Starting phenix.real_space_refine on Fri Dec 27 09:59:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7osl_13054/12_2024/7osl_13054_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7osl_13054/12_2024/7osl_13054.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/7osl_13054/12_2024/7osl_13054.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7osl_13054/12_2024/7osl_13054.map" model { file = "/net/cci-nas-00/data/ceres_data/7osl_13054/12_2024/7osl_13054_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7osl_13054/12_2024/7osl_13054_neut.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= 0.001 sd= 0.007 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 S 63 5.16 5 C 15151 2.51 5 N 3935 2.21 5 O 4511 1.98 5 H 24225 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 225 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 47885 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 5319 Classifications: {'peptide': 326} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 316} Chain: "B" Number of atoms: 5333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 5333 Classifications: {'peptide': 327} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 317} Chain: "C" Number of atoms: 5319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 5319 Classifications: {'peptide': 326} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 316} Chain: "D" Number of atoms: 5319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 5319 Classifications: {'peptide': 326} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 316} Chain: "E" Number of atoms: 5319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 5319 Classifications: {'peptide': 326} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 316} Chain: "F" Number of atoms: 5319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 5319 Classifications: {'peptide': 326} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 316} Chain: "G" Number of atoms: 5319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 5319 Classifications: {'peptide': 326} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 316} Chain: "H" Number of atoms: 5319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 5319 Classifications: {'peptide': 326} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 316} Chain: "I" Number of atoms: 5319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 5319 Classifications: {'peptide': 326} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 316} Time building chain proxies: 16.21, per 1000 atoms: 0.34 Number of scatterers: 47885 At special positions: 0 Unit cell: (182.6, 180.4, 75.9, 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) S 63 16.00 O 4511 8.00 N 3935 7.00 C 15151 6.00 H 24225 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 9.33 Conformation dependent library (CDL) restraints added in 2.7 seconds 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5582 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 36 sheets defined 49.7% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.98 Creating SS restraints... Processing helix chain 'A' and resid 365 through 382 removed outlier: 3.928A pdb=" N TRP A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 458 Processing helix chain 'A' and resid 464 through 480 Processing helix chain 'A' and resid 481 through 485 removed outlier: 3.858A pdb=" N ILE A 485 " --> pdb=" O LYS A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 496 Processing helix chain 'A' and resid 501 through 512 Processing helix chain 'A' and resid 513 through 526 removed outlier: 3.674A pdb=" N ASP A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 545 removed outlier: 3.601A pdb=" N ILE A 537 " --> pdb=" O ASP A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 562 removed outlier: 4.266A pdb=" N GLU A 556 " --> pdb=" O VAL A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 571 Processing helix chain 'A' and resid 583 through 593 Processing helix chain 'A' and resid 606 through 621 Processing helix chain 'A' and resid 632 through 644 removed outlier: 4.846A pdb=" N ARG A 637 " --> pdb=" O LEU A 633 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N TYR A 638 " --> pdb=" O ASP A 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 382 removed outlier: 3.898A pdb=" N TRP B 375 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 458 Processing helix chain 'B' and resid 464 through 480 Processing helix chain 'B' and resid 481 through 485 removed outlier: 3.874A pdb=" N ILE B 485 " --> pdb=" O LYS B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 496 Processing helix chain 'B' and resid 501 through 512 Processing helix chain 'B' and resid 513 through 526 removed outlier: 3.688A pdb=" N ASP B 519 " --> pdb=" O SER B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 545 removed outlier: 3.588A pdb=" N ILE B 537 " --> pdb=" O ASP B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 562 removed outlier: 4.247A pdb=" N GLU B 556 " --> pdb=" O VAL B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 571 Processing helix chain 'B' and resid 583 through 593 Processing helix chain 'B' and resid 606 through 621 Processing helix chain 'B' and resid 632 through 644 removed outlier: 4.854A pdb=" N ARG B 637 " --> pdb=" O LEU B 633 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N TYR B 638 " --> pdb=" O ASP B 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 382 removed outlier: 3.863A pdb=" N TRP C 375 " --> pdb=" O GLU C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 458 removed outlier: 3.572A pdb=" N ALA C 454 " --> pdb=" O ASN C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 480 Processing helix chain 'C' and resid 481 through 485 removed outlier: 3.879A pdb=" N ILE C 485 " --> pdb=" O LYS C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 496 Processing helix chain 'C' and resid 501 through 512 Processing helix chain 'C' and resid 513 through 526 removed outlier: 3.662A pdb=" N ASP C 519 " --> pdb=" O SER C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 545 removed outlier: 3.601A pdb=" N ILE C 537 " --> pdb=" O ASP C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 562 removed outlier: 3.505A pdb=" N CYS C 555 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU C 556 " --> pdb=" O VAL C 552 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR C 557 " --> pdb=" O ILE C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 571 Processing helix chain 'C' and resid 583 through 593 Processing helix chain 'C' and resid 606 through 621 Processing helix chain 'C' and resid 632 through 644 removed outlier: 4.844A pdb=" N ARG C 637 " --> pdb=" O LEU C 633 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N TYR C 638 " --> pdb=" O ASP C 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 382 removed outlier: 3.868A pdb=" N TRP D 375 " --> pdb=" O GLU D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 458 Processing helix chain 'D' and resid 464 through 480 Processing helix chain 'D' and resid 481 through 485 removed outlier: 3.861A pdb=" N ILE D 485 " --> pdb=" O LYS D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 496 Processing helix chain 'D' and resid 501 through 512 Processing helix chain 'D' and resid 513 through 526 removed outlier: 3.690A pdb=" N ASP D 519 " --> pdb=" O SER D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 545 removed outlier: 3.615A pdb=" N ILE D 537 " --> pdb=" O ASP D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 562 removed outlier: 4.277A pdb=" N GLU D 556 " --> pdb=" O VAL D 552 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR D 557 " --> pdb=" O ILE D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 571 Processing helix chain 'D' and resid 583 through 593 Processing helix chain 'D' and resid 606 through 621 Processing helix chain 'D' and resid 632 through 644 removed outlier: 4.838A pdb=" N ARG D 637 " --> pdb=" O LEU D 633 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N TYR D 638 " --> pdb=" O ASP D 634 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 382 removed outlier: 3.882A pdb=" N TRP E 375 " --> pdb=" O GLU E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 450 through 458 Processing helix chain 'E' and resid 464 through 480 Processing helix chain 'E' and resid 481 through 485 removed outlier: 3.872A pdb=" N ILE E 485 " --> pdb=" O LYS E 482 " (cutoff:3.500A) Processing helix chain 'E' and resid 486 through 496 Processing helix chain 'E' and resid 501 through 512 Processing helix chain 'E' and resid 513 through 526 removed outlier: 3.698A pdb=" N ASP E 519 " --> pdb=" O SER E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 545 removed outlier: 3.605A pdb=" N ILE E 537 " --> pdb=" O ASP E 533 " (cutoff:3.500A) Processing helix chain 'E' and resid 550 