Starting phenix.real_space_refine on Wed Aug 7 16:36:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k7u_36943/08_2024/8k7u_36943.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k7u_36943/08_2024/8k7u_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k7u_36943/08_2024/8k7u_36943.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k7u_36943/08_2024/8k7u_36943.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k7u_36943/08_2024/8k7u_36943.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k7u_36943/08_2024/8k7u_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 Residue "D ARG 491": "NH1" <-> "NH2" Residue "D PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 10.42, per 1000 atoms: 0.50 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 - 3.50 Amino acid : False - 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: 7.67 Conformation dependent library (CDL) restraints added in 3.7 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: 2.84 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: 7.64 Time building geometry restraints manager: 8.56 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: 98.56 - 105.71: 338 105.71 - 112.86: 10885 112.86 - 120.00: 7752 120.00 - 127.15: 9456 127.15 - 134.30: 182 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: 0.570 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: 0.860 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 52.940 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.710 ------------------------------------------------------------------------------- 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= 0.380 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 2.566 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: 0.3269 time to fit residues: 150.6003 Evaluate side-chains 244 residues out of total 2234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 2.433 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 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= 0.337 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 *********************** 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 fitting. rotamer outliers: 22 poor density : 245 time to evaluate : 2.396 Fit side-chains REVERT: A 573 MET cc_start: 0.8398 (mmt) cc_final: 0.8182 (mmt) REVERT: A 733 MET cc_start: 0.8887 (mtm) cc_final: 0.8608 (ttm) REVERT: C 189 MET cc_start: 0.8602 (ptm) cc_final: 0.8349 (ttp) REVERT: C 203 GLU cc_start: 0.8745 (pm20) cc_final: 0.8348 (pm20) REVERT: D 190 ASP cc_start: 0.8532 (t0) cc_final: 0.8252 (t0) REVERT: D 247 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7729 (mm-30) REVERT: D 547 TRP cc_start: 0.8152 (t60) cc_final: 0.7432 (t60) REVERT: D 671 ARG cc_start: 0.7697 (tpt170) cc_final: 0.7372 (tpm170) REVERT: B 17 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7422 (ptt-90) REVERT: B 669 TYR cc_start: 0.9010 (m-80) cc_final: 0.8753 (m-80) REVERT: B 682 PHE cc_start: 0.8423 (OUTLIER) cc_final: 0.7699 (p90) outliers start: 22 outliers final: 14 residues processed: 261 average time/residue: 0.3219 time to fit residues: 129.9637 Evaluate side-chains 247 residues out of total 2234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 231 time to evaluate : 2.226 ------------------------------------------------------------------------------- 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 128 optimal weight: 7.9990 chunk 71 optimal weight: 20.0000 chunk 191 optimal weight: 9.9990 chunk 157 optimal weight: 9.9990 chunk 63 optimal weight: 0.0570 chunk 231 optimal weight: 0.6980 chunk 249 optimal weight: 5.9990 chunk 205 optimal weight: 20.0000 chunk 229 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 185 optimal weight: 10.0000 overall best weight: 4.3504 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21196 Z= 0.253 Angle : 0.560 10.124 28613 Z= 0.302 Chirality : 0.043 0.159 3071 Planarity : 0.004 0.050 3649 Dihedral : 4.367 19.389 2837 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.85 % Allowed : 11.42 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.44 (0.23), residues: 516 sheet: -0.46 (0.19), residues: 841 loop : -2.22 (0.16), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 654 HIS 0.003 0.001 HIS D 219 PHE 0.030 0.001 PHE D 520 TYR 0.021 0.001 TYR B 599 ARG 0.007 0.000 ARG D 681 *********************** 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 287 residues out of total 2234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 246 time to evaluate : 2.335 Fit side-chains REVERT: A 573 MET cc_start: 0.8466 (mmt) cc_final: 0.8181 (mmt) REVERT: A 733 MET cc_start: 0.8921 (mtm) cc_final: 0.8659 (ttm) REVERT: C 103 PHE cc_start: 0.8014 (OUTLIER) cc_final: 0.7445 (p90) REVERT: C 189 