Starting phenix.real_space_refine on Tue Jun 17 20:41:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k7u_36943/06_2025/8k7u_36943.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k7u_36943/06_2025/8k7u_36943.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k7u_36943/06_2025/8k7u_36943.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k7u_36943/06_2025/8k7u_36943.map" model { file = "/net/cci-nas-00/data/ceres_data/8k7u_36943/06_2025/8k7u_36943.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k7u_36943/06_2025/8k7u_36943.cif" } resolution = 3.37 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 101 5.16 5 C 13277 2.51 5 N 3454 2.21 5 O 3915 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20747 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 5450 Classifications: {'peptide': 673} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 21, 'TRANS': 651} Chain breaks: 6 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 5459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 5459 Classifications: {'peptide': 673} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 651} Chain breaks: 6 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 4966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 4966 Classifications: {'peptide': 609} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 589} Chain breaks: 9 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 4872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4872 Classifications: {'peptide': 600} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 19, 'TRANS': 580} Chain breaks: 11 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Time building chain proxies: 14.51, per 1000 atoms: 0.70 Number of scatterers: 20747 At special positions: 0 Unit cell: (133.4, 116.84, 138.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 101 16.00 O 3915 8.00 N 3454 7.00 C 13277 6.00 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: 4.78 Conformation dependent library (CDL) restraints added in 2.7 seconds 4966 Ramachandran restraints generated. 2483 Oldfield, 0 Emsley, 2483 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4794 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 34 sheets defined 23.2% alpha, 33.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.90 Creating SS restraints... Processing helix chain 'A' and resid 46 through 50 Processing helix chain 'A' and resid 278 through 282 removed outlier: 4.432A pdb=" N ASP A 281 " --> pdb=" O ASN A 278 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE A 282 " --> pdb=" O PRO A 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 278 through 282' Processing helix chain 'A' and resid 305 through 321 removed outlier: 3.651A pdb=" N LEU A 321 " --> pdb=" O TYR A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 356 Processing helix chain 'A' and resid 356 through 361 Processing helix chain 'A' and resid 397 through 406 removed outlier: 3.569A pdb=" N ARG A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 406 " --> pdb=" O LYS A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 429 Processing helix chain 'A' and resid 454 through 472 removed outlier: 3.890A pdb=" N VAL A 458 " --> pdb=" O ARG A 454 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU A 471 " --> pdb=" O LYS A 467 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER A 472 " --> pdb=" O VAL A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 520 removed outlier: 4.014A pdb=" N ILE A 506 " --> pdb=" O MET A 502 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU A 507 " --> pdb=" O HIS A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 543 Processing helix chain 'A' and resid 557 through 565 removed outlier: 3.659A pdb=" N TYR A 562 " --> pdb=" O THR A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 573 removed outlier: 3.521A pdb=" N MET A 573 " --> pdb=" O VAL A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 599 removed outlier: 3.693A pdb=" N ARG A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 597 " --> pdb=" O THR A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 636 removed outlier: 3.763A pdb=" N LYS A 621 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS A 622 " --> pdb=" O GLU A 618 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N GLU A 632 " --> pdb=" O LYS A 628 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N LEU A 633 " --> pdb=" O GLU A 629 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 636 " --> pdb=" O GLU A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 735 Processing helix chain 'A' and resid 740 through 747 removed outlier: 3.871A pdb=" N LEU A 744 " --> pdb=" O ASP A 740 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN A 745 " --> pdb=" O ARG A 741 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A 746 " --> pdb=" O GLU A 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 321 removed outlier: 3.744A pdb=" N LEU C 321 " --> pdb=" O TYR C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 361 removed outlier: 4.369A pdb=" N LYS C 349 " --> pdb=" O PHE C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 407 removed outlier: 3.725A pdb=" N ARG C 401 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS C 402 " --> pdb=" O GLY C 398 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY C 407 " --> pdb=" O VAL C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 433 Processing helix chain 'C' and resid 454 through 469 removed outlier: 3.667A pdb=" N VAL C 458 " --> pdb=" O ARG C 454 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL C 468 " --> pdb=" O MET C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 498 removed outlier: 3.510A pdb=" N GLN C 498 " --> pdb=" O ALA C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 520 Processing helix chain 'C' and resid 536 through 543 Processing helix chain 'C' and resid 555 through 565 Processing helix chain 'C' and resid 590 through 599 removed outlier: 3.926A pdb=" N ARG C 594 " --> pdb=" O PRO C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 612 removed outlier: 3.708A pdb=" N LEU C 612 " --> pdb=" O LEU C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 636 removed outlier: 5.288A pdb=" N GLU C 632 " --> pdb=" O LYS C 628 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU C 633 " --> pdb=" O GLU C 629 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL C 636 " --> pdb=" O GLU C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 728 through 735 Processing helix chain 'C' and resid 740 through 748 removed outlier: 3.779A pdb=" N LEU C 744 " --> pdb=" O ASP C 740 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN C 745 " --> pdb=" O ARG C 741 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY C 748 " --> pdb=" O LEU C 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 73 removed outlier: 3.851A pdb=" N THR D 73 " --> pdb=" O MET D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 129 No H-bonds generated for 'chain 'D' and resid 127 through 129' Processing helix chain 'D' and resid 305 through 321 removed outlier: 4.052A pdb=" N MET D 309 " --> pdb=" O GLY D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 327 Processing helix chain 'D' and resid 350 through 358 removed outlier: 3.927A pdb=" N LYS D 358 " --> pdb=" O ALA D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 471 removed outlier: 3.506A pdb=" N LYS D 467 " --> pdb=" O LYS D 463 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL D 468 " --> pdb=" O MET D 464 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU D 471 " --> pdb=" O LYS D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 499 removed outlier: 4.058A pdb=" N GLY D 499 " --> pdb=" O SER D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 520 removed outlier: 3.728A pdb=" N ILE D 506 " --> pdb=" O MET D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 543 removed outlier: 4.236A pdb=" N PHE D 542 " --> pdb=" O ALA D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 565 removed outlier: 3.838A pdb=" N ILE D 560 " --> pdb=" O GLU D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 599 removed outlier: 3.640A pdb=" N ARG D 594 " --> pdb=" O PRO D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 615 through 636 removed outlier: 4.988A pdb=" N GLU D 632 " --> pdb=" O LYS D 628 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LEU D 633 " --> pdb=" O GLU D 629 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL D 636 " --> pdb=" O GLU D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 728 through 736 removed outlier: 3.686A pdb=" N LEU D 732 " --> pdb=" O TYR D 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 321 removed outlier: 3.990A pdb=" N MET B 309 " --> pdb=" O GLY B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 357 Processing helix chain 'B' and resid 454 through 469 removed outlier: 4.298A pdb=" N VAL B 458 " --> pdb=" O ARG B 454 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL B 468 " --> pdb=" O MET B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 499 No H-bonds generated for 'chain 'B' and resid 497 through 499' Processing helix chain 'B' and resid 500 through 520 Processing helix chain 'B' and resid 538 through 543 removed outlier: 3.919A