through 562 removed outlier: 4.233A pdb=" N GLU E 556 " --> pdb=" O VAL E 552 " (cutoff:3.500A) Processing helix chain 'E' and resid 562 through 571 Processing helix chain 'E' and resid 583 through 593 Processing helix chain 'E' and resid 606 through 621 Processing helix chain 'E' and resid 632 through 644 removed outlier: 4.844A pdb=" N ARG E 637 " --> pdb=" O LEU E 633 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N TYR E 638 " --> pdb=" O ASP E 634 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 382 removed outlier: 3.886A pdb=" N TRP F 375 " --> pdb=" O GLU F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 450 through 458 Processing helix chain 'F' and resid 464 through 480 Processing helix chain 'F' and resid 481 through 485 removed outlier: 3.885A pdb=" N ILE F 485 " --> pdb=" O LYS F 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 486 through 496 Processing helix chain 'F' and resid 501 through 512 Processing helix chain 'F' and resid 513 through 526 removed outlier: 3.719A pdb=" N ASP F 519 " --> pdb=" O SER F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 533 through 545 removed outlier: 3.590A pdb=" N ILE F 537 " --> pdb=" O ASP F 533 " (cutoff:3.500A) Processing helix chain 'F' and resid 550 through 562 removed outlier: 4.269A pdb=" N GLU F 556 " --> pdb=" O VAL F 552 " (cutoff:3.500A) Processing helix chain 'F' and resid 562 through 571 Processing helix chain 'F' and resid 583 through 593 Processing helix chain 'F' and resid 606 through 621 Processing helix chain 'F' and resid 632 through 644 removed outlier: 4.845A pdb=" N ARG F 637 " --> pdb=" O LEU F 633 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N TYR F 638 " --> pdb=" O ASP F 634 " (cutoff:3.500A) Processing helix chain 'G' and resid 365 through 382 removed outlier: 3.902A pdb=" N TRP G 375 " --> pdb=" O GLU G 371 " (cutoff:3.500A) Processing helix chain 'G' and resid 450 through 458 Processing helix chain 'G' and resid 464 through 480 Processing helix chain 'G' and resid 481 through 485 removed outlier: 3.873A pdb=" N ILE G 485 " --> pdb=" O LYS G 482 " (cutoff:3.500A) Processing helix chain 'G' and resid 486 through 496 Processing helix chain 'G' and resid 501 through 512 Processing helix chain 'G' and resid 513 through 526 removed outlier: 3.652A pdb=" N ASP G 519 " --> pdb=" O SER G 515 " (cutoff:3.500A) Processing helix chain 'G' and resid 533 through 545 removed outlier: 3.611A pdb=" N ILE G 537 " --> pdb=" O ASP G 533 " (cutoff:3.500A) Processing helix chain 'G' and resid 550 through 562 removed outlier: 4.217A pdb=" N GLU G 556 " --> pdb=" O VAL G 552 " (cutoff:3.500A) Processing helix chain 'G' and resid 562 through 571 Processing helix chain 'G' and resid 583 through 593 Processing helix chain 'G' and resid 606 through 621 Processing helix chain 'G' and resid 632 through 644 removed outlier: 4.858A pdb=" N ARG G 637 " --> pdb=" O LEU G 633 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N TYR G 638 " --> pdb=" O ASP G 634 " (cutoff:3.500A) Processing helix chain 'H' and resid 365 through 382 removed outlier: 3.888A pdb=" N TRP H 375 " --> pdb=" O GLU H 371 " (cutoff:3.500A) Processing helix chain 'H' and resid 450 through 458 Processing helix chain 'H' and resid 464 through 480 Processing helix chain 'H' and resid 481 through 485 removed outlier: 3.877A pdb=" N ILE H 485 " --> pdb=" O LYS H 482 " (cutoff:3.500A) Processing helix chain 'H' and resid 486 through 496 Processing helix chain 'H' and resid 501 through 512 Processing helix chain 'H' and resid 513 through 526 removed outlier: 3.701A pdb=" N ASP H 519 " --> pdb=" O SER H 515 " (cutoff:3.500A) Processing helix chain 'H' and resid 533 through 545 removed outlier: 3.618A pdb=" N ILE H 537 " --> pdb=" O ASP H 533 " (cutoff:3.500A) Processing helix chain 'H' and resid 550 through 562 removed outlier: 4.238A pdb=" N GLU H 556 " --> pdb=" O VAL H 552 " (cutoff:3.500A) Processing helix chain 'H' and resid 562 through 571 Processing helix chain 'H' and resid 583 through 593 Processing helix chain 'H' and resid 606 through 621 Processing helix chain 'H' and resid 632 through 644 removed outlier: 4.836A pdb=" N ARG H 637 " --> pdb=" O LEU H 633 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N TYR H 638 " --> pdb=" O ASP H 634 " (cutoff:3.500A) Processing helix chain 'I' and resid 365 through 382 removed outlier: 3.894A pdb=" N TRP I 375 " --> pdb=" O GLU I 371 " (cutoff:3.500A) Processing helix chain 'I' and resid 450 through 458 Processing helix chain 'I' and resid 464 through 480 Processing helix chain 'I' and resid 481 through 485 removed outlier: 3.885A pdb=" N ILE I 485 " --> pdb=" O LYS I 482 " (cutoff:3.500A) Processing helix chain 'I' and resid 486 through 496 Processing helix chain 'I' and resid 501 through 512 Processing helix chain 'I' and resid 513 through 526 removed outlier: 3.690A pdb=" N ASP I 519 " --> pdb=" O SER I 515 " (cutoff:3.500A) Processing helix chain 'I' and resid 533 through 545 removed outlier: 3.619A pdb=" N ILE I 537 " --> pdb=" O ASP I 533 " (cutoff:3.500A) Processing helix chain 'I' and resid 550 through 562 removed outlier: 4.252A pdb=" N GLU I 556 " --> pdb=" O VAL I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 562 through 571 Processing helix chain 'I' and resid 583 through 593 Processing helix chain 'I' and resid 606 through 621 Processing helix chain 'I' and resid 632 through 644 removed outlier: 4.881A pdb=" N ARG I 637 " --> pdb=" O LEU I 633 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N TYR I 638 " --> pdb=" O ASP I 634 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 389 through 393 removed outlier: 6.837A pdb=" N LEU A 353 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ASN A 391 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU A 355 " --> pdb=" O ASN A 391 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL A 393 " --> pdb=" O LEU A 355 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU A 357 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ALA A 399 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR A 410 " --> pdb=" O PHE A 402 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU A 404 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N SER A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 433 through 438 removed outlier: 6.316A pdb=" N SER A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TYR A 444 " --> pdb=" O PHE A 421 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 652 through 654 removed outlier: 6.346A pdb=" N ILE A 629 " --> pdb=" O LEU A 653 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU A 577 " --> pdb=" O LYS A 665 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LEU A 667 " --> pdb=" O LEU A 577 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N VAL A 579 " --> pdb=" O LEU A 667 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR A 669 " --> pdb=" O VAL A 579 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU A 581 " --> pdb=" O THR A 669 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 594 through 597 Processing sheet with id=AA5, first strand: chain 'B' and resid 389 through 393 removed outlier: 6.833A pdb=" N LEU B 353 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ASN B 391 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU B 355 " --> pdb=" O ASN B 391 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL B 393 " --> pdb=" O LEU B 355 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU B 357 " --> pdb=" O VAL B 393 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ALA B 399 " --> pdb=" O SER B 358 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR B 410 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LEU B 404 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N SER B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 433 through 438 removed outlier: 6.310A pdb=" N SER B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TYR B 444 " --> pdb=" O PHE B 421 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 652 through 654 removed outlier: 6.329A pdb=" N ILE B 629 " --> pdb=" O LEU B 653 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU B 577 " --> pdb=" O LYS B 665 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LEU B 667 " --> pdb=" O LEU B 577 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL B 579 " --> pdb=" O LEU B 667 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR B 669 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU B 581 " --> pdb=" O THR B 669 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 594 through 597 Processing sheet with id=AA9, first strand: chain 'C' and resid 389 through 393 removed outlier: 6.861A pdb=" N LEU C 353 " --> pdb=" O ILE C 389 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ASN C 391 