MET cc_start: 0.8680 (ptm) cc_final: 0.8348 (ttp) REVERT: C 203 GLU cc_start: 0.8688 (pm20) cc_final: 0.8267 (pm20) REVERT: C 679 TRP cc_start: 0.8194 (OUTLIER) cc_final: 0.7484 (p90) REVERT: C 743 ASP cc_start: 0.7883 (m-30) cc_final: 0.7626 (m-30) REVERT: D 190 ASP cc_start: 0.8562 (t0) cc_final: 0.8234 (t0) REVERT: D 247 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7718 (mm-30) REVERT: D 547 TRP cc_start: 0.8176 (t60) cc_final: 0.7405 (t60) REVERT: B 321 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8272 (tm) REVERT: B 326 TRP cc_start: 0.8160 (m100) cc_final: 0.7792 (m100) REVERT: B 669 TYR cc_start: 0.8954 (m-80) cc_final: 0.8713 (m-80) REVERT: B 682 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.7557 (p90) outliers start: 41 outliers final: 25 residues processed: 277 average time/residue: 0.3145 time to fit residues: 135.5126 Evaluate side-chains 255 residues out of total 2234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 226 time to evaluate : 2.338 ------------------------------------------------------------------------------- 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 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 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 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 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 682 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 228 optimal weight: 20.0000 chunk 173 optimal weight: 20.0000 chunk 119 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 chunk 231 optimal weight: 8.9990 chunk 245 optimal weight: 8.9990 chunk 121 optimal weight: 10.0000 chunk 219 optimal weight: 0.3980 chunk 66 optimal weight: 9.9990 overall best weight: 7.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN A 222 ASN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 21196 Z= 0.420 Angle : 0.644 9.300 28613 Z= 0.345 Chirality : 0.046 0.172 3071 Planarity : 0.004 0.050 3649 Dihedral : 4.693 20.406 2837 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 2.48 % Allowed : 14.35 % Favored : 83.17 % 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: -1.65 (0.17), residues: 2483 helix: 0.29 (0.23), residues: 515 sheet: -0.48 (0.19), residues: 850 loop : -2.27 (0.16), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 413 HIS 0.005 0.001 HIS D 219 PHE 0.025 0.002 PHE B 682 TYR 0.020 0.002 TYR B 599 ARG 0.006 0.000 ARG D 681 *********************** 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 284 residues out of total 2234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 229 time to evaluate : 2.243 Fit side-chains REVERT: A 733 MET cc_start: 0.8912 (mtm) cc_final: 0.8610 (ttm) REVERT: C 103 PHE cc_start: 0.8124 (OUTLIER) cc_final: 0.7213 (p90) REVERT: C 679 TRP cc_start: 0.8353 (OUTLIER) cc_final: 0.7606 (p90) REVERT: C 743 ASP cc_start: 0.7890 (m-30) cc_final: 0.7603 (m-30) REVERT: D 18 GLU cc_start: 0.8467 (mp0) cc_final: 0.7847 (mp0) REVERT: D 190 ASP cc_start: 0.8601 (t0) cc_final: 0.8292 (t0) REVERT: D 247 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7808 (mm-30) REVERT: B 311 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8142 (mt0) REVERT: B 321 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8285 (tm) REVERT: B 326 TRP cc_start: 0.8214 (m100) cc_final: 0.7926 (m100) REVERT: B 669 TYR cc_start: 0.8981 (m-80) cc_final: 0.8772 (m-80) REVERT: B 682 PHE cc_start: 0.9048 (OUTLIER) cc_final: 0.7316 (p90) outliers start: 55 outliers final: 37 residues processed: 271 average time/residue: 0.3078 time to fit residues: 131.5134 Evaluate side-chains 261 residues out of total 2234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 219 time to evaluate : 2.535 ------------------------------------------------------------------------------- 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 273 VAL Chi-restraints excluded: chain A residue 362 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 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 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 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 23 MET 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 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 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 Chi-restraints excluded: chain B residue 682 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 204 optimal weight: 4.9990 chunk 139 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 182 optimal weight: 20.0000 chunk 101 optimal weight: 20.0000 chunk 209 optimal weight: 10.0000 chunk 169 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 125 optimal weight: 3.9990 chunk 220 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 676 ASN B 337 