pdb=" N PHE B 542 " --> pdb=" O ALA B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 565 removed outlier: 3.753A pdb=" N ILE B 560 " --> pdb=" O GLU B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 599 removed outlier: 4.478A pdb=" N ARG B 594 " --> pdb=" O PRO B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 635 removed outlier: 3.708A pdb=" N GLU B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR B 630 " --> pdb=" O PHE B 626 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N GLU B 632 " --> pdb=" O LYS B 628 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N LEU B 633 " --> pdb=" O GLU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 735 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 removed outlier: 6.839A pdb=" N SER A 20 " --> pdb=" O TYR A 36 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TYR A 36 " --> pdb=" O SER A 20 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU A 22 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 94 removed outlier: 6.092A pdb=" N THR A 91 " --> pdb=" O GLU A 177 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA A 182 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 275 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY A 276 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY A 214 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN D 216 " --> pdb=" O ALA D 263 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET D 274 " --> pdb=" O GLN D 262 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU D 275 " --> pdb=" O ALA D 182 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA D 182 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ILE D 277 " --> pdb=" O MET D 180 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N MET D 180 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N THR D 91 " --> pdb=" O GLU D 177 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 285 through 286 removed outlier: 4.059A pdb=" N ALA A 182 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 275 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY A 276 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY A 214 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN D 216 " --> pdb=" O ALA D 263 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET D 274 " --> pdb=" O GLN D 262 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU D 275 " --> pdb=" O ALA D 182 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA D 182 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ILE D 277 " --> pdb=" O MET D 180 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N MET D 180 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE D 174 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 112 removed outlier: 5.865A pdb=" N TYR A 105 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N HIS A 139 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER A 107 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR A 111 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE A 153 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 150 " --> pdb=" O ASN A 163 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN A 163 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG A 162 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLU A 296 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 104 through 112 removed outlier: 5.865A pdb=" N TYR A 105 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N HIS A 139 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER A 107 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR A 111 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE A 153 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 150 " --> pdb=" O ASN A 163 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN A 163 " --> pdb=" O THR A 150 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 524 through 526 removed outlier: 3.507A pdb=" N ASP A 480 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N PHE A 365 " --> pdb=" O GLY A 411 " (cutoff:3.500A) removed outlier: 9.013A pdb=" N TRP A 413 " --> pdb=" O PHE A 365 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU A 335 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N VAL A 577 " --> pdb=" O GLU A 606 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 639 through 644 removed outlier: 6.415A pdb=" N ALA A 653 " --> pdb=" O LEU A 643 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP A 654 " --> pdb=" O ALA A 667 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 668 " --> pdb=" O LEU A 754 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA A 752 " --> pdb=" O GLN A 670 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 680 through 682 removed outlier: 4.678A pdb=" N ILE A 680 " --> pdb=" O ILE A 739 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 739 " --> pdb=" O ILE A 680 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.884A pdb=" N MET C 23 " --> pdb=" O PHE C 12 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR C 21 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N SER C 20 " --> pdb=" O TYR C 36 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N TYR C 36 " --> pdb=" O SER C 20 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU C 22 " --> pdb=" O LEU C 34 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 90 through 93 removed outlier: 6.304A pdb=" N THR C 91 " --> pdb=" O GLU C 177 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N MET C 180 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE C 277 " --> pdb=" O MET C 180 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA C 182 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU C 275 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY C 214 " --> pdb=" O VAL C 265 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY B 214 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER B 220 " --> pdb=" O PHE B 259 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE B 259 " --> pdb=" O SER B 220 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET B 274 " --> pdb=" O GLN B 262 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR B 271 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLU B 185 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL B 273 " --> pdb=" O SER B 183 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N SER B 183 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU B 275 " --> pdb=" O SER B 181 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE B 277 " --> pdb=" O ALA B 179 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ALA B 179 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR B 91 " --> pdb=" O GLU B 177 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 285 through 286 removed outlier: 3.610A pdb=" N ILE C 174 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N MET C 180 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE C 277 " --> pdb=" O MET C 180 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA C 182 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU C 275 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY C 214 " --> pdb=" O VAL C 265 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY B 214 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER B 220 " --> pdb=" O PHE B 259 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE B 259 " --> pdb=" O SER B 220 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET B 274 " --> pdb=" O GLN B 262 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR B 271 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLU B 185 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL B 273 " --> pdb=" O SER B 183 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N SER B 183 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU B 275 " --> pdb=" O SER B 181 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE B 277 " --> pdb=" O ALA B 179 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ALA B 179 " --> pdb=" O ILE B 277 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 104 through 112 removed outlier: 5.747A pdb=" N TYR C 105 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N HIS C 139 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER C 107 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR C 150 " --> pdb=" O ASN C 163 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR C 154 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N VAL C 159 " --> pdb=" O TYR C 154 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N PHE C 233 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N LEU C 196 " --> pdb=" O PHE C 233 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL C 194 " --> pdb=" O ALA C 235 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 104 through 112 removed outlier: 5.747A pdb=" N TYR C 105 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N HIS C 139 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER C 107 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR C 150 " --> pdb=" O ASN C 163 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR C 154 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N VAL C 159 " --> pdb=" O TYR C 154 