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU C 355 " --> pdb=" O ASN C 391 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL C 393 " --> pdb=" O LEU C 355 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU C 357 " --> pdb=" O VAL C 393 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ALA C 399 " --> pdb=" O SER C 358 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR C 410 " --> pdb=" O PHE C 402 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LEU C 404 " --> pdb=" O SER C 408 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N SER C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 433 through 438 removed outlier: 6.292A pdb=" N SER C 441 " --> pdb=" O LEU C 437 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR C 444 " --> pdb=" O PHE C 421 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 652 through 654 removed outlier: 6.333A pdb=" N ILE C 629 " --> pdb=" O LEU C 653 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU C 577 " --> pdb=" O LYS C 665 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N LEU C 667 " --> pdb=" O LEU C 577 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL C 579 " --> pdb=" O LEU C 667 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N THR C 669 " --> pdb=" O VAL C 579 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU C 581 " --> pdb=" O THR C 669 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 594 through 597 Processing sheet with id=AB4, first strand: chain 'D' and resid 389 through 393 removed outlier: 6.849A pdb=" N LEU D 353 " --> pdb=" O ILE D 389 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N ASN D 391 " --> pdb=" O LEU D 353 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU D 355 " --> pdb=" O ASN D 391 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N VAL D 393 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU D 357 " --> pdb=" O VAL D 393 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA D 399 " --> pdb=" O SER D 358 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR D 410 " --> pdb=" O PHE D 402 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU D 404 " --> pdb=" O SER D 408 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N SER D 408 " --> pdb=" O LEU D 404 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 433 through 438 removed outlier: 6.310A pdb=" N SER D 441 " --> pdb=" O LEU D 437 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N TYR D 444 " --> pdb=" O PHE D 421 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 652 through 654 removed outlier: 6.336A pdb=" N ILE D 629 " --> pdb=" O LEU D 653 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU D 577 " --> pdb=" O LYS D 665 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEU D 667 " --> pdb=" O LEU D 577 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N VAL D 579 " --> pdb=" O LEU D 667 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR D 669 " --> pdb=" O VAL D 579 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU D 581 " --> pdb=" O THR D 669 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 594 through 597 Processing sheet with id=AB8, first strand: chain 'E' and resid 389 through 393 removed outlier: 6.852A pdb=" N LEU E 353 " --> pdb=" O ILE E 389 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ASN E 391 " --> pdb=" O LEU E 353 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU E 355 " --> pdb=" O ASN E 391 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL E 393 " --> pdb=" O LEU E 355 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU E 357 " --> pdb=" O VAL E 393 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ALA E 399 " --> pdb=" O SER E 358 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR E 410 " --> pdb=" O PHE E 402 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU E 404 " --> pdb=" O SER E 408 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N SER E 408 " --> pdb=" O LEU E 404 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 433 through 438 removed outlier: 6.308A pdb=" N SER E 441 " --> pdb=" O LEU E 437 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TYR E 444 " --> pdb=" O PHE E 421 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 652 through 654 removed outlier: 6.352A pdb=" N ILE E 629 " --> pdb=" O LEU E 653 " (cutoff:3.500A) removed outlier: 9.430A pdb=" N VAL E 628 " --> pdb=" O LEU E 576 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ASN E 578 " --> pdb=" O VAL E 628 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU E 630 " --> pdb=" O ASN E 578 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TRP E 580 " --> pdb=" O LEU E 630 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU E 577 " --> pdb=" O LYS E 665 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEU E 667 " --> pdb=" O LEU E 577 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N VAL E 579 " --> pdb=" O LEU E 667 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N THR E 669 " --> pdb=" O VAL E 579 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU E 581 " --> pdb=" O THR E 669 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 594 through 597 Processing sheet with id=AC3, first strand: chain 'F' and resid 389 through 393 removed outlier: 6.856A pdb=" N LEU F 353 " --> pdb=" O ILE F 389 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N ASN F 391 " --> pdb=" O LEU F 353 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU F 355 " --> pdb=" O ASN F 391 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL F 393 " --> pdb=" O LEU F 355 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU F 357 " --> pdb=" O VAL F 393 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ALA F 399 " --> pdb=" O SER F 358 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR F 410 " --> pdb=" O PHE F 402 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU F 404 " --> pdb=" O SER F 408 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N SER F 408 " --> pdb=" O LEU F 404 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 433 through 438 removed outlier: 6.308A pdb=" N SER F 441 " --> pdb=" O LEU F 437 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N TYR F 444 " --> pdb=" O PHE F 421 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 652 through 654 removed outlier: 6.346A pdb=" N ILE F 629 " --> pdb=" O LEU F 653 " (cutoff:3.500A) removed outlier: 9.480A pdb=" N VAL F 628 " --> pdb=" O LEU F 576 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN F 578 " --> pdb=" O VAL F 628 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N LEU F 630 " --> pdb=" O ASN F 578 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TRP F 580 " --> pdb=" O LEU F 630 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU F 577 " --> pdb=" O LYS F 665 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N LEU F 667 " --> pdb=" O LEU F 577 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL F 579 " --> pdb=" O LEU F 667 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N THR F 669 " --> pdb=" O VAL F 579 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU F 581 " --> pdb=" O THR F 669 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'F' and resid 594 through 597 Processing sheet with id=AC7, first strand: chain 'G' and resid 389 through 393 removed outlier: 6.851A pdb=" N LEU G 353 " --> pdb=" O ILE G 389 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ASN G 391 " --> pdb=" O LEU G 353 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU G 355 " --> pdb=" O ASN G 391 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL G 393 " --> pdb=" O LEU G 355 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU G 357 " --> pdb=" O VAL G 393 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ALA G 399 " --> pdb=" O SER G 358 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR G 410 " --> pdb=" O PHE G 402 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU G 404 " --> pdb=" O SER G 408 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N SER G 408 " --> pdb=" O LEU G 404 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 433 through 438 removed outlier: 6.294A pdb=" N SER G 441 " --> pdb=" O LEU G 437 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N TYR G 444 " --> pdb=" O PHE G 421 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 652 through 654 removed outlier: 6.335A pdb=" N ILE G 629 " --> pdb=" O LEU G 653 " (cutoff:3.500A) removed outlier: 9.465A pdb=" N VAL G 628 " --> pdb=" O LEU G 576 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASN G 578 " --> pdb=" O VAL G 628 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU G 630 " --> pdb=" O ASN G 578 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TRP G 580 " --> pdb=" O LEU G 630 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU G 577 " --> pdb=" O LYS G 665 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU G 667 " --> pdb=" O LEU G 577 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N VAL G 579 " --> pdb=" O LEU G 667 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N THR G 669 " --> pdb=" O VAL G 579 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU G 581 " --> pdb=" O THR G 669 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'G' and resid 594 through 597 Processing sheet with id=AD2, first strand: chain 'H' and resid 389 through 393 removed outlier: 6.851A pdb=" N LEU H 353 " --> pdb=" O ILE H 389 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ASN H 391 " --> pdb=" O LEU H 353 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU H 355 " --> pdb=" O ASN H 391 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL H 393 " --> pdb=" O LEU H 355 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU H 357 " --> pdb=" O VAL H 393 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ALA H 399 " --> pdb=" O SER H 358 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR H 410 " --> pdb=" O PHE H 402 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU H 404 " --> pdb=" O SER H 408 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N SER H 408 " --> pdb=" O LEU H 404 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 433 through 438 removed outlier: 6.302A pdb=" N SER H 441 " --> pdb=" O LEU H 437 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N TYR H 444 " --> pdb=" O PHE H 421 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 652 through 654 removed outlier: 6.349A pdb=" N ILE H 629 " --> pdb=" O LEU H 653 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU H 577 " --> pdb=" O LYS H 665 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LEU H 667 " --> pdb=" O LEU H 577 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VAL H 579 " --> pdb=" O LEU H 667 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N THR H 669 " --> pdb=" O VAL H 579 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU H 581 " --> pdb=" O THR H 669 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 594 through 597 Processing sheet with id=AD6, first strand: chain 'I' and resid 389 through 393 removed outlier: 6.847A pdb=" N LEU I 353 " --> pdb=" O ILE I 389 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ASN I 391 " --> pdb=" O LEU I 353 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU I 355 " --> pdb=" O ASN I 391 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL I 393 " --> pdb=" O LEU I 355 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU I 357 " --> pdb=" O VAL I 393 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ALA I 399 " --> pdb=" O SER I 358 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR I 410 " --> pdb=" O PHE I 402 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU I 404 " --> pdb=" O SER I 408 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N SER I 408 " --> pdb=" O LEU I 404 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 433 through 438 removed outlier: 6.301A pdb=" N SER I 441 " --> pdb=" O LEU I 437 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N TYR I 444 " --> pdb=" O PHE I 421 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 652 through 654 removed outlier: 6.319A pdb=" N ILE I 629 " --> pdb=" O LEU I 653 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU I 577 " --> pdb=" O LYS I 665 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LEU I 667 " --> pdb=" O LEU I 577 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N VAL I 579 " --> pdb=" O LEU I 667 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR I 669 " --> pdb=" O VAL I 579 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU I 581 " --> pdb=" O THR I 669 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 594 through 597 1166 hydrogen bonds defined for protein. 3372 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: 14.36 Time building geometry restraints manager: 11.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.02: 24216 1.02 - 1.22: 9 1.22 - 1.41: 9636 1.41 - 1.61: 14285 1.61 - 1.81: 117 Bond restraints: 48263 Sorted by residual: bond pdb=" N ASN G 345 " pdb=" H1 ASN G 345 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" N ASN B 345 " pdb=" H1 ASN B 345 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" N ASN E 345 " pdb=" H1 ASN E 345 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" N ASN D 345 " pdb=" H1 ASN D 345 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" N ASN C 345 " pdb=" H1 ASN C 345 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.48e+01 ... (remaining 48258 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 83394 2.08 - 4.17: 3737 4.17 - 6.25: 298 6.25 - 8.33: 75 8.33 - 10.42: 18 Bond angle restraints: 87522 Sorted by residual: angle pdb=" C ARG E 499 " pdb=" N LYS E 500 " pdb=" CA LYS E 500 " ideal model delta sigma weight residual 121.85 132.23 -10.38 1.77e+00 3.19e-01 3.44e+01 angle pdb=" C ARG B 499 " pdb=" N LYS B 500 " pdb=" CA LYS B 500 " ideal model delta sigma weight residual 121.85 132.15 -10.30 1.77e+00 3.19e-01 3.39e+01 angle pdb=" C ARG H 499 " pdb=" N LYS H 500 " pdb=" CA LYS H 500 " ideal model delta sigma weight residual 121.85 132.12 -10.27 1.77e+00 3.19e-01 3.37e+01 angle pdb=" C ARG G 499 " pdb=" N LYS G 500 " pdb=" CA LYS G 500 " ideal model delta sigma weight residual 121.85 132.12 -10.27 1.77e+00 3.19e-01 3.36e+01 angle pdb=" C ARG D 499 " pdb=" N LYS D 500 " pdb=" CA LYS D 500 " ideal model delta sigma weight residual 121.85 132.10 -10.25 1.77e+00 3.19e-01 3.35e+01 ... (remaining 87517 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 20582 17.99 - 35.99: 1118 35.99 - 53.98: 340 53.98 - 71.98: 348 71.98 - 89.97: 11 Dihedral angle restraints: 22399 sinusoidal: 12505 harmonic: 9894 Sorted by residual: dihedral pdb=" CD ARG C 510 " pdb=" NE ARG C 510 " pdb=" CZ ARG C 510 " pdb=" NH1 ARG C 510 " ideal model delta sinusoidal sigma weight residual 0.00 -32.44 32.44 1 1.00e+01 1.00e-02 1.50e+01 dihedral pdb=" CD ARG F 510 " pdb=" NE ARG F 510 " pdb=" CZ ARG F 510 " pdb=" NH1 ARG F 510 " ideal model delta sinusoidal sigma weight residual 0.00 -32.18 32.18 1 1.00e+01 1.00e-02 1.47e+01 dihedral pdb=" CD ARG B 510 " pdb=" NE ARG B 510 " pdb=" CZ ARG B 510 " pdb=" NH1 ARG B 510 " ideal model delta sinusoidal sigma weight residual 0.00 -32.15 32.15 1 1.00e+01 1.00e-02 1.47e+01 ... (remaining 22396 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2540 0.061 - 0.121: 994 0.121 - 0.182: 222 0.182 - 0.242: 53 0.242 - 0.303: 35 Chirality restraints: 3844 Sorted by residual: chirality pdb=" CA ILE I 496 " pdb=" N ILE I 496 " pdb=" C ILE I 496 " pdb=" CB ILE I 496 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA ILE G 496 " pdb=" N ILE G 496 " pdb=" C ILE G 496 " pdb=" CB ILE G 496 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CA ILE H 496 " pdb=" N ILE H 496 " pdb=" C ILE H 496 " pdb=" CB ILE H 496 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 3841 not shown) Planarity restraints: 6960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 535 " -0.095 9.50e-02 1.11e+02 6.57e-02 7.54e+01 pdb=" NE ARG B 535 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG B 535 " -0.056 2.00e-02 2.50e+03 pdb=" NH1 ARG B 535 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG B 535 " 0.115 2.00e-02 2.50e+03 pdb="HH11 ARG B 535 " -0.014 2.00e-02 2.50e+03 pdb="HH12 ARG B 535 " 0.052 2.00e-02 2.50e+03 pdb="HH21 ARG B 535 " 0.009 2.00e-02 2.50e+03 pdb="HH22 ARG B 535 " -0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 535 " -0.096 9.50e-02 1.11e+02 6.54e-02 7.42e+01 pdb=" NE ARG C 535 " 0.006 2.00e-02 2.50e+03 pdb=" CZ ARG C 535 " -0.055 2.00e-02 2.50e+03 pdb=" NH1 ARG C 535 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 535 " 0.115 2.00e-02 2.50e+03 pdb="HH11 ARG C 535 " -0.015 2.00e-02 2.50e+03 pdb="HH12 ARG C 535 " 0.049 2.00e-02 2.50e+03 pdb="HH21 ARG C 535 " 0.010 2.00e-02 2.50e+03 pdb="HH22 ARG C 535 " -0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 535 " 0.097 9.50e-02 1.11e+02 6.55e-02 7.41e+01 pdb=" NE ARG G 535 " -0.007 2.00e-02 2.50e+03 pdb=" CZ ARG G 535 " 0.056 2.00e-02 2.50e+03 pdb=" NH1 ARG G 535 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG G 535 " -0.115 2.00e-02 2.50e+03 pdb="HH11 ARG G 535 " 0.014 2.00e-02 2.50e+03 pdb="HH12 ARG G 535 " -0.049 2.00e-02 2.50e+03 pdb="HH21 ARG G 535 " -0.009 2.00e-02 2.50e+03 pdb="HH22 ARG G 535 " 0.100 2.00e-02 2.50e+03 ... (remaining 6957 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 2504 2.21 - 2.81: 98298 2.81 - 3.40: 120593 3.40 - 4.00: 156727 4.00 - 4.60: 246052 Nonbonded interactions: 624174 Sorted by model distance: nonbonded pdb=" O PRO E 648 " pdb=" HG SER E 649 " model vdw 1.610 2.450 nonbonded pdb=" O PRO A 648 " pdb=" HG SER A 649 " model vdw 1.613 2.450 nonbonded pdb=" O PRO H 648 " pdb=" HG SER H 649 " model vdw 1.618 2.450 nonbonded pdb=" O PRO C 648 " pdb=" HG SER C 649 " model vdw 1.618 2.450 nonbonded pdb=" O PRO D 648 " pdb=" HG SER D 649 " model vdw 1.618 2.450 ... (remaining 624169 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' selection = (chain 'B' and resid 345 through 670) selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 0.530 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.630 Extract box with map and model: 1.470 Check model and map are aligned: 0.270 Set scattering table: 0.350 Process input model: 71.580 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6516 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 : 0.010 0.063 24038 Z= 0.609 Angle : 1.263 10.417 32537 Z= 0.790 Chirality : 0.071 0.303 3844 Planarity : 0.008 0.116 4115 Dihedral : 12.138 83.575 9084 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 0.