : bond 0.03549 ( 176) hydrogen bonds : angle 4.88737 ( 477) link_BETA1-4 : bond 0.00147 ( 2) link_BETA1-4 : angle 2.46829 ( 6) link_NAG-ASN : bond 0.01161 ( 4) link_NAG-ASN : angle 6.32691 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.150 Fit side-chains revert: symmetry clash REVERT: B 542 ARG cc_start: 0.8821 (ptt-90) cc_final: 0.8518 (ptt180) REVERT: B 563 MET cc_start: 0.8299 (tpp) cc_final: 0.8071 (tpt) outliers start: 8 outliers final: 5 residues processed: 71 average time/residue: 0.0820 time to fit residues: 7.0567 Evaluate side-chains 66 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain C residue 37 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 2 optimal weight: 0.5980 chunk 14 optimal weight: 0.0870 chunk 15 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 4 optimal weight: 4.9990 chunk 0 optimal weight: 0.1980 chunk 25 optimal weight: 0.5980 chunk 30 optimal weight: 0.3980 chunk 10 optimal weight: 0.8980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 427 GLN ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.161773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.135110 restraints weight = 4692.818| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.75 r_work: 0.3285 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 1.6007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 3883 Z= 0.150 Angle : 0.781 21.309 5341 Z= 0.359 Chirality : 0.048 0.568 639 Planarity : 0.004 0.036 677 Dihedral : 5.578 34.974 668 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.41 % Allowed : 15.48 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.38), residues: 499 helix: 1.90 (0.50), residues: 117 sheet: 0.22 (0.42), residues: 158 loop : -1.08 (0.38), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 542 TYR 0.012 0.001 TYR A 445 PHE 0.008 0.001 PHE B 399 TRP 0.008 0.001 TRP D 34 HIS 0.002 0.001 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 3869) covalent geometry : angle 0.64524 ( 5307) SS BOND : bond 0.00806 ( 8) SS BOND : angle 2.47061 ( 16) hydrogen bonds : bond 0.03184 ( 176) hydrogen bonds : angle 4.80706 ( 477) link_BETA1-4 : bond 0.01024 ( 2) link_BETA1-4 : angle 3.56504 ( 6) link_NAG-ASN : bond 0.00497 ( 4) link_NAG-ASN : angle 8.55151 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 70 average time/residue: 0.0680 time to fit residues: 6.1204 Evaluate side-chains 72 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain C residue 37 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 12 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 39 optimal weight: 0.3980 chunk 9 optimal weight: 0.0070 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 427 GLN ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.159993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.135850 restraints weight = 4721.077| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.05 r_work: 0.3280 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 1.6760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 3883 Z= 0.165 Angle : 0.748 20.304 5341 Z= 0.348 Chirality : 0.048 0.581 639 Planarity : 0.006 0.114 677 Dihedral : 5.898 36.847 668 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.41 % Allowed : 17.34 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.38), residues: 499 helix: 1.55 (0.49), residues: 119 sheet: 0.56 (0.44), residues: 148 loop : -1.34 (0.38), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 542 TYR 0.012 0.002 TYR A 445 PHE 0.016 0.002 PHE C 55 TRP 0.023 0.002 TRP A 553 HIS 0.003 0.002 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 3869) covalent geometry : angle 0.63068 ( 5307) SS BOND : bond 0.01211 ( 8) SS BOND : angle 2.65169 ( 16) hydrogen bonds : bond 0.03248 ( 176) hydrogen bonds : angle 4.84434 ( 477) link_BETA1-4 : bond 0.00888 ( 2) link_BETA1-4 : angle 1.74623 ( 6) link_NAG-ASN : bond 0.01178 ( 4) link_NAG-ASN : angle 7.88742 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: B 563 MET cc_start: 0.8433 (tpp) cc_final: 0.8225 (tpt) REVERT: B 588 LEU cc_start: 0.6002 (OUTLIER) cc_final: 0.5794 (mp) REVERT: A 433 ILE cc_start: 0.8040 (tp) cc_final: 0.7819 (tp) REVERT: A 507 LEU cc_start: 0.3950 (OUTLIER) cc_final: 0.3736 (mt) REVERT: C 33 LEU cc_start: 0.8690 (tt) cc_final: 0.8351 (tp) outliers start: 11 outliers final: 5 residues processed: 66 average time/residue: 0.0619 time to fit residues: 5.2832 Evaluate side-chains 65 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain C residue 37 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 10 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 19 optimal weight: 0.0770 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 427 GLN ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN A 522 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.157088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.127352 restraints weight = 4717.504| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.92 r_work: 0.3191 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 1.7087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 3883 Z= 0.168 Angle : 0.676 10.586 5341 Z= 0.328 Chirality : 0.045 0.251 639 Planarity : 0.004 0.035 677 Dihedral : 9.663 102.322 668 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.79 % Allowed : 17.96 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.38), residues: 499 helix: 1.63 (0.49), residues: 119 sheet: 0.61 (0.44), residues: 148 loop : -1.37 (0.38), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 542 TYR 0.014 0.002 TYR A 409 PHE 0.009 0.001 PHE A 385 TRP 0.012 0.001 TRP A 553 HIS 0.002 0.001 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 3869) covalent geometry : angle 0.64823 ( 5307) SS BOND : bond 0.00888 ( 8) SS BOND : angle 2.76950 ( 16) hydrogen bonds : bond 0.03185 ( 176) hydrogen bonds : angle 4.81000 ( 477) link_BETA1-4 : bond 0.01840 ( 2) link_BETA1-4 : angle 2.38218 ( 6) link_NAG-ASN : bond 0.00910 ( 4) link_NAG-ASN : angle 2.08853 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 33 LEU cc_start: 0.8760 (tt) cc_final: 0.8468 (tp) outliers start: 9 outliers final: 6 residues processed: 71 average time/residue: 0.0623 time to fit residues: 5.7202 Evaluate side-chains 64 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain C residue 37 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 17 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 427 GLN B 468 ASN B 522 GLN A 466 GLN A 501 ASN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.152786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.122554 restraints weight = 4702.488| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.97 r_work: 0.3128 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 1.7946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 3883 Z= 0.207 Angle : 0.721 11.333 5341 Z= 0.351 Chirality : 0.046 0.283 639 Planarity : 0.005 0.039 677 Dihedral : 10.167 105.885 668 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.79 % Allowed : 18.27 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.37), residues: 499 helix: 1.45 (0.49), residues: 120 sheet: 0.52 (0.45), residues: 148 loop : -1.35 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 542 TYR 0.012 0.002 TYR A 523 PHE 0.019 0.002 PHE C 55 TRP 0.013 0.002 TRP A 553 HIS 0.004 0.002 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00507 ( 3869) covalent geometry : angle 0.68410 ( 5307) SS BOND : bond 0.00968 ( 8) SS BOND : angle 3.04498 ( 16) hydrogen bonds : bond 0.03623 ( 176) hydrogen bonds : angle 4.92842 ( 477) link_BETA1-4 : bond 0.01110 ( 2) link_BETA1-4 : angle 3.66504 ( 6) link_NAG-ASN : bond 0.01085 ( 4) link_NAG-ASN : angle 2.27974 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 491 ILE cc_start: 0.7814 (OUTLIER) cc_final: 0.7481 (mt) REVERT: B 588 LEU cc_start: 0.6341 (tt) cc_final: 0.6094 (mp) REVERT: A 563 MET cc_start: 0.7754 (mmt) cc_final: 0.7412 (mmt) REVERT: C 33 LEU cc_start: 0.8749 (tt) cc_final: 0.8467 (tp) outliers start: 9 outliers final: 6 residues processed: 66 average time/residue: 0.0438 time to fit residues: 3.7199 Evaluate side-chains 66 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain C residue 37 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 16 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 0.0980 chunk 6 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 42 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 468 ASN B 522 GLN A 421 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.153944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.124333 restraints weight = 4732.767| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.95 r_work: 0.3151 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 1.8153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 3883 Z= 0.151 Angle : 0.634 10.678 5341 Z= 0.315 Chirality : 0.043 0.213 639 Planarity : 0.004 0.031 677 Dihedral : 9.489 100.056 668 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.79 % Allowed : 18.58 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.38), residues: 499 helix: 1.59 (0.49), residues: 120 sheet: 0.62 (0.45), residues: 148 loop : -1.28 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 542 TYR 0.012 0.001 TYR A 445 PHE 0.013 0.001 PHE C 55 TRP 0.010 0.001 TRP B 553 HIS 0.003 0.002 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 3869) covalent geometry : angle 0.60324 ( 5307) SS BOND : bond 0.00873 ( 8) SS BOND : angle 3.01892 ( 16) hydrogen bonds : bond 0.03225 ( 176) hydrogen bonds : angle 4.84508 ( 477) link_BETA1-4 : bond 0.00242 ( 2) link_BETA1-4 : angle 1.82101 ( 6) link_NAG-ASN : bond 0.00515 ( 4) link_NAG-ASN : angle 2.07636 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 998 Ramachandran restraints generated. 499 Oldfield, 0 Emsley, 499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 34 TRP cc_start: 0.5390 (t-100) cc_final: 0.4506 (t60) REVERT: A 543 LYS cc_start: 0.8257 (ttmt) cc_final: 0.8041 (ttmt) REVERT: A 563 MET cc_start: 0.7677 (mmt) cc_final: 0.7458 (mmt) REVERT: C 33 LEU cc_start: 0.8671 (tt) cc_final: 0.8428 (tp) outliers start: 9 outliers final: 8 residues processed: 68 average time/residue: 0.0666 time to fit residues: 5.7439 Evaluate side-chains 70 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 383 CYS Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 522 GLN Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain A residue 496 LYS Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain C residue 37 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 16 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 29 optimal weight: 0.1980 chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 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 421 ASN A 522 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.153730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.123041 restraints weight = 4690.836| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.03 r_work: 0.3139 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 1.8119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.123 3883 Z= 0.264 Angle : 1.218 59.200 5341 Z= 0.729 Chirality : 0.046 0.332 639 Planarity : 0.004 0.032 677 Dihedral : 9.508 100.190 668 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.10 % Allowed : 18.27 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.38), residues: 499 helix: 1.63 (0.49), residues: 120 sheet: 0.62 (0.45), residues: 148 loop : -1.29 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 542 TYR 0.011 0.001 TYR A 445 PHE 0.012 0.001 PHE C 55 TRP 0.010 0.001 TRP B 553 HIS 0.002 0.001 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00557 ( 3869) covalent geometry : angle 1.20148 ( 5307) SS BOND : bond 0.00967 ( 8) SS BOND : angle 3.45193 ( 16) hydrogen bonds : bond 0.03235 ( 176) hydrogen bonds : angle 4.84284 ( 477) link_BETA1-4 : bond 0.00368 ( 2) link_BETA1-4 : angle 1.89539 ( 6) link_NAG-ASN : bond 0.00486 ( 4) link_NAG-ASN : angle 2.03362 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1507.75 seconds wall clock time: 26 minutes 25.88 seconds (1585.88 seconds total)