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 334 through 336 Processing sheet with id=AB6, first strand: chain 'C' and resid 364 through 366 removed outlier: 3.763A pdb=" N PHE C 365 " --> pdb=" O LYS C 409 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 414 through 415 Processing sheet with id=AB8, first strand: chain 'C' and resid 639 through 644 removed outlier: 6.319A pdb=" N ALA C 653 " --> pdb=" O LEU C 643 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR C 652 " --> pdb=" O TYR C 669 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 680 through 682 removed outlier: 3.999A pdb=" N ILE C 680 " --> pdb=" O ILE C 739 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 693 through 695 Processing sheet with id=AC2, first strand: chain 'D' and resid 3 through 6 removed outlier: 6.993A pdb=" N SER D 20 " --> pdb=" O TYR D 36 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TYR D 36 " --> pdb=" O SER D 20 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU D 22 " --> pdb=" O LEU D 34 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 104 through 110 removed outlier: 5.819A pdb=" N TYR D 105 " --> pdb=" O HIS D 139 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N HIS D 139 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER D 107 " --> pdb=" O THR D 137 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR D 145 " --> pdb=" O ASP D 140 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR D 150 " --> pdb=" O ASN D 163 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN D 163 " --> pdb=" O THR D 150 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR D 154 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N VAL D 159 " --> pdb=" O TYR D 154 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU D 296 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL D 300 " --> pdb=" O GLY D 250 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU D 236 " --> pdb=" O TYR D 249 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU D 253 " --> pdb=" O PRO D 232 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU D 196 " --> pdb=" O ASN D 231 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N PHE D 233 " --> pdb=" O VAL D 194 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL D 194 " --> pdb=" O PHE D 233 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ALA D 235 " --> pdb=" O GLU D 192 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N GLU D 192 " --> pdb=" O ALA D 235 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 104 through 110 removed outlier: 5.819A pdb=" N TYR D 105 " --> pdb=" O HIS D 139 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N HIS D 139 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER D 107 " --> pdb=" O THR D 137 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR D 145 " --> pdb=" O ASP D 140 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG D 165 " --> pdb=" O VAL D 148 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 410 through 411 removed outlier: 6.922A pdb=" N PHE D 365 " --> pdb=" O GLY D 411 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU D 335 " --> pdb=" O VAL D 366 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU D 334 " --> pdb=" O TYR D 605 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 476 through 480 removed outlier: 6.327A pdb=" N PHE D 525 " --> pdb=" O GLN D 545 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N TRP D 547 " --> pdb=" O PHE D 525 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N SER D 527 " --> pdb=" O TRP D 547 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR D 546 " --> pdb=" O GLY D 574 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 639 through 644 removed outlier: 6.365A pdb=" N ALA D 653 " --> pdb=" O LEU D 643 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA D 664 " --> pdb=" O LEU D 758 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE D 668 " --> pdb=" O LEU D 754 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA D 752 " --> pdb=" O GLN D 670 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 680 through 682 removed outlier: 3.896A pdb=" N ILE D 680 " --> pdb=" O ILE D 739 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE D 682 " --> pdb=" O ILE D 737 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 3 through 4 removed outlier: 6.993A pdb=" N SER B 20 " --> pdb=" O TYR B 36 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N TYR B 36 " --> pdb=" O SER B 20 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU B 22 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG B 24 " --> pdb=" O GLU B 32 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 104 through 110 removed outlier: 7.174A pdb=" N THR B 137 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N HIS B 108 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N GLU B 135 " --> pdb=" O HIS B 108 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ILE B 110 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N THR B 133 " --> pdb=" O ILE B 110 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR B 150 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN B 163 " --> pdb=" O THR B 150 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR B 154 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N VAL B 159 " --> pdb=" O TYR B 154 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHE B 233 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU B 196 " --> pdb=" O PHE B 233 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL B 194 " --> pdb=" O ALA B 235 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 104 through 110 removed outlier: 7.174A pdb=" N THR B 137 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N HIS B 108 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N GLU B 135 " --> pdb=" O HIS B 108 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ILE B 110 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N THR B 133 " --> pdb=" O ILE B 110 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR B 150 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN B 163 " --> pdb=" O THR B 150 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR B 154 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N VAL B 159 " --> pdb=" O TYR B 154 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 365 through 366 removed outlier: 7.109A pdb=" N PHE B 365 " --> pdb=" O GLY B 411 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 476 through 477 Processing sheet with id=AD5, first strand: chain 'B' and resid 546 through 547 removed outlier: 7.263A pdb=" N THR B 546 " --> pdb=" O GLY B 574 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 639 through 642 removed outlier: 3.527A pdb=" N TRP B 654 " --> pdb=" O ALA B 667 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA B 664 " --> pdb=" O LEU B 758 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE B 668 " --> pdb=" O LEU B 754 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU B 754 " --> pdb=" O PHE B 668 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR B 757 " --> pdb=" O SER B 696 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS B 759 " --> pdb=" O GLU B 694 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR B 725 " --> pdb=" O VAL B 695 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 680 through 682 860 hydrogen bonds defined for protein. 2382 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: 8.74 Time building geometry restraints manager: 5.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3871 1.32 - 1.45: 5546 1.45 - 1.57: 11589 1.57 - 1.69: 0 1.69 - 1.81: 190 Bond restraints: 21196 Sorted by residual: bond pdb=" N ILE D 117 " pdb=" CA ILE D 117 " ideal model delta sigma weight residual 1.460 1.496 -0.036 7.50e-03 1.78e+04 2.36e+01 bond pdb=" N ILE A 117 " pdb=" CA ILE A 117 " ideal model delta sigma weight residual 1.460 1.491 -0.031 7.30e-03 1.88e+04 1.78e+01 bond pdb=" CA SER D 122 " pdb=" CB SER D 122 " ideal model delta sigma weight residual 1.539 1.488 0.051 1.36e-02 5.41e+03 1.38e+01 bond pdb=" N VAL B 567 " pdb=" CA VAL B 567 " ideal model delta sigma weight residual 1.458 1.490 -0.032 9.00e-03 1.23e+04 1.30e+01 bond pdb=" N VAL B 19 " pdb=" CA VAL B 19 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.11e-02 8.12e+03 1.17e+01 ... (remaining 21191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 27893 2.16 - 4.33: 657 4.33 - 6.49: 58 6.49 - 8.65: 3 8.65 - 10.81: 2 Bond angle restraints: 28613 Sorted by residual: angle pdb=" N PRO D 118 " pdb=" CA PRO D 118 " pdb=" C PRO D 118 " ideal model delta sigma weight residual 110.70 121.51 -10.81 1.22e+00 6.72e-01 7.86e+01 angle pdb=" N PRO A 118 " pdb=" CA PRO A 118 " pdb=" C PRO A 118 " ideal model delta sigma weight residual 110.70 119.67 -8.97 1.22e+00 6.72e-01 5.40e+01 angle pdb=" C LYS D 115 " pdb=" N GLY D 116 " pdb=" CA GLY D 116 " ideal model delta sigma weight residual 121.57 116.66 4.91 9.70e-01 1.06e+00 2.56e+01 angle pdb=" CA GLY D 81 " pdb=" C GLY D 81 " pdb=" O GLY D 81 " ideal model delta sigma weight residual 122.59 117.82 4.77 1.04e+00 9.25e-01 2.11e+01 angle pdb=" O LYS D 115 " pdb=" C LYS D 115 " pdb=" N GLY D 116 " ideal model delta sigma weight residual 122.94 118.21 4.73 1.12e+00 