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1963 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= 0.339 Angle : 0.595 8.849 28613 Z= 0.319 Chirality : 0.044 0.155 3071 Planarity : 0.004 0.050 3649 Dihedral : 4.572 20.485 2837 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.11 % Allowed : 15.12 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.17), residues: 2483 helix: 0.35 (0.23), residues: 516 sheet: -0.50 (0.19), residues: 845 loop : -2.24 (0.16), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 479 HIS 0.005 0.001 HIS A 50 PHE 0.021 0.002 PHE B 682 TYR 0.018 0.001 TYR B 599 ARG 0.006 0.000 ARG D 681 *********************** 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 297 residues out of total 2234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 228 time to evaluate : 2.590 Fit side-chains REVERT: A 505 TYR cc_start: 0.7010 (OUTLIER) cc_final: 0.6088 (p90) REVERT: A 733 MET cc_start: 0.8921 (mtm) cc_final: 0.8650 (ttm) REVERT: C 103 PHE cc_start: 0.8050 (OUTLIER) cc_final: 0.7167 (p90) REVERT: C 189 MET cc_start: 0.8623 (ptm) cc_final: 0.8335 (ttp) REVERT: C 203 GLU cc_start: 0.8718 (pm20) cc_final: 0.8292 (pm20) REVERT: C 671 ARG cc_start: 0.8322 (ttp-170) cc_final: 0.8036 (ttp-170) REVERT: C 679 TRP cc_start: 0.8344 (OUTLIER) cc_final: 0.7593 (p90) REVERT: C 743 ASP cc_start: 0.7888 (m-30) cc_final: 0.7598 (m-30) REVERT: D 18 GLU cc_start: 0.8462 (mp0) cc_final: 0.7867 (mp0) REVERT: D 190 ASP cc_start: 0.8562 (t0) cc_final: 0.8253 (t0) REVERT: D 247 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7839 (mm-30) REVERT: D 516 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8818 (tt) REVERT: D 547 TRP cc_start: 0.8570 (t60) cc_final: 0.7445 (t60) REVERT: D 575 SER cc_start: 0.8717 (OUTLIER) cc_final: 0.8516 (t) REVERT: D 671 ARG cc_start: 0.7714 (tpt170) cc_final: 0.7398 (tpm170) REVERT: B 311 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8105 (mt0) REVERT: B 321 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8227 (tm) REVERT: B 599 TYR cc_start: 0.8594 (m-80) cc_final: 0.8147 (m-80) outliers start: 69 outliers final: 46 residues processed: 281 average time/residue: 0.3174 time to fit residues: 139.8971 Evaluate side-chains 274 residues out of total 2234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 221 time to evaluate : 2.439 ------------------------------------------------------------------------------- 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 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 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 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 161 THR Chi-restraints excluded: chain D residue 177 GLU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 216 GLN Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 575 SER 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 23 MET 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 82 optimal weight: 6.9990 chunk 221 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 chunk 144 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 chunk 245 optimal weight: 9.9990 chunk 204 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 20 optimal weight: 20.0000 chunk 81 optimal weight: 7.9990 chunk 129 optimal weight: 0.5980 overall best weight: 4.5188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21196 Z= 0.256 Angle : 0.554 8.118 28613 Z= 0.298 Chirality : 0.043 0.153 3071 Planarity : 0.004 0.049 3649 Dihedral : 4.370 19.571 2837 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.16 % Allowed : 16.38 % Favored : 80.46 % 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: -1.51 (0.17), residues: 2483 helix: 0.52 (0.24), residues: 510 sheet: -0.44 (0.19), residues: 847 loop : -2.20 (0.16), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 338 HIS 0.003 0.001 HIS A 50 PHE 0.021 0.001 PHE B 5 TYR 0.016 0.001 TYR B 599 ARG 0.006 0.000 ARG D 681 *********************** 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 308 residues out of total 2234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 238 time to evaluate : 2.589 Fit side-chains REVERT: A 17 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7414 (ptm-80) REVERT: A 304 ARG cc_start: 0.7980 (mmm-85) cc_final: 0.7725 (mtp85) REVERT: A 505 TYR cc_start: 0.6988 (OUTLIER) cc_final: 0.5926 (p90) REVERT: A 733 MET cc_start: 0.8926 (mtm) cc_final: 0.8654 (ttm) REVERT: C 103 PHE cc_start: 0.7966 (OUTLIER) cc_final: 0.7206 (p90) REVERT: C 189 MET cc_start: 0.8604 (ptm) cc_final: 0.8393 (ttp) REVERT: C 203 GLU cc_start: 0.8713 (pm20) cc_final: 0.8303 (pm20) REVERT: C 671 ARG cc_start: 0.8292 (ttp-170) cc_final: 0.7725 (ttp-170) REVERT: C 679 TRP cc_start: 0.8320 (OUTLIER) cc_final: 0.7580 (p90) REVERT: C 743 ASP cc_start: 0.7918 (m-30) cc_final: 0.7641 (m-30) REVERT: D 18 GLU cc_start: 0.8440 (mp0) cc_final: 0.7809 (mp0) REVERT: D 190 ASP cc_start: 0.8530 (t0) cc_final: 0.8232 (t0) REVERT: D 516 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8829 (tt) REVERT: D 547 TRP cc_start: 0.8566 (t60) cc_final: 0.7539 (t60) REVERT: D 671 ARG cc_start: 0.7773 (tpt170) cc_final: 0.7423 (tpm170) REVERT: B 203 GLU cc_start: 0.8317 (mt-10) cc_final: 0.7938 (mp0) REVERT: B 311 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8092 (mt0) REVERT: B 321 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8279 (tm) REVERT: B 326 TRP cc_start: 0.8208 (m100) cc_final: 0.7958 (m100) REVERT: B 599 TYR cc_start: 0.8567 (m-80) cc_final: 0.8181 (m-80) outliers start: 70 outliers final: 51 residues processed: 291 average time/residue: 0.3312 time to fit residues: 148.9869 Evaluate side-chains 288 residues out of total 2234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 230 time to evaluate : 2.487 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 675 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 236 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 179 optimal weight: 8.9990 chunk 139 optimal weight: 6.9990 chunk 206 optimal weight: 8.9990 chunk 137 optimal weight: 6.9990 chunk 244 optimal weight: 9.9990 chunk 153 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 113 optimal weight: 1.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 596 ASN C 610 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 21196 Z= 0.341 Angle : 0.596 8.887 28613 Z= 0.319 Chirality : 0.044 0.154 3071 Planarity : 0.004 0.049 3649 Dihedral : 4.509 19.851 2837 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.43 % Allowed : 17.06 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.17), residues: 2483 helix: 0.47 (0.24), residues: 508 sheet: -0.47 (0.19), residues: 845 loop : -2.20 (0.16), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 338 HIS 0.004 0.001 HIS D 219 PHE 0.022 0.002 PHE B 682 TYR 0.015 0.001 TYR B 21 ARG 0.005 0.000 ARG D 304 *********************** 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 308 residues out of total 2234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 232 time to evaluate : 2.487 Fit side-chains REVERT: A 17 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7507 (ptm-80) REVERT: A 505 TYR cc_start: 0.7234 (OUTLIER) cc_final: 0.5973 (p90) REVERT: A 733 MET cc_start: 0.8930 (mtm) cc_final: 0.8658 (ttm) REVERT: C 103 PHE cc_start: 0.8020 (OUTLIER) cc_final: 0.7099 (p90) REVERT: C 189 MET cc_start: 0.8619 (ptm) cc_final: 0.8410 (ttp) REVERT: C 203 GLU cc_start: 0.8730 (pm20) cc_final: 0.8308 (pm20) REVERT: C 679 TRP cc_start: 0.8357 (OUTLIER) cc_final: 0.7535 (p90) REVERT: C 743 ASP cc_start: 0.7895 (m-30) cc_final: 0.7605 (m-30) REVERT: D 18 GLU cc_start: 0.8438 (mp0) cc_final: 0.7811 (mp0) REVERT: D 190 ASP cc_start: 0.8535 (t0) cc_final: 0.8237 (t0) REVERT: D 487 GLU cc_start: 0.4251 (tm-30) cc_final: 0.3900 (tm-30) REVERT: D 516 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8831 (tt) REVERT: D 547 TRP cc_start: 0.8532 (t60) cc_final: 0.7568 (t60) REVERT: D 671 ARG cc_start: 0.7752 (tpt170) cc_final: 0.7407 (tpm170) REVERT: B 132 GLU cc_start: 0.7655 (tt0) cc_final: 0.7430 (tt0) REVERT: B 311 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8132 (mt0) REVERT: B 321 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8237 (tm) REVERT: B 326 TRP cc_start: 0.8152 (m100) cc_final: 0.7867 (m100) REVERT: B 599 TYR cc_start: 0.8587 (m-80) cc_final: 0.8152 (m-80) outliers start: 76 outliers final: 58 residues processed: 290 average time/residue: 0.3123 time to fit residues: 140.3673 Evaluate side-chains 282 residues out of total 2234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 217 time to evaluate : 2.290 ------------------------------------------------------------------------------- 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 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 668 PHE 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 103 PHE Chi-restraints excluded: chain D residue 129 ASP 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 23 MET 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 274 MET 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 151 optimal weight: 8.9990 chunk 97 optimal weight: 7.9990 chunk 146 optimal weight: 10.0000 chunk 73 optimal weight: 0.7980 chunk 48 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 155 optimal weight: 0.9980 chunk 166 optimal weight: 7.9990 chunk 121 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 192 optimal weight: 9.