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: -2.09 (0.13), residues: 2917 helix: -1.89 (0.11), residues: 1386 sheet: -0.16 (0.20), residues: 560 loop : -0.98 (0.17), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP D 375 HIS 0.011 0.004 HIS B 565 PHE 0.028 0.003 PHE I 647 TYR 0.025 0.006 TYR C 405 ARG 0.126 0.016 ARG F 510 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 444 time to evaluate : 2.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 MET cc_start: 0.6626 (ttp) cc_final: 0.6215 (ttt) REVERT: A 626 ASN cc_start: 0.6954 (t0) cc_final: 0.6665 (m110) REVERT: B 371 GLU cc_start: 0.7039 (mm-30) cc_final: 0.6598 (tp30) REVERT: B 380 GLU cc_start: 0.7001 (tt0) cc_final: 0.6774 (tt0) REVERT: B 409 ILE cc_start: 0.7770 (tp) cc_final: 0.7354 (pt) REVERT: C 371 GLU cc_start: 0.6922 (mm-30) cc_final: 0.6585 (tm-30) REVERT: C 373 MET cc_start: 0.6779 (ttp) cc_final: 0.6331 (ttt) REVERT: C 375 TRP cc_start: 0.6038 (m100) cc_final: 0.5771 (m100) REVERT: C 626 ASN cc_start: 0.6933 (t0) cc_final: 0.6720 (m110) REVERT: D 371 GLU cc_start: 0.7068 (mm-30) cc_final: 0.6297 (tp30) REVERT: D 397 ASP cc_start: 0.5679 (t0) cc_final: 0.5396 (t0) REVERT: D 626 ASN cc_start: 0.6845 (t0) cc_final: 0.6537 (m-40) REVERT: E 371 GLU cc_start: 0.7136 (mm-30) cc_final: 0.6917 (tm-30) REVERT: E 387 LYS cc_start: 0.7645 (mtpt) cc_final: 0.7326 (mmmt) REVERT: E 409 ILE cc_start: 0.7461 (tp) cc_final: 0.7044 (pt) REVERT: E 543 PHE cc_start: 0.8160 (t80) cc_final: 0.7884 (t80) REVERT: E 550 ASP cc_start: 0.7518 (m-30) cc_final: 0.7280 (m-30) REVERT: E 626 ASN cc_start: 0.6600 (t0) cc_final: 0.6352 (m-40) REVERT: E 637 ARG cc_start: 0.6919 (tpt170) cc_final: 0.6554 (tpp-160) REVERT: F 387 LYS cc_start: 0.7610 (mtpt) cc_final: 0.7401 (mttp) REVERT: F 516 LYS cc_start: 0.7852 (tttt) cc_final: 0.7569 (ttmt) REVERT: F 626 ASN cc_start: 0.6641 (t0) cc_final: 0.6372 (m-40) REVERT: G 543 PHE cc_start: 0.8367 (t80) cc_final: 0.8128 (t80) REVERT: G 626 ASN cc_start: 0.6673 (t0) cc_final: 0.6282 (m-40) REVERT: H 371 GLU cc_start: 0.7021 (mm-30) cc_final: 0.6172 (tp30) REVERT: H 626 ASN cc_start: 0.6968 (t0) cc_final: 0.6586 (m-40) REVERT: H 637 ARG cc_start: 0.7087 (tpt170) cc_final: 0.6665 (tpp-160) REVERT: I 371 GLU cc_start: 0.6968 (mm-30) cc_final: 0.6563 (tp30) REVERT: I 387 LYS cc_start: 0.7573 (mtpt) cc_final: 0.7355 (mtpp) REVERT: I 407 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7260 (mm-30) REVERT: I 626 ASN cc_start: 0.6934 (t0) cc_final: 0.6423 (m-40) outliers start: 0 outliers final: 0 residues processed: 444 average time/residue: 0.6741 time to fit residues: 456.7056 Evaluate side-chains 236 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 2.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 0.9990 chunk 218 optimal weight: 9.9990 chunk 121 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 chunk 147 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 225 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 168 optimal weight: 10.0000 chunk 261 optimal weight: 6.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN B 360 ASN B 395 ASN C 395 ASN D 395 ASN E 395 ASN F 395 ASN G 395 ASN H 395 ASN I 395 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6446 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24038 Z= 0.215 Angle : 0.648 6.313 32537 Z= 0.372 Chirality : 0.047 0.184 3844 Planarity : 0.005 0.045 4115 Dihedral : 4.730 23.017 3178 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.48 % Allowed : 3.65 % Favored : 95.87 % 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: -0.24 (0.15), residues: 2917 helix: 0.30 (0.14), residues: 1386 sheet: -0.14 (0.20), residues: 576 loop : -0.62 (0.19), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 580 HIS 0.002 0.001 HIS G 565 PHE 0.015 0.002 PHE I 647 TYR 0.008 0.001 TYR H 557 ARG 0.009 0.001 ARG G 510 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 226 time to evaluate : 2.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 626 ASN cc_start: 0.6906 (t0) cc_final: 0.6591 (m110) REVERT: B 371 GLU cc_start: 0.6970 (mm-30) cc_final: 0.6393 (tp30) REVERT: B 409 ILE cc_start: 0.7740 (tp) cc_final: 0.7352 (pt) REVERT: B 642 MET cc_start: 0.6452 (ttm) cc_final: 0.5997 (mtp) REVERT: C 626 ASN cc_start: 0.7054 (t0) cc_final: 0.6437 (m-40) REVERT: C 655 PHE cc_start: 0.7162 (m-80) cc_final: 0.6466 (m-80) REVERT: D 397 ASP cc_start: 0.5538 (t0) cc_final: 0.5264 (t0) REVERT: D 626 ASN cc_start: 0.6951 (t0) cc_final: 0.6429 (m-40) REVERT: E 371 GLU cc_start: 0.6967 (mm-30) cc_final: 0.6487 (tp30) REVERT: E 387 LYS cc_start: 0.7658 (mtpt) cc_final: 0.7280 (mmmt) REVERT: E 409 ILE cc_start: 0.7476 (tp) cc_final: 0.7169 (pt) REVERT: E 516 LYS cc_start: 0.7358 (tttt) cc_final: 0.7081 (ttmt) REVERT: E 626 ASN cc_start: 0.6535 (t0) cc_final: 0.6122 (m-40) REVERT: F 387 LYS cc_start: 0.7577 (mtpt) cc_final: 0.7376 (mmtt) REVERT: F 626 ASN cc_start: 0.6966 (t0) cc_final: 0.6452 (m-40) REVERT: G 626 ASN cc_start: 0.6771 (t0) cc_final: 0.6263 (m-40) REVERT: H 626 ASN cc_start: 0.7086 (t0) cc_final: 0.6526 (m-40) REVERT: H 637 ARG cc_start: 0.7098 (tpt170) cc_final: 0.6499 (tpp-160) REVERT: I 371 GLU cc_start: 0.6992 (mm-30) cc_final: 0.6699 (tp30) REVERT: I 407 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7407 (mm-30) REVERT: I 626 ASN cc_start: 0.7065 (t0) cc_final: 0.6669 (t0) REVERT: I 655 PHE cc_start: 0.7396 (m-80) cc_final: 0.7122 (m-80) outliers start: 13 outliers final: 12 residues processed: 230 average time/residue: 0.7237 time to fit residues: 249.4545 Evaluate side-chains 197 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 185 time to evaluate : 2.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain D residue 619 ASN Chi-restraints excluded: chain D residue 631 THR Chi-restraints excluded: chain E residue 368 GLN Chi-restraints excluded: chain E residue 631 THR Chi-restraints excluded: chain F residue 631 THR Chi-restraints excluded: chain G residue 631 THR Chi-restraints excluded: chain G residue 642 MET Chi-restraints excluded: chain H residue 368 GLN Chi-restraints excluded: chain H residue 631 THR Chi-restraints excluded: chain I residue 631 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 217 optimal weight: 10.0000 chunk 178 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 262 optimal weight: 0.4980 chunk 283 optimal weight: 0.7980 chunk 233 optimal weight: 0.3980 chunk 259 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 210 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6444 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24038 Z= 0.177 Angle : 0.533 6.170 32537 Z= 0.303 Chirality : 0.044 0.174 3844 Planarity : 0.003 0.035 4115 Dihedral : 4.549 23.910 3178 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.63 % Allowed : 4.98 % Favored : 94.39 % 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: 0.31 (0.15), residues: 2917 helix: 0.93 (0.14), residues: 1386 sheet: -0.26 (0.20), residues: 576 loop : -0.39 (0.20), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 580 HIS 0.002 0.001 HIS D 565 PHE 0.010 0.001 PHE D 378 TYR 0.006 0.001 TYR C 405 ARG 0.005 0.000 ARG A 510 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 201 time to evaluate : 2.