7.97e-01 1.78e+01 ... (remaining 28608 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 11339 17.82 - 35.64: 1049 35.64 - 53.46: 191 53.46 - 71.28: 32 71.28 - 89.10: 15 Dihedral angle restraints: 12626 sinusoidal: 5141 harmonic: 7485 Sorted by residual: dihedral pdb=" CA TRP C 679 " pdb=" C TRP C 679 " pdb=" N ILE C 680 " pdb=" CA ILE C 680 " ideal model delta harmonic sigma weight residual -180.00 -159.65 -20.35 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA ASP B 42 " pdb=" C ASP B 42 " pdb=" N LYS B 43 " pdb=" CA LYS B 43 " ideal model delta harmonic sigma weight residual 180.00 160.43 19.57 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA LYS B 759 " pdb=" C LYS B 759 " pdb=" N LYS B 760 " pdb=" CA LYS B 760 " ideal model delta harmonic sigma weight residual -180.00 -160.48 -19.52 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 12623 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2361 0.055 - 0.110: 575 0.110 - 0.165: 117 0.165 - 0.220: 16 0.220 - 0.275: 2 Chirality restraints: 3071 Sorted by residual: chirality pdb=" CA PHE B 668 " pdb=" N PHE B 668 " pdb=" C PHE B 668 " pdb=" CB PHE B 668 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA ILE D 117 " pdb=" N ILE D 117 " pdb=" C ILE D 117 " pdb=" CB ILE D 117 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA LEU A 196 " pdb=" N LEU A 196 " pdb=" C LEU A 196 " pdb=" CB LEU A 196 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 3068 not shown) Planarity restraints: 3649 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 654 " 0.023 2.00e-02 2.50e+03 2.19e-02 1.19e+01 pdb=" CG TRP C 654 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP C 654 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP C 654 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 654 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 654 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 654 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 654 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 654 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 654 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 194 " 0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C VAL A 194 " -0.058 2.00e-02 2.50e+03 pdb=" O VAL A 194 " 0.021 2.00e-02 2.50e+03 pdb=" N GLN A 195 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 654 " -0.020 2.00e-02 2.50e+03 1.81e-02 8.16e+00 pdb=" CG TRP A 654 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP A 654 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP A 654 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 654 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 654 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 654 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 654 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 654 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 654 " -0.003 2.00e-02 2.50e+03 ... (remaining 3646 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 207 2.62 - 3.19: 17359 3.19 - 3.76: 28490 3.76 - 4.33: 39889 4.33 - 4.90: 69571 Nonbonded interactions: 155516 Sorted by model distance: nonbonded pdb=" O THR A 224 " pdb=" SG CYS A 225 " model vdw 2.046 3.400 nonbonded pdb=" ND2 ASN A 16 " pdb=" O TYR A 154 " model vdw 2.199 3.120 nonbonded pdb=" NZ LYS B 43 " pdb=" OH TYR B 48 " model vdw 2.233 3.120 nonbonded pdb=" OG1 THR C 267 " pdb=" OE2 GLU B 229 " model vdw 2.233 3.040 nonbonded pdb=" NE2 GLN C 168 " pdb=" O GLN C 172 " model vdw 2.235 3.120 ... (remaining 155511 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 49 or resid 69 through 337 or resid 352 through \ 355 or (resid 356 through 357 and (name N or name CA or name C or name O or name \ CB )) or resid 358 or (resid 359 through 360 and (name N or name CA or name C o \ r name O or name CB )) or resid 361 through 367 or resid 409 through 414 or (res \ id 415 and (name N or name CA or name C or name O or name CB )) or resid 416 thr \ ough 419 or resid 456 through 469 or resid 475 through 491 or resid 495 through \ 518 or (resid 519 through 520 and (name N or name CA or name C or name O or name \ CB )) or resid 521 through 529 or resid 533 through 535 or (resid 536 and (name \ N or name CA or name C or name O or name CB )) or resid 537 through 548 or resi \ d 555 through 579 or resid 589 through 606 or resid 615 through 647 or (resid 64 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 649 through \ 730 or (resid 731 and (name N or name CA or name C or name O or name CB )) or re \ sid 732 through 741 or (resid 742 through 743 and (name N or name CA or name C o \ r name O or name CB )) or resid 744 through 761)) selection = (chain 'B' and (resid 2 through 40 or (resid 41 and (name N or name CA or name C \ or name O or name CB )) or resid 42 through 83 or (resid 84 and (name N or name \ CA or name C or name O or name CB )) or resid 85 through 354 or (resid 355 thro \ ugh 357 and (name N or name CA or name C or name O or name CB )) or resid 358 or \ (resid 359 through 360 and (name N or name CA or name C or name O or name CB )) \ or resid 361 through 419 or resid 456 through 555 or (resid 556 and (name N or \ name CA or name C or name O or name CB )) or resid 557 through 697 or resid 723 \ through 742 or (resid 743 and (name N or name CA or name C or name O or name CB \ )) or resid 744 through 761)) selection = (chain 'C' and (resid 2 through 40 or (resid 41 and (name N or name CA or name C \ or name O or name CB )) or resid 42 through 83 or (resid 84 and (name N or name \ CA or name C or name O or name CB )) or resid 85 through 337 or resid 352 throu \ gh 354 or (resid 355 through 357 and (name N or name CA or name C or name O or n \ ame CB )) or resid 358 through 367 or resid 409 through 414 or (resid 415 and (n \ ame N or name CA or name C or name O or name CB )) or resid 416 through 419 or r \ esid 456 through 469 or resid 475 through 491 or resid 495 through 518 or (resid \ 519 through 520 and (name N or name CA or name C or name O or name CB )) or res \ id 521 through 529 or resid 533 through 535 or (resid 536 and (name N or name CA \ or name C or name O or name CB )) or resid 537 through 548 or resid 555 or (res \ id 556 and (name N or name CA or name C or name O or name CB )) or resid 557 thr \ ough 606 or resid 615 through 647 or (resid 648 and (name N or name CA or name C \ or name O or name CB )) or resid 649 through 730 or (resid 731 and (name N or n \ ame CA or name C or name O or name CB )) or resid 732 through 741 or (resid 742 \ through 743 and (name N or name CA or name C or name O or name CB )) or resid 74 \ 4 through 761)) selection = (chain 'D' and (resid 2 through 40 or (resid 41 and (name N or name CA or name C \ or name O or name CB )) or resid 42 through 83 or (resid 84 and (name N or name \ CA or name C or name O or name CB )) or resid 85 through 337 or resid 352 throu \ gh 354 or (resid 355 through 357 and (name N or name CA or name C or name O or n \ ame CB )) or resid 358 or (resid 359 through 360 and (name N or name CA or name \ C or name O or name CB )) or resid 361 through 414 or (resid 415 and (name N or \ name CA or name C or name O or name CB )) or resid 416 through 419 or resid 456 \ through 469 or resid 475 through 491 or resid 495 through 518 or (resid 519 thro \ ugh 520 and (name N or name CA or name C or name O or name CB )) or resid 521 th \ rough 535 or (resid 536 and (name N or name CA or name C or name O or name CB )) \ or resid 537 through 555 or (resid 556 and (name N or name CA or name C or name \ O or name CB )) or resid 557 through 579 or resid 589 through 606 or resid 615 \ through 647 or (resid 648 and (name N or name CA or name C or name O or name CB \ )) or resid 649 through 697 or resid 723 through 730 or (resid 731 and (name N o \ r name CA or name C or name O or name CB )) or resid 732 through 741 or (resid 7 \ 42 through 743 and (name N or name CA or name C or name O or name CB )) or resid \ 744 through 761)) } 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: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.840 Check model and map are aligned: 0.140 Set scattering table: 0.200 Process input model: 51.000 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.090 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 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 : 0.006 0.051 21196 Z= 0.324 Angle : 0.740 10.814 28613 Z= 0.473 Chirality : 0.051 0.275 3071 Planarity : 0.004 0.050 3649 Dihedral : 14.047 89.100 7832 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % 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: -2.17 (0.16), residues: 2483 helix: -0.32 (0.23), residues: 497 sheet: -0.88 (0.19), residues: 804 loop : -2.35 (0.16), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP C 654 HIS 0.004 0.001 HIS A 219 PHE 0.030 0.002 PHE A 668 TYR 0.030 0.002 TYR B 599 ARG 0.008 0.001 ARG D 681 Details of bonding type rmsd hydrogen bonds : bond 0.24944 ( 730) hydrogen bonds : angle 8.20236 ( 2382) covalent geometry : bond 0.00584 (21196) covalent geometry : angle 0.73997 (28613) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4966 Ramachandran restraints generated. 2483 Oldfield, 0 Emsley, 2483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4966 Ramachandran restraints generated. 2483 Oldfield, 0 Emsley, 2483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 2.346 Fit side-chains REVERT: A 189 MET cc_start: 0.8684 (ptm) cc_final: 0.8418 (ptp) REVERT: A 426 TYR cc_start: 0.8782 (t80) cc_final: 0.8560 (t80) REVERT: D 547 TRP cc_start: 0.8094 (t60) cc_final: 0.7433 (t60) REVERT: B 22 LEU cc_start: 0.8656 (mp) cc_final: 0.8388 (mt) REVERT: B 23 MET cc_start: 0.8106 (mtm) cc_final: 0.7727 (mtp) REVERT: B 326 TRP cc_start: 0.8183 (m100) cc_final: 0.7950 (m100) REVERT: B 669 TYR cc_start: 0.9096 (m-80) cc_final: 0.8732 (m-80) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.3218 time to fit residues: 148.4574 Evaluate side-chains 244 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 2.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 214 optimal weight: 20.0000 chunk 192 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 65 optimal weight: 0.6980 chunk 129 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 199 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 121 optimal weight: 9.9990 chunk 148 optimal weight: 10.0000 chunk 230 optimal weight: 10.0000 overall best weight: 5.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 ASN A 596 ASN C 168 GLN C 685 GLN D 168 GLN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.111418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.083441 restraints weight = 35904.805| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 3.07 r_work: 0.2826 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 21196 Z= 0.219 Angle : 0.630 11.974 28613 Z= 0.337 Chirality : 0.045 0.163 3071 Planarity : 0.004 0.050 3649 Dihedral : 4.605 19.348 2837 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.99 % Allowed : 8.66 % Favored : 90.34 % 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: -1.81 (0.16), residues: 2483 helix: 0.11 (0.23), residues: 520 sheet: -0.64 (0.19), residues: 837 loop : -2.29 (0.16), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 654 HIS 0.005 0.001 HIS A 219 PHE 0.029 0.002 PHE D 682 TYR 0.019 0.001 TYR C 566 ARG 0.006 0.001 ARG D 681 Details of bonding type rmsd hydrogen bonds : bond 0.05982 ( 730) hydrogen bonds : angle 5.47475 ( 2382) covalent geometry : bond 0.00523 (21196) covalent geometry : angle 0.63018 (28613) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4966 Ramachandran restraints generated. 2483 Oldfield, 0 Emsley, 2483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4966 Ramachandran restraints generated. 2483 Oldfield, 0 Emsley, 2483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 245 time to evaluate : 2.370 Fit side-chains REVERT: A 733 MET cc_start: 0.9173 (mtm) cc_final: 0.8906 (ttm) REVERT: C 189 MET cc_start: 0.9216 (ptm) cc_final: 0.8919 (ttp) REVERT: C 203 GLU cc_start: 0.9078 (pm20) cc_final: 0.8750 (pm20) REVERT: D 190 ASP cc_start: 0.8786 (t0) cc_final: 0.8536 (t0) REVERT: D 247 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8329 (mm-30) REVERT: D 547 TRP cc_start: 0.8390 (t60) cc_final: 0.7560 (t60) REVERT: D 671 ARG cc_start: 0.7958 (tpt170) cc_final: 0.7665 (tpm170) REVERT: D 679 TRP cc_start: 0.8376 (p90) cc_final: 0.8167 (p90) REVERT: B 17 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7364 (ptt-90) REVERT: B 669 TYR cc_start: 0.9173 (m-80) cc_final: 0.8910 (m-80) REVERT: B 682 PHE cc_start: 0.8501 (OUTLIER) cc_final: 0.7796 (p90) outliers start: 22 outliers final: 14 residues processed: 261 average time/residue: 0.3271 time to fit residues: 132.0707 Evaluate side-chains 247 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 231 time to evaluate : 2.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 479 TRP Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain B residue 17 ARG Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 545 GLN Chi-restraints excluded: chain B residue 682 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 141 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 chunk 142 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 131 optimal weight: 9.9990 chunk 233 optimal weight: 8.9990 chunk 4 optimal weight: 8.9990 chunk 228 optimal weight: 20.0000 chunk 205 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 596 ASN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.110012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.082533 restraints weight = 36112.313| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 3.02 r_work: 0.2786 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 21196 Z= 0.261 Angle : 0.639 9.991 28613 Z= 0.343 Chirality : 0.046 0.159 3071 Planarity : 0.004 0.051 3649 Dihedral : 4.711 20.643 2837 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 2.12 % Allowed : 12.27 % Favored : 85.60 % 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: -1.71 (0.17), residues: 2483 helix: 0.25 (0.23), residues: 515 sheet: -0.53 (0.19), residues: 849 loop : -2.31 (0.16), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 654 HIS 0.005 0.001 HIS A 219 PHE 0.031 0.002 PHE D 520 TYR 0.021 0.002 TYR B 599 ARG 0.006 0.000 ARG D 681 Details of bonding type rmsd hydrogen bonds : bond 0.06218 ( 730) hydrogen bonds : angle 5.19823 ( 2382) covalent geometry : bond 0.00629 (21196) covalent geometry : angle 0.63857 (28613) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4966 Ramachandran restraints generated. 2483 Oldfield, 0 Emsley, 2483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4966 Ramachandran restraints generated. 2483 Oldfield, 0 Emsley, 2483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 231 time to evaluate : 2.699 Fit side-chains REVERT: A 242 THR cc_start: 0.8855 (t) cc_final: 0.8628 (p) REVERT: A 733 MET cc_start: 0.9190 (mtm) cc_final: 0.8912 (ttm) REVERT: C 103 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.7231 (p90) REVERT: C 203 GLU cc_start: 0.9063 (pm20) cc_final: 0.8711 (pm20) REVERT: C 679 TRP cc_start: 0.8367 (OUTLIER) cc_final: 0.7614 (p90) REVERT: C 743 ASP cc_start: 0.8023 (m-30) cc_final: 0.7758 (m-30) REVERT: D 190 ASP cc_start: 0.8879 (t0) cc_final: 0.8590 (t0) REVERT: D 487 GLU cc_start: 0.4114 (tm-30) cc_final: 0.3790 (tm-30) REVERT: B 311 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8272 (mt0) REVERT: B 321 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8379 (tm) REVERT: B 326 TRP cc_start: 0.8285 (m100) cc_final: 0.7948 (m100) REVERT: B 669 TYR cc_start: 0.9171 (m-80) cc_final: 0.8939 (m-80) REVERT: B 682 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.7550 (p90) outliers start: 47 outliers final: 30 residues processed: 268 average time/residue: 0.3084 time to fit residues: 129.8748 Evaluate side-chains 252 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 217 time to evaluate : 2.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 200 TRP Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 479 TRP Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 679 TRP Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 575 SER Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 668 PHE Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain B residue 26 MET Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 545 GLN Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 682 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 117 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 176 optimal weight: 20.0000 chunk 15 optimal weight: 8.9990 chunk 235 optimal weight: 30.0000 chunk 108 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 202 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN A 596 ASN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.111158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.083330 restraints weight = 36086.107| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 3.05 r_work: 0.2828 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21196 Z= 0.172 Angle : 0.562 8.941 28613 Z= 0.302 Chirality : 0.043 0.151 3071 Planarity : 0.004 0.050 3649 Dihedral : 4.439 19.745 2837 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.08 % Allowed : 14.67 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.17), residues: 2483 helix: 0.43 (0.23), residues: 515 sheet: -0.46 (0.19), residues: 845 loop : -2.23 (0.16), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 654 HIS 0.004 0.001 HIS A 50 PHE 0.023 0.001 PHE A 751 TYR 0.021 0.001 TYR B 599 ARG 0.008 0.000 ARG D 681 Details of bonding type rmsd hydrogen bonds : bond 0.05070 ( 730) hydrogen bonds : angle 4.95101 ( 2382) covalent geometry : bond 0.00408 (21196) covalent geometry : angle 0.56167 (28613) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4966 Ramachandran restraints generated. 2483 Oldfield, 0 Emsley, 2483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4966 Ramachandran restraints generated. 