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 626 ASN cc_start: 0.6971 (t0) cc_final: 0.6625 (m110) REVERT: B 371 GLU cc_start: 0.6913 (mm-30) cc_final: 0.6436 (tp30) REVERT: B 409 ILE cc_start: 0.7731 (tp) cc_final: 0.7356 (pt) REVERT: B 642 MET cc_start: 0.6519 (ttm) cc_final: 0.6164 (mtp) REVERT: B 655 PHE cc_start: 0.7587 (m-80) cc_final: 0.7193 (m-80) REVERT: C 626 ASN cc_start: 0.7137 (t0) cc_final: 0.6503 (m-40) REVERT: C 655 PHE cc_start: 0.7062 (m-80) cc_final: 0.6271 (m-80) REVERT: D 397 ASP cc_start: 0.5689 (t0) cc_final: 0.5413 (t0) REVERT: D 626 ASN cc_start: 0.7010 (t0) cc_final: 0.6673 (t0) REVERT: E 387 LYS cc_start: 0.7657 (mtpt) cc_final: 0.7284 (mmmt) REVERT: E 409 ILE cc_start: 0.7490 (tp) cc_final: 0.7165 (pt) REVERT: E 516 LYS cc_start: 0.7333 (tttt) cc_final: 0.7045 (mttp) REVERT: E 626 ASN cc_start: 0.6508 (t0) cc_final: 0.6192 (t0) REVERT: F 387 LYS cc_start: 0.7571 (mtpt) cc_final: 0.7371 (mmtt) REVERT: F 516 LYS cc_start: 0.7252 (tttt) cc_final: 0.6975 (ttmt) REVERT: F 543 PHE cc_start: 0.8006 (t80) cc_final: 0.7780 (t80) REVERT: F 626 ASN cc_start: 0.6916 (t0) cc_final: 0.6397 (m-40) REVERT: F 655 PHE cc_start: 0.7196 (m-80) cc_final: 0.6502 (m-80) REVERT: G 655 PHE cc_start: 0.7169 (m-80) cc_final: 0.6896 (m-80) REVERT: H 626 ASN cc_start: 0.7093 (t0) cc_final: 0.6487 (m-40) REVERT: I 371 GLU cc_start: 0.6914 (mm-30) cc_final: 0.6612 (tp30) REVERT: I 407 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7523 (mm-30) REVERT: I 626 ASN cc_start: 0.7052 (t0) cc_final: 0.6677 (t0) REVERT: I 655 PHE cc_start: 0.7390 (m-80) cc_final: 0.7149 (m-80) outliers start: 17 outliers final: 15 residues processed: 211 average time/residue: 0.7545 time to fit residues: 237.7667 Evaluate side-chains 188 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 173 time to evaluate : 2.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain D residue 631 THR Chi-restraints excluded: chain E residue 368 GLN Chi-restraints excluded: chain E residue 397 ASP Chi-restraints excluded: chain E residue 631 THR Chi-restraints excluded: chain F residue 631 THR Chi-restraints excluded: chain G residue 579 VAL Chi-restraints excluded: chain G residue 631 THR Chi-restraints excluded: chain H residue 368 GLN Chi-restraints excluded: chain H residue 631 THR Chi-restraints excluded: chain H residue 642 MET Chi-restraints excluded: chain I residue 631 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 6.9990 chunk 196 optimal weight: 0.9990 chunk 135 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 262 optimal weight: 4.9990 chunk 278 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 249 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6483 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24038 Z= 0.233 Angle : 0.535 6.176 32537 Z= 0.303 Chirality : 0.044 0.182 3844 Planarity : 0.003 0.038 4115 Dihedral : 4.527 23.997 3178 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.74 % Allowed : 5.35 % Favored : 93.91 % 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: 0.36 (0.16), residues: 2917 helix: 1.06 (0.14), residues: 1386 sheet: -0.38 (0.19), residues: 576 loop : -0.41 (0.21), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 375 HIS 0.002 0.001 HIS B 565 PHE 0.011 0.001 PHE E 378 TYR 0.009 0.001 TYR C 405 ARG 0.007 0.001 ARG F 637 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 2.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 626 ASN cc_start: 0.7035 (t0) cc_final: 0.6649 (m110) REVERT: B 371 GLU cc_start: 0.6967 (mm-30) cc_final: 0.6456 (tp30) REVERT: B 409 ILE cc_start: 0.7713 (tp) cc_final: 0.7338 (pt) REVERT: B 642 MET cc_start: 0.6583 (ttm) cc_final: 0.6199 (mtp) REVERT: B 655 PHE cc_start: 0.7469 (m-80) cc_final: 0.6985 (m-80) REVERT: C 626 ASN cc_start: 0.7325 (t0) cc_final: 0.6636 (m-40) REVERT: C 637 ARG cc_start: 0.6624 (tpt170) cc_final: 0.6388 (tpt170) REVERT: C 655 PHE cc_start: 0.7012 (m-80) cc_final: 0.6169 (m-80) REVERT: D 397 ASP cc_start: 0.5513 (t0) cc_final: 0.5302 (t0) REVERT: D 626 ASN cc_start: 0.7036 (t0) cc_final: 0.6706 (t0) REVERT: E 387 LYS cc_start: 0.7634 (mtpt) cc_final: 0.7232 (mmmt) REVERT: E 409 ILE cc_start: 0.7439 (tp) cc_final: 0.7166 (pt) REVERT: E 516 LYS cc_start: 0.7312 (tttt) cc_final: 0.7017 (mttp) REVERT: E 626 ASN cc_start: 0.6711 (t0) cc_final: 0.6421 (t0) REVERT: F 516 LYS cc_start: 0.7261 (tttt) cc_final: 0.7058 (ttmt) REVERT: F 626 ASN cc_start: 0.6903 (t0) cc_final: 0.6383 (m-40) REVERT: G 642 MET cc_start: 0.6892 (OUTLIER) cc_final: 0.5948 (mtp) REVERT: G 655 PHE cc_start: 0.7182 (m-80) cc_final: 0.6879 (m-80) REVERT: H 626 ASN cc_start: 0.7187 (t0) cc_final: 0.6552 (m-40) REVERT: I 371 GLU cc_start: 0.6992 (mm-30) cc_final: 0.6722 (tp30) REVERT: I 626 ASN cc_start: 0.6988 (t0) cc_final: 0.6613 (t0) REVERT: I 642 MET cc_start: 0.6489 (ttm) cc_final: 0.5995 (mtp) REVERT: I 655 PHE cc_start: 0.7398 (m-80) cc_final: 0.7082 (m-80) outliers start: 20 outliers final: 16 residues processed: 199 average time/residue: 0.6894 time to fit residues: 219.3731 Evaluate side-chains 190 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 2.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain D residue 631 THR Chi-restraints excluded: chain E residue 368 GLN Chi-restraints excluded: chain E residue 397 ASP Chi-restraints excluded: chain E residue 631 THR Chi-restraints excluded: chain F residue 631 THR Chi-restraints excluded: chain F residue 642 MET Chi-restraints excluded: chain G residue 579 VAL Chi-restraints excluded: chain G residue 631 THR Chi-restraints excluded: chain G residue 642 MET Chi-restraints excluded: chain H residue 368 GLN Chi-restraints excluded: chain H residue 397 ASP Chi-restraints excluded: chain H residue 631 THR Chi-restraints excluded: chain I residue 631 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 2.9990 chunk 158 optimal weight: 0.0570 chunk 4 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 237 optimal weight: 3.9990 chunk 192 optimal weight: 0.0870 chunk 0 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 249 optimal weight: 0.0870 chunk 70 optimal weight: 3.9990 overall best weight: 0.6256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 450 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 24038 Z= 0.123 Angle : 0.466 5.202 32537 Z= 0.261 Chirality : 0.043 0.159 3844 Planarity : 0.003 0.040 4115 Dihedral : 4.313 23.812 3178 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.44 % Allowed : 5.94 % Favored : 93.62 % 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: 0.78 (0.16), residues: 2917 helix: 1.45 (0.14), residues: 1386 sheet: -0.28 (0.19), residues: 576 loop : -0.18 (0.21), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP E 580 HIS 0.001 0.000 HIS G 425 PHE 0.011 0.001 PHE F 543 TYR 0.004 0.001 TYR G 444 ARG 0.004 0.000 ARG F 637 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 180 time to evaluate : 3.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 PHE cc_start: 0.7667 (t80) cc_final: 0.7432 (t80) REVERT: A 626 ASN cc_start: 0.6979 (t0) cc_final: 0.6627 (m110) REVERT: B 371 GLU cc_start: 0.6864 (mm-30) cc_final: 0.6473 (tp30) REVERT: B 375 TRP cc_start: 0.5727 (m100) cc_final: 0.5473 (t-100) REVERT: B 409 ILE cc_start: 0.7713 (tp) cc_final: 0.7365 (pt) REVERT: B 642 MET cc_start: 0.6490 (ttm) cc_final: 0.6210 (mtp) REVERT: B 655 PHE cc_start: 0.7399 (m-80) cc_final: 0.6943 (m-80) REVERT: C 626 ASN cc_start: 0.7043 (t0) cc_final: 0.6381 (m-40) REVERT: C 637 ARG cc_start: 0.6642 (tpt170) cc_final: 0.6418 (tpt170) REVERT: C 655 PHE cc_start: 0.7109 (m-80) cc_final: 0.6325 (m-80) REVERT: D 397 ASP cc_start: 0.5474 (t0) cc_final: 0.5132 (t0) REVERT: D 626 ASN cc_start: 0.6998 (t0) cc_final: 0.6646 (t0) REVERT: E 387 LYS cc_start: 0.7621 (mtpt) cc_final: 0.7245 (mmmt) REVERT: E 409 ILE cc_start: 0.7450 (tp) cc_final: 0.7203 (pt) REVERT: E 626 ASN cc_start: 0.6601 (t0) cc_final: 0.6322 (t0) REVERT: F 516 LYS cc_start: 0.7216 (tttt) cc_final: 0.6988 (ttmt) REVERT: F 626 ASN cc_start: 0.6857 (t0) cc_final: 0.6343 (m-40) REVERT: F 637 ARG cc_start: 0.7057 (tpt-90) cc_final: 0.6377 (tpt170) REVERT: G 642 MET cc_start: 0.6858 (ttm) cc_final: 0.6242 (mtp) REVERT: G 655 PHE cc_start: 0.7197 (m-80) cc_final: 0.6833 (m-80) REVERT: H 626 ASN cc_start: 0.7152 (t0) cc_final: 0.6510 (m-40) REVERT: H 637 ARG cc_start: 0.6776 (tpt170) cc_final: 0.6214 (tpt170) REVERT: I 371 GLU cc_start: 0.6848 (mm-30) cc_final: 0.6555 (tp30) REVERT: I 626 ASN cc_start: 0.7087 (t0) cc_final: 0.6712 (t0) REVERT: I 642 MET cc_start: 0.6357 (ttm) cc_final: 0.5924 (mtp) REVERT: I 655 PHE cc_start: 0.7399 (m-80) cc_final: 0.7094 (m-80) outliers start: 12 outliers final: 12 residues processed: 188 average time/residue: 0.6582 time to fit residues: 196.3091 Evaluate side-chains 182 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 170 time to evaluate : 3.