2483 Oldfield, 0 Emsley, 2483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 242 time to evaluate : 2.685 Fit side-chains REVERT: A 242 THR cc_start: 0.8807 (t) cc_final: 0.8569 (p) REVERT: A 733 MET cc_start: 0.9206 (mtm) cc_final: 0.8948 (ttm) REVERT: C 103 PHE cc_start: 0.8046 (OUTLIER) cc_final: 0.7326 (p90) REVERT: C 189 MET cc_start: 0.9271 (ptm) cc_final: 0.8982 (ttp) REVERT: C 203 GLU cc_start: 0.9028 (pm20) cc_final: 0.8681 (pm20) REVERT: C 671 ARG cc_start: 0.8583 (ttp-170) cc_final: 0.8271 (ttp80) REVERT: C 679 TRP cc_start: 0.8375 (OUTLIER) cc_final: 0.7604 (p90) REVERT: C 743 ASP cc_start: 0.8011 (m-30) cc_final: 0.7770 (m-30) REVERT: C 750 ASP cc_start: 0.7961 (m-30) cc_final: 0.7419 (t70) REVERT: D 18 GLU cc_start: 0.8795 (mp0) cc_final: 0.8201 (mp0) REVERT: D 190 ASP cc_start: 0.8803 (t0) cc_final: 0.8515 (t0) REVERT: D 247 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8253 (mm-30) REVERT: D 487 GLU cc_start: 0.4090 (tm-30) cc_final: 0.3767 (tm-30) REVERT: D 516 LEU cc_start: 0.9179 (tt) cc_final: 0.8859 (tt) REVERT: D 547 TRP cc_start: 0.8721 (t60) cc_final: 0.7516 (t60) REVERT: D 671 ARG cc_start: 0.7929 (tpt170) cc_final: 0.7655 (tpm170) REVERT: B 18 GLU cc_start: 0.8041 (mp0) cc_final: 0.7748 (mp0) REVERT: B 321 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8342 (tm) REVERT: B 326 TRP cc_start: 0.8260 (m100) cc_final: 0.7938 (m100) REVERT: B 669 TYR cc_start: 0.9123 (m-80) cc_final: 0.8913 (m-80) outliers start: 46 outliers final: 34 residues processed: 277 average time/residue: 0.3347 time to fit residues: 144.8028 Evaluate side-chains 263 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 226 time to evaluate : 2.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 200 TRP Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 479 TRP Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 679 TRP Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 539 MET Chi-restraints excluded: chain D residue 575 SER Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 668 PHE Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain B residue 26 MET Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 675 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 245 optimal weight: 9.9990 chunk 228 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 chunk 170 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 163 optimal weight: 0.9980 chunk 109 optimal weight: 20.0000 chunk 128 optimal weight: 10.0000 chunk 209 optimal weight: 20.0000 chunk 249 optimal weight: 0.7980 chunk 236 optimal weight: 20.0000 overall best weight: 4.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 596 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.112016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.084395 restraints weight = 36076.085| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.03 r_work: 0.2817 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21196 Z= 0.164 Angle : 0.553 8.053 28613 Z= 0.296 Chirality : 0.043 0.151 3071 Planarity : 0.004 0.050 3649 Dihedral : 4.342 19.258 2837 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.02 % Allowed : 15.34 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.17), residues: 2483 helix: 0.49 (0.24), residues: 516 sheet: -0.40 (0.19), residues: 846 loop : -2.18 (0.16), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 338 HIS 0.003 0.001 HIS D 219 PHE 0.026 0.001 PHE D 520 TYR 0.022 0.001 TYR B 599 ARG 0.006 0.000 ARG D 681 Details of bonding type rmsd hydrogen bonds : bond 0.04908 ( 730) hydrogen bonds : angle 4.84860 ( 2382) covalent geometry : bond 0.00391 (21196) covalent geometry : angle 0.55258 (28613) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4966 Ramachandran restraints generated. 2483 Oldfield, 0 Emsley, 2483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4966 Ramachandran restraints generated. 2483 Oldfield, 0 Emsley, 2483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 246 time to evaluate : 2.895 Fit side-chains REVERT: A 128 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8547 (pp20) REVERT: A 242 THR cc_start: 0.8800 (t) cc_final: 0.8560 (p) REVERT: A 304 ARG cc_start: 0.8554 (mmm-85) cc_final: 0.8308 (mtp85) REVERT: A 505 TYR cc_start: 0.7248 (OUTLIER) cc_final: 0.6445 (p90) REVERT: A 733 MET cc_start: 0.9196 (mtm) cc_final: 0.8934 (ttm) REVERT: C 103 PHE cc_start: 0.8047 (OUTLIER) cc_final: 0.7285 (p90) REVERT: C 189 MET cc_start: 0.9263 (ptm) cc_final: 0.9002 (ttp) REVERT: C 203 GLU cc_start: 0.9028 (pm20) cc_final: 0.8662 (pm20) REVERT: C 671 ARG cc_start: 0.8554 (ttp-170) cc_final: 0.8117 (ttp-170) REVERT: C 679 TRP cc_start: 0.8350 (OUTLIER) cc_final: 0.7488 (p90) REVERT: C 743 ASP cc_start: 0.8011 (m-30) cc_final: 0.7771 (m-30) REVERT: C 750 ASP cc_start: 0.7943 (m-30) cc_final: 0.7362 (t70) REVERT: D 18 GLU cc_start: 0.8825 (mp0) cc_final: 0.8209 (mp0) REVERT: D 190 ASP cc_start: 0.8834 (t0) cc_final: 0.8530 (t0) REVERT: D 247 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8292 (mm-30) REVERT: D 487 GLU cc_start: 0.4073 (tm-30) cc_final: 0.3746 (tm-30) REVERT: D 516 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8834 (tt) REVERT: D 671 ARG cc_start: 0.7965 (tpt170) cc_final: 0.7654 (tpm170) REVERT: B 132 GLU cc_start: 0.7914 (tt0) cc_final: 0.7669 (mm-30) REVERT: B 203 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8348 (mp0) REVERT: B 311 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8287 (mt0) REVERT: B 321 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8339 (tm) REVERT: B 326 TRP cc_start: 0.8278 (m100) cc_final: 0.7987 (m100) outliers start: 67 outliers final: 46 residues processed: 296 average time/residue: 0.3318 time to fit residues: 154.4312 Evaluate side-chains 287 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 234 time to evaluate : 2.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 200 TRP Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 479 TRP Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 111 TYR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 679 TRP Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 539 MET Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 668 PHE Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 26 MET Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 545 GLN Chi-restraints excluded: chain B residue 675 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 98 optimal weight: 8.9990 chunk 235 optimal weight: 20.0000 chunk 136 optimal weight: 0.4980 chunk 75 optimal weight: 8.9990 chunk 214 optimal weight: 0.8980 chunk 48 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 145 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 169 optimal weight: 9.9990 chunk 182 optimal weight: 0.8980 overall best weight: 3.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 337 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.112115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.084241 restraints weight = 35820.414| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.07 r_work: 0.2841 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21196 Z= 0.138 Angle : 0.531 7.541 28613 Z= 0.285 Chirality : 0.042 0.150 3071 Planarity : 0.004 0.049 3649 Dihedral : 4.203 18.328 2837 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.11 % Allowed : 16.02 % Favored : 80.87 % 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: -1.38 (0.17), residues: 2483 helix: 0.61 (0.24), residues: 511 sheet: -0.35 (0.19), residues: 847 loop : -2.11 (0.16), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 338 HIS 0.002 0.001 HIS D 219 PHE 0.024 0.001 PHE B 5 TYR 0.021 0.001 TYR B 599 ARG 0.006 0.000 ARG D 681 Details of bonding type rmsd hydrogen bonds : bond 0.04508 ( 730) hydrogen bonds : angle 4.73153 ( 2382) covalent geometry : bond 0.00323 (21196) covalent geometry : angle 0.53117 (28613) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4966 Ramachandran restraints generated. 2483 Oldfield, 0 Emsley, 2483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4966 Ramachandran restraints generated. 2483 Oldfield, 0 Emsley, 2483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 246 time to evaluate : 2.290 Fit side-chains REVERT: A 17 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7883 (ptm-80) REVERT: A 242 THR cc_start: 0.8790 (t) cc_final: 0.8532 (p) REVERT: A 304 ARG cc_start: 0.8535 (mmm-85) cc_final: 0.8291 (mtp85) REVERT: A 505 TYR cc_start: 0.7197 (OUTLIER) cc_final: 0.6383 (p90) REVERT: A 733 MET cc_start: 0.9215 (mtm) cc_final: 0.8954 (ttm) REVERT: C 33 ASN cc_start: 0.9212 (t0) cc_final: 0.8849 (t0) REVERT: C 103 PHE cc_start: 0.7969 (OUTLIER) cc_final: 0.7365 (p90) REVERT: C 189 MET cc_start: 0.9275 (ptm) cc_final: 0.9042 (ttp) REVERT: C 203 GLU cc_start: 0.9012 (pm20) cc_final: 0.8635 (pm20) REVERT: C 671 ARG cc_start: 0.8585 (ttp-170) cc_final: 0.8056 (ttp-170) REVERT: C 679 TRP cc_start: 0.8348 (OUTLIER) cc_final: 0.7490 (p90) REVERT: C 743 ASP cc_start: 0.8018 (m-30) cc_final: 0.7787 (m-30) REVERT: C 750 ASP cc_start: 0.7907 (m-30) cc_final: 0.7431 (t70) REVERT: D 190 ASP cc_start: 0.8760 (t0) cc_final: 0.8465 (t0) REVERT: D 487 GLU cc_start: 0.4012 (tm-30) cc_final: 0.3674 (tm-30) REVERT: D 516 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8821 (tt) REVERT: D 671 ARG cc_start: 0.7963 (tpt170) cc_final: 0.7641 (tpm170) REVERT: B 132 GLU cc_start: 0.7844 (tt0) cc_final: 0.7629 (mm-30) REVERT: B 203 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8372 (mp0) REVERT: B 311 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8267 (mt0) REVERT: B 321 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8295 (tm) REVERT: B 326 TRP cc_start: 0.8268 (m100) cc_final: 0.8007 (m100) outliers start: 69 outliers final: 49 residues processed: 296 average time/residue: 0.3157 time to fit residues: 145.1075 Evaluate side-chains 290 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 234 time to evaluate : 2.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 200 TRP Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 479 TRP Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 669 TYR Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 477 ILE Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 679 TRP Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 668 PHE Chi-restraints excluded: chain D residue 679 TRP Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 26 MET Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 675 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 1 optimal weight: 10.0000 chunk 98 optimal weight: 20.0000 chunk 62 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 43 optimal weight: 20.0000 chunk 181 optimal weight: 9.9990 chunk 174 optimal weight: 6.9990 chunk 35 optimal weight: 20.0000 chunk 205 optimal weight: 20.0000 chunk 194 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 676 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.108717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.081513 restraints weight = 35758.982| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.97 r_work: 0.2754 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 21196 Z= 0.290 Angle : 0.653 10.098 28613 Z= 0.349 Chirality : 0.046 0.166 3071 Planarity : 0.004 0.049 3649 Dihedral : 4.691 20.270 2837 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 3.34 % Allowed : 17.06 % Favored : 79.60 % 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: -1.60 (0.17), residues: 2483 helix: 0.35 (0.23), residues: 510 sheet: -0.47 (0.19), residues: 844 loop : -2.23 (0.16), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 479 HIS 0.005 0.001 HIS D 219 PHE 0.030 0.002 PHE D 520 TYR 0.022 0.002 TYR B 599 ARG 0.005 0.000 ARG D 304 Details of bonding type rmsd hydrogen bonds : bond 0.06162 ( 730) hydrogen bonds : angle 5.02937 ( 2382) covalent geometry : bond 0.00703 (21196) covalent geometry : angle 0.65269 (28613) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4966 Ramachandran restraints generated. 2483 Oldfield, 0 Emsley, 2483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4966 Ramachandran restraints generated. 2483 Oldfield, 0 Emsley, 2483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 223 time to evaluate : 2.349 Fit side-chains REVERT: A 17 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8110 (ptm-80) REVERT: A 505 TYR cc_start: 0.7538 (OUTLIER) cc_final: 0.6325 (p90) REVERT: A 733 MET cc_start: 0.9227 (mtm) cc_final: 0.8959 (ttm) REVERT: C 103 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7068 (p90) REVERT: C 189 MET cc_start: 0.9296 (ptm) cc_final: 0.9047 (ttp) REVERT: C 203 GLU cc_start: 0.9093 (pm20) cc_final: 0.8889 (pm20) REVERT: C 679 TRP cc_start: 0.8391 (OUTLIER) cc_final: 0.7648 (p90) REVERT: C 743 ASP cc_start: 0.8025 (m-30) cc_final: 0.7754 (m-30) REVERT: D 190 ASP cc_start: 0.8915 (t0) cc_final: 0.8606 (t0) REVERT: D 487 GLU cc_start: 0.4000 (tm-30) cc_final: 0.3513 (tm-30) REVERT: D 516 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8850 (tt) REVERT: D 547 TRP cc_start: 0.8639 (t60) cc_final: 0.7521 (t60) REVERT: D 671 ARG cc_start: 0.7974 (tpt170) cc_final: 0.7636 (tpm170) REVERT: B 311 GLN cc_start: 0.9074 (OUTLIER) cc_final: 0.8329 (mt0) REVERT: B 321 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8354 (tm) REVERT: B 326 TRP cc_start: 0.8259 (m100) cc_final: 0.7988 (m100) outliers start: 74 outliers final: 54 residues processed: 277 average time/residue: 0.3115 time to fit residues: 135.5673 Evaluate side-chains 277 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 216 time to evaluate : 2.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 200 TRP Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 479 TRP Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 111 TYR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 477 ILE Chi-restraints excluded: chain C residue 556 GLU Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 679 TRP Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 539 MET Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 668 PHE Chi-restraints excluded: chain D residue 679 TRP Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain B residue 26 MET Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 545 GLN Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 675 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 203 optimal weight: 7.9990 chunk 212 optimal weight: 9.9990 chunk 246 optimal weight: 9.9990 chunk 113 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 171 optimal weight: 10.0000 chunk 220 optimal weight: 9.9990 chunk 236 optimal weight: 10.0000 chunk 209 optimal weight: 9.9990 chunk 180 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN C 610 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.109750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.082612 restraints weight = 35700.754| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.97 r_work: 0.2773 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 21196 Z= 0.225 Angle : 0.605 8.960 28613 Z= 0.323 Chirality : 0.044 0.153 3071 Planarity : 0.004 0.050 3649 Dihedral : 4.581 20.279 2837 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.25 % Allowed : 17.42 % Favored : 79.33 % 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: -1.61 (0.17), residues: 2483 helix: 0.42 (0.23), residues: 508 sheet: -0.47 (0.19), residues: 837 loop : -2.27 (0.16), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 338 HIS 0.004 0.001 HIS D 219 PHE 0.026 0.002 PHE B 5 TYR 0.021 0.001 TYR B 599 ARG 0.007 0.000 ARG D 681 Details of bonding type rmsd hydrogen bonds : bond 0.05489 ( 730) hydrogen bonds : angle 4.93607 ( 2382) covalent geometry : bond 0.00542 (21196) covalent geometry : angle 0.60518 (28613) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4966 Ramachandran restraints generated. 2483 Oldfield, 0 Emsley, 2483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4966 Ramachandran restraints generated. 2483 Oldfield, 0 Emsley, 2483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 221 time to evaluate : 2.311 Fit side-chains REVERT: A 17 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7988 (ptm-80) REVERT: A 304 ARG cc_start: 0.8579 (mmm-85) cc_final: 0.8337 (mtp85) REVERT: A 505 TYR cc_start: 0.7602 (OUTLIER) cc_final: 0.6224 (p90) REVERT: A 733 MET cc_start: 0.9225 (mtm) cc_final: 0.8962 (ttm) REVERT: C 103 PHE cc_start: 0.8071 (OUTLIER) cc_final: 0.7070 (p90) REVERT: C 189 MET cc_start: 0.9268 (ptm) cc_final: 0.9040 (ttp) REVERT: C 203 GLU cc_start: 0.9094 (pm20) cc_final: 0.8736 (pm20) REVERT: C 679 TRP cc_start: 0.8440 (OUTLIER) cc_final: 0.7703 (p90) REVERT: C 743 ASP cc_start: 0.8031 (m-30) cc_final: 0.7755 (m-30) REVERT: D 190 ASP cc_start: 0.8860 (t0) cc_final: 0.8555 (t0) REVERT: D 487 GLU cc_start: 0.3947 (tm-30) cc_final: 0.3532 (tm-30) REVERT: D 516 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8868 (tt) REVERT: D 547 TRP cc_start: 0.8631 (t60) cc_final: 0.7587 (t60) REVERT: D 671 ARG cc_start: 0.7928 (tpt170) cc_final: 0.7619 (tpm170) REVERT: B 311 GLN cc_start: 0.9033 (OUTLIER) cc_final: 0.8304 (mt0) REVERT: B 321 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8311 (tm) REVERT: B 326 TRP cc_start: 0.8259 (m100) cc_final: 0.7994 (m100) outliers start: 72 outliers final: 58 residues processed: 275 average time/residue: 0.3251 time to fit residues: 140.0618 Evaluate side-chains 283 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 218 time to evaluate : 2.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 200 TRP Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 479 TRP Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 669 TYR Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 111 TYR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 477 ILE Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 679 TRP Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 539 MET Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 668 PHE Chi-restraints excluded: chain D residue 679 TRP Chi-restraints excluded: chain D residue 684 LEU Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain B residue 26 MET Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 545 GLN Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 675 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 126 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 221 optimal weight: 9.9990 chunk 203 optimal weight: 0.0010 chunk 227 optimal weight: 8.9990 chunk 84 optimal weight: 3.9990 overall best weight: 3.