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain D residue 631 THR Chi-restraints excluded: chain E residue 368 GLN Chi-restraints excluded: chain E residue 397 ASP Chi-restraints excluded: chain E residue 631 THR Chi-restraints excluded: chain F residue 631 THR Chi-restraints excluded: chain G residue 579 VAL Chi-restraints excluded: chain H residue 368 GLN Chi-restraints excluded: chain H residue 397 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 6.9990 chunk 250 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 163 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 278 optimal weight: 4.9990 chunk 231 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 92 optimal weight: 8.9990 chunk 146 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6520 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 24038 Z= 0.337 Angle : 0.572 6.671 32537 Z= 0.322 Chirality : 0.046 0.196 3844 Planarity : 0.004 0.036 4115 Dihedral : 4.493 23.805 3178 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.92 % Allowed : 5.94 % Favored : 93.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.15), residues: 2917 helix: 1.13 (0.14), residues: 1386 sheet: -0.44 (0.19), residues: 576 loop : -0.50 (0.21), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 375 HIS 0.003 0.001 HIS B 565 PHE 0.013 0.002 PHE E 471 TYR 0.013 0.002 TYR I 405 ARG 0.004 0.001 ARG I 510 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 2.948 Fit side-chains revert: symmetry clash REVERT: A 626 ASN cc_start: 0.7004 (t0) cc_final: 0.6550 (m-40) REVERT: B 371 GLU cc_start: 0.6986 (mm-30) cc_final: 0.6464 (tp30) REVERT: B 409 ILE cc_start: 0.7602 (tp) cc_final: 0.7252 (pt) REVERT: B 655 PHE cc_start: 0.7423 (m-80) cc_final: 0.6882 (m-80) REVERT: C 626 ASN cc_start: 0.7075 (t0) cc_final: 0.6416 (m-40) REVERT: C 637 ARG cc_start: 0.6646 (tpt170) cc_final: 0.6369 (tpt170) REVERT: C 655 PHE cc_start: 0.7027 (m-80) cc_final: 0.6196 (m-80) REVERT: D 626 ASN cc_start: 0.6998 (t0) cc_final: 0.6478 (m-40) REVERT: E 387 LYS cc_start: 0.7532 (mtpt) cc_final: 0.7151 (mmmt) REVERT: E 409 ILE cc_start: 0.7438 (tp) cc_final: 0.7129 (pt) REVERT: E 626 ASN cc_start: 0.6733 (t0) cc_final: 0.6384 (t0) REVERT: F 626 ASN cc_start: 0.6916 (t0) cc_final: 0.6612 (t0) REVERT: G 642 MET cc_start: 0.6794 (ttm) cc_final: 0.6189 (mtp) REVERT: H 637 ARG cc_start: 0.6831 (tpt170) cc_final: 0.6272 (tpt170) REVERT: H 642 MET cc_start: 0.6648 (OUTLIER) cc_final: 0.5872 (mtp) REVERT: I 371 GLU cc_start: 0.6944 (mm-30) cc_final: 0.6685 (tp30) REVERT: I 437 LEU cc_start: 0.6973 (OUTLIER) cc_final: 0.6711 (mp) REVERT: I 642 MET cc_start: 0.6274 (ttm) cc_final: 0.5906 (mtp) REVERT: I 655 PHE cc_start: 0.7340 (m-80) cc_final: 0.7013 (m-80) outliers start: 25 outliers final: 21 residues processed: 188 average time/residue: 0.6560 time to fit residues: 195.6241 Evaluate side-chains 185 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 2.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain D residue 631 THR Chi-restraints excluded: chain E residue 368 GLN Chi-restraints excluded: chain E residue 397 ASP Chi-restraints excluded: chain E residue 621 MET Chi-restraints excluded: chain E residue 631 THR Chi-restraints excluded: chain F residue 631 THR Chi-restraints excluded: chain F residue 642 MET Chi-restraints excluded: chain G residue 397 ASP Chi-restraints excluded: chain G residue 579 VAL Chi-restraints excluded: chain G residue 631 THR Chi-restraints excluded: chain H residue 368 GLN Chi-restraints excluded: chain H residue 397 ASP Chi-restraints excluded: chain H residue 631 THR Chi-restraints excluded: chain H residue 642 MET Chi-restraints excluded: chain I residue 437 LEU Chi-restraints excluded: chain I residue 621 MET Chi-restraints excluded: chain I residue 631 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 158 optimal weight: 1.9990 chunk 203 optimal weight: 4.9990 chunk 157 optimal weight: 0.9980 chunk 234 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 277 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 450 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 24038 Z= 0.216 Angle : 0.511 6.142 32537 Z= 0.286 Chirality : 0.044 0.177 3844 Planarity : 0.003 0.045 4115 Dihedral : 4.419 24.450 3178 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.74 % Allowed : 6.24 % Favored : 93.03 % 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: 0.51 (0.16), residues: 2917 helix: 1.28 (0.14), residues: 1386 sheet: -0.42 (0.19), residues: 576 loop : -0.40 (0.21), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 580 HIS 0.002 0.001 HIS G 425 PHE 0.009 0.001 PHE B 421 TYR 0.008 0.001 TYR C 405 ARG 0.005 0.000 ARG F 637 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 2.966 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 626 ASN cc_start: 0.6981 (t0) cc_final: 0.6551 (m-40) REVERT: B 371 GLU cc_start: 0.6963 (mm-30) cc_final: 0.6520 (tp30) REVERT: B 375 TRP cc_start: 0.5804 (m100) cc_final: 0.5518 (t-100) REVERT: B 409 ILE cc_start: 0.7566 (tp) cc_final: 0.7236 (pt) REVERT: B 642 MET cc_start: 0.6633 (ttm) cc_final: 0.6335 (mtp) REVERT: C 626 ASN cc_start: 0.7053 (t0) cc_final: 0.6414 (m-40) REVERT: C 637 ARG cc_start: 0.6641 (tpt170) cc_final: 0.6371 (tpt170) REVERT: C 655 PHE cc_start: 0.7194 (m-80) cc_final: 0.6440 (m-80) REVERT: D 626 ASN cc_start: 0.7027 (t0) cc_final: 0.6526 (m-40) REVERT: E 387 LYS cc_start: 0.7527 (mtpt) cc_final: 0.7137 (mmmt) REVERT: E 409 ILE cc_start: 0.7416 (tp) cc_final: 0.7129 (pt) REVERT: E 524 LEU cc_start: 0.6928 (OUTLIER) cc_final: 0.6540 (mp) REVERT: E 626 ASN cc_start: 0.6718 (t0) cc_final: 0.6385 (t0) REVERT: F 626 ASN cc_start: 0.6861 (t0) cc_final: 0.6593 (t0) REVERT: G 642 MET cc_start: 0.6824 (ttm) cc_final: 0.6286 (mtp) REVERT: H 637 ARG cc_start: 0.6827 (tpt170) cc_final: 0.6270 (tpt170) REVERT: I 371 GLU cc_start: 0.6925 (mm-30) cc_final: 0.6630 (tp30) REVERT: I 437 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6713 (mp) REVERT: I 626 ASN cc_start: 0.7110 (t0) cc_final: 0.6768 (t0) REVERT: I 642 MET cc_start: 0.6203 (ttm) cc_final: 0.5874 (mtp) REVERT: I 655 PHE cc_start: 0.7340 (m-80) cc_final: 0.7025 (m-80) outliers start: 20 outliers final: 17 residues processed: 180 average time/residue: 0.6697 time to fit residues: 193.2339 Evaluate side-chains 178 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 2.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain D residue 631 THR Chi-restraints excluded: chain E residue 368 GLN Chi-restraints excluded: chain E residue 397 ASP Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 631 THR Chi-restraints excluded: chain F residue 631 THR Chi-restraints excluded: chain G residue 397 ASP Chi-restraints excluded: chain G residue 579 VAL Chi-restraints excluded: chain G residue 631 THR Chi-restraints excluded: chain H residue 368 GLN Chi-restraints excluded: chain H residue 397 ASP Chi-restraints excluded: chain H residue 442 ILE Chi-restraints excluded: chain I residue 437 LEU Chi-restraints excluded: chain I residue 631 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 chunk 165 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 176 optimal weight: 2.9990 chunk 189 optimal weight: 5.9990 chunk 137 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 218 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6473 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 24038 Z= 0.148 Angle : 0.470 6.137 32537 Z= 0.262 Chirality : 0.043 0.167 3844 Planarity : 0.003 0.048 4115 Dihedral : 4.264 24.138 3178 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.63 % Allowed : 6.53 % Favored : 92.84 % 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: 0.77 (0.16), residues: 2917 helix: 1.50 (0.14), residues: 1386 sheet: -0.34 (0.19), residues: 576 loop : -0.26 (0.21), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 580 HIS 0.002 0.000 HIS G 425 PHE 0.009 0.001 PHE B 421 TYR 0.005 0.001 TYR I 405 ARG 0.006 0.000 ARG F 637 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 2.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 621 MET cc_start: 0.5184 (tmm) cc_final: 0.4957 (tpp) REVERT: A 626 ASN cc_start: 0.7008 (t0) cc_final: 0.6611 (m110) REVERT: B 371 GLU cc_start: 0.6882 (mm-30) cc_final: 0.6483 (tp30) REVERT: B 375 TRP cc_start: 0.5758 (m100) cc_final: 0.5507 (t-100) REVERT: B 409 ILE cc_start: 0.7572 (tp) cc_final: 0.7289 (pt) REVERT: B 642 MET cc_start: 0.6556 (ttm) cc_final: 0.6299 (mtp) REVERT: C 626 ASN cc_start: 0.7033 (t0) cc_final: 0.6474 (m-40) REVERT: C 637 ARG cc_start: 0.6631 (tpt170) cc_final: 0.6369 (tpt170) REVERT: C 655 PHE cc_start: 0.7033 (m-80) cc_final: 0.6202 (m-80) REVERT: D 626 ASN cc_start: 0.7008 (t0) cc_final: 0.6768 (m110) REVERT: E 380 GLU cc_start: 0.6676 (tt0) cc_final: 0.6422 (tt0) REVERT: E 387 LYS cc_start: 0.7617 (mtpt) cc_final: 0.7211 (mmmt) REVERT: E 409 ILE cc_start: 0.7423 (tp) cc_final: 0.7149 (pt) REVERT: E 543 PHE cc_start: 0.7752 (t80) cc_final: 0.7481 (t80) REVERT: E 626 ASN cc_start: 0.6671 (t0) cc_final: 0.6344 (t0) REVERT: F 626 ASN cc_start: 0.6852 (t0) cc_final: 0.6271 (m-40) REVERT: F 655 PHE cc_start: 0.7088 (m-80) cc_final: 0.6566 (m-80) REVERT: G 642 MET cc_start: 0.6900 (ttm) cc_final: 0.6456 (mtp) REVERT: H 637 ARG cc_start: 0.6786 (tpt170) cc_final: 0.6239 (tpt170) REVERT: I 626 ASN cc_start: 0.7057 (t0) cc_final: 0.6692 (t0) REVERT: I 642 MET cc_start: 0.6255 (ttm) cc_final: 0.5947 (mtp) REVERT: I 655 PHE cc_start: 0.7329 (m-80) cc_final: 0.7000 (m-80) outliers start: 17 outliers final: 14 residues processed: 180 average time/residue: 0.6503 time to fit residues: 185.0347 Evaluate side-chains 175 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 161 time to evaluate : 2.