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.111764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.083917 restraints weight = 36050.478| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 3.08 r_work: 0.2832 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21196 Z= 0.137 Angle : 0.544 8.203 28613 Z= 0.290 Chirality : 0.042 0.153 3071 Planarity : 0.004 0.050 3649 Dihedral : 4.249 18.646 2837 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.98 % Allowed : 17.87 % Favored : 79.15 % 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: -1.43 (0.17), residues: 2483 helix: 0.58 (0.24), residues: 509 sheet: -0.36 (0.19), residues: 827 loop : -2.14 (0.16), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 338 HIS 0.002 0.001 HIS A 219 PHE 0.027 0.001 PHE B 5 TYR 0.020 0.001 TYR B 599 ARG 0.007 0.000 ARG D 681 Details of bonding type rmsd hydrogen bonds : bond 0.04437 ( 730) hydrogen bonds : angle 4.73895 ( 2382) covalent geometry : bond 0.00321 (21196) covalent geometry : angle 0.54386 (28613) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4966 Ramachandran restraints generated. 2483 Oldfield, 0 Emsley, 2483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4966 Ramachandran restraints generated. 2483 Oldfield, 0 Emsley, 2483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 236 time to evaluate : 2.451 Fit side-chains REVERT: A 17 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7868 (ptm-80) REVERT: A 304 ARG cc_start: 0.8532 (mmm-85) cc_final: 0.8279 (mtp85) REVERT: A 338 TRP cc_start: 0.6804 (t60) cc_final: 0.6433 (t-100) REVERT: A 505 TYR cc_start: 0.7294 (OUTLIER) cc_final: 0.5938 (p90) REVERT: A 733 MET cc_start: 0.9228 (mtm) cc_final: 0.8972 (ttm) REVERT: C 33 ASN cc_start: 0.9235 (t0) cc_final: 0.8870 (t0) REVERT: C 103 PHE cc_start: 0.7934 (OUTLIER) cc_final: 0.7312 (p90) REVERT: C 189 MET cc_start: 0.9273 (ptm) cc_final: 0.9037 (ttp) REVERT: C 203 GLU cc_start: 0.9060 (pm20) cc_final: 0.8701 (pm20) REVERT: C 247 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8422 (mm-30) REVERT: C 679 TRP cc_start: 0.8358 (OUTLIER) cc_final: 0.7523 (p90) REVERT: C 743 ASP cc_start: 0.8035 (m-30) cc_final: 0.7780 (m-30) REVERT: C 750 ASP cc_start: 0.7835 (m-30) cc_final: 0.7456 (t70) REVERT: D 190 ASP cc_start: 0.8768 (t0) cc_final: 0.8481 (t0) REVERT: D 487 GLU cc_start: 0.3913 (tm-30) cc_final: 0.3555 (tm-30) REVERT: D 516 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8848 (tt) REVERT: D 547 TRP cc_start: 0.8607 (t60) cc_final: 0.7500 (t60) REVERT: D 671 ARG cc_start: 0.7930 (tpt170) cc_final: 0.7509 (tpm170) REVERT: B 132 GLU cc_start: 0.7961 (tt0) cc_final: 0.7696 (tt0) REVERT: B 203 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8350 (mp0) REVERT: B 311 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8294 (mt0) REVERT: B 321 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8303 (tm) REVERT: B 326 TRP cc_start: 0.8220 (m100) cc_final: 0.7969 (m100) outliers start: 66 outliers final: 52 residues processed: 286 average time/residue: 0.3222 time to fit residues: 144.2821 Evaluate side-chains 288 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 229 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 200 TRP Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 479 TRP Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 669 TYR Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 111 TYR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 477 ILE Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 679 TRP Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 539 MET Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 668 PHE Chi-restraints excluded: chain D residue 679 TRP Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain B residue 26 MET Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 675 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 159 optimal weight: 10.0000 chunk 188 optimal weight: 7.9990 chunk 152 optimal weight: 9.9990 chunk 209 optimal weight: 20.0000 chunk 67 optimal weight: 10.0000 chunk 227 optimal weight: 0.0980 chunk 250 optimal weight: 20.0000 chunk 117 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.110764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.082397 restraints weight = 35875.964| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 3.09 r_work: 0.2795 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21196 Z= 0.160 Angle : 0.558 8.043 28613 Z= 0.297 Chirality : 0.043 0.155 3071 Planarity : 0.004 0.048 3649 Dihedral : 4.246 19.066 2837 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.02 % Allowed : 18.01 % Favored : 78.97 % 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: -1.37 (0.17), residues: 2483 helix: 0.58 (0.23), residues: 510 sheet: -0.31 (0.19), residues: 839 loop : -2.11 (0.16), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 338 HIS 0.003 0.001 HIS D 219 PHE 0.025 0.001 PHE B 5 TYR 0.023 0.001 TYR B 599 ARG 0.007 0.000 ARG D 681 Details of bonding type rmsd hydrogen bonds : bond 0.04753 ( 730) hydrogen bonds : angle 4.74796 ( 2382) covalent geometry : bond 0.00382 (21196) covalent geometry : angle 0.55798 (28613) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4966 Ramachandran restraints generated. 2483 Oldfield, 0 Emsley, 2483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4966 Ramachandran restraints generated. 2483 Oldfield, 0 Emsley, 2483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 232 time to evaluate : 2.841 Fit side-chains REVERT: A 17 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7970 (ptm-80) REVERT: A 304 ARG cc_start: 0.8569 (mmm-85) cc_final: 0.8320 (mtp85) REVERT: A 505 TYR cc_start: 0.7415 (OUTLIER) cc_final: 0.6041 (p90) REVERT: A 733 MET cc_start: 0.9223 (mtm) cc_final: 0.8960 (ttm) REVERT: C 103 PHE cc_start: 0.7866 (OUTLIER) cc_final: 0.7023 (p90) REVERT: C 189 MET cc_start: 0.9261 (ptm) cc_final: 0.9006 (ttp) REVERT: C 203 GLU cc_start: 0.9089 (pm20) cc_final: 0.8730 (pm20) REVERT: C 679 TRP cc_start: 0.8356 (OUTLIER) cc_final: 0.7530 (p90) REVERT: C 743 ASP cc_start: 0.8052 (m-30) cc_final: 0.7789 (m-30) REVERT: C 750 ASP cc_start: 0.7880 (m-30) cc_final: 0.7453 (t70) REVERT: D 190 ASP cc_start: 0.8847 (t0) cc_final: 0.8559 (t0) REVERT: D 487 GLU cc_start: 0.3952 (tm-30) cc_final: 0.3585 (tm-30) REVERT: D 516 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8844 (tt) REVERT: D 547 TRP cc_start: 0.8581 (t60) cc_final: 0.7491 (t60) REVERT: D 605 TYR cc_start: 0.8853 (m-80) cc_final: 0.8647 (m-80) REVERT: D 671 ARG cc_start: 0.7934 (tpt170) cc_final: 0.7530 (tpm170) REVERT: B 132 GLU cc_start: 0.8005 (tt0) cc_final: 0.7730 (tt0) REVERT: B 203 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8341 (mp0) REVERT: B 311 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8281 (mt0) REVERT: B 321 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8296 (tm) REVERT: B 326 TRP cc_start: 0.8236 (m100) cc_final: 0.7991 (m100) outliers start: 67 outliers final: 56 residues processed: 282 average time/residue: 0.3223 time to fit residues: 142.6247 Evaluate side-chains 288 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 225 time to evaluate : 2.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 200 TRP Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 479 TRP Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 669 TYR Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 111 TYR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 477 ILE Chi-restraints excluded: chain C residue 556 GLU Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 679 TRP Chi-restraints excluded: chain C residue 735 VAL Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 103 PHE Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 539 MET Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 668 PHE Chi-restraints excluded: chain D residue 679 TRP Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain B residue 26 MET Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 675 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 63 optimal weight: 6.9990 chunk 176 optimal weight: 20.0000 chunk 210 optimal weight: 4.9990 chunk 102 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 194 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 225 optimal weight: 8.9990 chunk 156 optimal weight: 5.9990 chunk 87 optimal weight: 20.0000 chunk 6 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.109882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.081972 restraints weight = 36414.606| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 3.07 r_work: 0.2765 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 21196 Z= 0.235 Angle : 0.613 9.184 28613 Z= 0.327 Chirality : 0.044 0.163 3071 Planarity : 0.004 0.048 3649 Dihedral : 4.475 20.532 2837 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 3.02 % Allowed : 17.96 % Favored : 79.02 % 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: -1.49 (0.17), residues: 2483 helix: 0.49 (0.23), residues: 508 sheet: -0.38 (0.19), residues: 832 loop : -2.18 (0.16), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 338 HIS 0.005 0.001 HIS D 219 PHE 0.026 0.002 PHE B 5 TYR 0.027 0.001 TYR B 599 ARG 0.007 0.000 ARG D 681 Details of bonding type rmsd hydrogen bonds : bond 0.05538 ( 730) hydrogen bonds : angle 4.89773 ( 2382) covalent geometry : bond 0.00566 (21196) covalent geometry : angle 0.61326 (28613) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8669.01 seconds wall clock time: 149 minutes 45.52 seconds (8985.52 seconds total)