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain E residue 368 GLN Chi-restraints excluded: chain E residue 397 ASP Chi-restraints excluded: chain E residue 442 ILE Chi-restraints excluded: chain E residue 631 THR Chi-restraints excluded: chain F residue 631 THR Chi-restraints excluded: chain G residue 397 ASP Chi-restraints excluded: chain G residue 579 VAL Chi-restraints excluded: chain G residue 631 THR Chi-restraints excluded: chain H residue 368 GLN Chi-restraints excluded: chain H residue 397 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 7.9990 chunk 265 optimal weight: 7.9990 chunk 242 optimal weight: 0.9980 chunk 258 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 203 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 233 optimal weight: 0.8980 chunk 244 optimal weight: 0.4980 chunk 257 optimal weight: 4.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6470 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 24038 Z= 0.151 Angle : 0.467 6.660 32537 Z= 0.258 Chirality : 0.043 0.168 3844 Planarity : 0.003 0.051 4115 Dihedral : 4.136 22.770 3178 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.77 % Allowed : 6.61 % Favored : 92.62 % 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: 0.90 (0.16), residues: 2917 helix: 1.62 (0.14), residues: 1386 sheet: -0.30 (0.19), residues: 576 loop : -0.19 (0.22), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 580 HIS 0.002 0.000 HIS G 425 PHE 0.009 0.001 PHE F 421 TYR 0.006 0.001 TYR I 405 ARG 0.007 0.000 ARG F 637 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 2.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 626 ASN cc_start: 0.7021 (t0) cc_final: 0.6612 (m110) REVERT: B 371 GLU cc_start: 0.6852 (mm-30) cc_final: 0.6477 (tp30) REVERT: B 375 TRP cc_start: 0.5756 (m100) cc_final: 0.5530 (t-100) REVERT: B 409 ILE cc_start: 0.7570 (tp) cc_final: 0.7311 (pt) REVERT: B 642 MET cc_start: 0.6534 (ttm) cc_final: 0.6273 (mtp) REVERT: C 637 ARG cc_start: 0.6630 (tpt170) cc_final: 0.6368 (tpt170) REVERT: C 655 PHE cc_start: 0.7005 (m-80) cc_final: 0.6223 (m-80) REVERT: D 626 ASN cc_start: 0.7008 (t0) cc_final: 0.6474 (m-40) REVERT: E 380 GLU cc_start: 0.6626 (tt0) cc_final: 0.6393 (tt0) REVERT: E 387 LYS cc_start: 0.7603 (mtpt) cc_final: 0.7205 (mmmt) REVERT: E 409 ILE cc_start: 0.7422 (tp) cc_final: 0.7147 (pt) REVERT: E 543 PHE cc_start: 0.7804 (t80) cc_final: 0.7549 (t80) REVERT: F 626 ASN cc_start: 0.6903 (t0) cc_final: 0.6281 (m-40) REVERT: F 655 PHE cc_start: 0.7002 (m-80) cc_final: 0.6473 (m-80) REVERT: G 642 MET cc_start: 0.6880 (ttm) cc_final: 0.6471 (mtp) REVERT: H 436 LYS cc_start: 0.7426 (mtmm) cc_final: 0.7040 (mtpt) REVERT: H 637 ARG cc_start: 0.6781 (tpt170) cc_final: 0.6242 (tpt170) REVERT: I 612 GLN cc_start: 0.7128 (mt0) cc_final: 0.6925 (mp10) REVERT: I 642 MET cc_start: 0.6160 (ttm) cc_final: 0.5929 (mtp) REVERT: I 655 PHE cc_start: 0.7332 (m-80) cc_final: 0.7013 (m-80) outliers start: 21 outliers final: 17 residues processed: 185 average time/residue: 0.6362 time to fit residues: 186.3069 Evaluate side-chains 181 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 2.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain E residue 368 GLN Chi-restraints excluded: chain E residue 397 ASP Chi-restraints excluded: chain E residue 437 LEU Chi-restraints excluded: chain E residue 631 THR Chi-restraints excluded: chain F residue 631 THR Chi-restraints excluded: chain G residue 397 ASP Chi-restraints excluded: chain G residue 579 VAL Chi-restraints excluded: chain G residue 631 THR Chi-restraints excluded: chain H residue 368 GLN Chi-restraints excluded: chain H residue 397 ASP Chi-restraints excluded: chain H residue 442 ILE Chi-restraints excluded: chain I residue 371 GLU Chi-restraints excluded: chain I residue 631 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 0.9990 chunk 273 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 190 optimal weight: 0.5980 chunk 286 optimal weight: 0.9990 chunk 264 optimal weight: 9.9990 chunk 228 optimal weight: 0.4980 chunk 23 optimal weight: 8.9990 chunk 176 optimal weight: 2.9990 chunk 140 optimal weight: 0.7980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 612 GLN H 612 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 24038 Z= 0.118 Angle : 0.449 7.073 32537 Z= 0.247 Chirality : 0.042 0.160 3844 Planarity : 0.003 0.053 4115 Dihedral : 4.034 22.611 3178 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.44 % Allowed : 6.97 % Favored : 92.58 % 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: 1.09 (0.16), residues: 2917 helix: 1.77 (0.14), residues: 1386 sheet: -0.23 (0.19), residues: 576 loop : -0.09 (0.22), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 580 HIS 0.002 0.000 HIS G 425 PHE 0.009 0.001 PHE B 421 TYR 0.005 0.001 TYR I 444 ARG 0.006 0.000 ARG F 637 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 174 time to evaluate : 3.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 626 ASN cc_start: 0.7025 (t0) cc_final: 0.6619 (m110) REVERT: B 371 GLU cc_start: 0.6808 (mm-30) cc_final: 0.6373 (tp30) REVERT: B 375 TRP cc_start: 0.5724 (m100) cc_final: 0.5503 (t-100) REVERT: B 409 ILE cc_start: 0.7551 (tp) cc_final: 0.7325 (pt) REVERT: B 642 MET cc_start: 0.6465 (ttm) cc_final: 0.6210 (mtp) REVERT: C 637 ARG cc_start: 0.6634 (tpt170) cc_final: 0.6374 (tpt170) REVERT: C 655 PHE cc_start: 0.6935 (m-80) cc_final: 0.6143 (m-80) REVERT: D 397 ASP cc_start: 0.5436 (t0) cc_final: 0.5086 (t0) REVERT: D 626 ASN cc_start: 0.7019 (t0) cc_final: 0.6484 (m-40) REVERT: E 380 GLU cc_start: 0.6606 (tt0) cc_final: 0.6405 (tt0) REVERT: E 387 LYS cc_start: 0.7592 (mtpt) cc_final: 0.7196 (mmmt) REVERT: E 409 ILE cc_start: 0.7454 (tp) cc_final: 0.7188 (pt) REVERT: E 543 PHE cc_start: 0.7770 (t80) cc_final: 0.7531 (t80) REVERT: F 626 ASN cc_start: 0.6894 (t0) cc_final: 0.6275 (m-40) REVERT: F 655 PHE cc_start: 0.7000 (m-80) cc_final: 0.6508 (m-80) REVERT: G 642 MET cc_start: 0.6850 (ttm) cc_final: 0.6447 (mtp) REVERT: H 436 LYS cc_start: 0.7429 (mtmm) cc_final: 0.7046 (mtpt) REVERT: H 637 ARG cc_start: 0.6771 (tpt170) cc_final: 0.6238 (tpt170) REVERT: I 375 TRP cc_start: 0.5630 (m100) cc_final: 0.5176 (t-100) REVERT: I 612 GLN cc_start: 0.7081 (mt0) cc_final: 0.6878 (mp10) REVERT: I 642 MET cc_start: 0.6216 (ttm) cc_final: 0.5998 (mtp) REVERT: I 655 PHE cc_start: 0.7369 (m-80) cc_final: 0.7062 (m-80) outliers start: 12 outliers final: 11 residues processed: 184 average time/residue: 0.6486 time to fit residues: 189.8775 Evaluate side-chains 175 residues out of total 2710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 164 time to evaluate : 2.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 612 GLN Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain E residue 368 GLN Chi-restraints excluded: chain E residue 397 ASP Chi-restraints excluded: chain E residue 437 LEU Chi-restraints excluded: chain E residue 631 THR Chi-restraints excluded: chain G residue 631 THR Chi-restraints excluded: chain H residue 368 GLN Chi-restraints excluded: chain H residue 397 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 2.9990 chunk 243 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 210 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 63 optimal weight: 0.0970 chunk 228 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 234 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 612 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.184411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.125129 restraints weight = 81680.010| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.35 r_work: 0.3258 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.156 24038 Z= 0.161 Angle : 0.623 59.151 32537 Z= 0.384 Chirality : 0.043 0.162 3844 Planarity : 0.003 0.053 4115 Dihedral : 4.032 22.597 3178 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.41 % Allowed : 7.12 % Favored : 92.47 % 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 (0.16), residues: 2917 helix: 1.76 (0.14), residues: 1386 sheet: -0.22 (0.19), residues: 576 loop : -0.08 (0.22), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 580 HIS 0.001 0.000 HIS G 425 PHE 0.009 0.001 PHE B 421 TYR 0.006 0.001 TYR I 405 ARG 0.004 0.000 ARG F 637 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6415.73 seconds wall clock time: 112 minutes 4.66 seconds (6724.66 seconds total)