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21196 Z= 0.251 Angle : 0.558 8.128 28613 Z= 0.299 Chirality : 0.043 0.154 3071 Planarity : 0.004 0.050 3649 Dihedral : 4.351 19.058 2837 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.25 % Allowed : 17.60 % 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: -1.45 (0.17), residues: 2483 helix: 0.55 (0.24), residues: 509 sheet: -0.41 (0.19), residues: 841 loop : -2.13 (0.16), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 338 HIS 0.003 0.001 HIS A 50 PHE 0.021 0.001 PHE B 5 TYR 0.019 0.001 TYR B 510 ARG 0.006 0.000 ARG D 304 *********************** 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 298 residues out of total 2234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 226 time to evaluate : 2.213 Fit side-chains REVERT: A 17 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7440 (ptm-80) REVERT: A 304 ARG cc_start: 0.7978 (mmm-85) cc_final: 0.7714 (mtp85) REVERT: A 505 TYR cc_start: 0.7188 (OUTLIER) cc_final: 0.5836 (p90) REVERT: A 733 MET cc_start: 0.8923 (mtm) cc_final: 0.8657 (ttm) REVERT: C 103 PHE cc_start: 0.7906 (OUTLIER) cc_final: 0.7123 (p90) REVERT: C 189 MET cc_start: 0.8651 (ptm) cc_final: 0.8436 (ttp) REVERT: C 203 GLU cc_start: 0.8720 (pm20) cc_final: 0.8299 (pm20) REVERT: C 247 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7865 (mm-30) REVERT: C 679 TRP cc_start: 0.8330 (OUTLIER) cc_final: 0.7512 (p90) REVERT: C 743 ASP cc_start: 0.7930 (m-30) cc_final: 0.7647 (m-30) REVERT: D 190 ASP cc_start: 0.8507 (t0) cc_final: 0.8205 (t0) REVERT: D 487 GLU cc_start: 0.4187 (tm-30) cc_final: 0.3880 (tm-30) REVERT: D 516 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8845 (tt) REVERT: D 547 TRP cc_start: 0.8516 (t60) cc_final: 0.7585 (t60) REVERT: D 671 ARG cc_start: 0.7676 (tpt170) cc_final: 0.7351 (tpm170) REVERT: B 132 GLU cc_start: 0.7621 (tt0) cc_final: 0.7384 (tt0) REVERT: B 203 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7932 (mp0) REVERT: B 311 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8121 (mt0) REVERT: B 321 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8226 (tm) REVERT: B 326 TRP cc_start: 0.8135 (m100) cc_final: 0.7867 (m100) REVERT: B 599 TYR cc_start: 0.8557 (m-80) cc_final: 0.8202 (m-80) outliers start: 72 outliers final: 58 residues processed: 278 average time/residue: 0.3180 time to fit residues: 137.6048 Evaluate side-chains 285 residues out of total 2234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 220 time to evaluate : 2.438 ------------------------------------------------------------------------------- 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 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 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 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 129 ASP 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 324 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 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 274 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 222 optimal weight: 5.9990 chunk 234 optimal weight: 20.0000 chunk 213 optimal weight: 2.9990 chunk 228 optimal weight: 1.9990 chunk 137 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 179 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 206 optimal weight: 5.9990 chunk 215 optimal weight: 0.9980 chunk 227 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN A 596 ASN B 231 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2319 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= 0.181 Angle : 0.524 7.489 28613 Z= 0.280 Chirality : 0.042 0.152 3071 Planarity : 0.004 0.049 3649 Dihedral : 4.120 18.419 2837 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.66 % Allowed : 18.37 % 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: -1.30 (0.17), residues: 2483 helix: 0.65 (0.24), residues: 510 sheet: -0.32 (0.19), residues: 838 loop : -2.02 (0.17), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 338 HIS 0.002 0.001 HIS A 50 PHE 0.025 0.001 PHE C 751 TYR 0.015 0.001 TYR B 599 ARG 0.007 0.000 ARG D 681 *********************** 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 299 residues out of total 2234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 240 time to evaluate : 2.344 Fit side-chains REVERT: A 17 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7330 (ptm-80) REVERT: A 338 TRP cc_start: 0.6536 (t60) cc_final: 0.6274 (t-100) REVERT: A 505 TYR cc_start: 0.7055 (OUTLIER) cc_final: 0.5796 (p90) REVERT: A 733 MET cc_start: 0.8925 (mtm) cc_final: 0.8655 (ttm) REVERT: C 103 PHE cc_start: 0.7904 (OUTLIER) cc_final: 0.7255 (p90) REVERT: C 189 MET cc_start: 0.8669 (ptm) cc_final: 0.8412 (ttp) REVERT: C 203 GLU cc_start: 0.8678 (pm20) cc_final: 0.8240 (pm20) REVERT: C 229 GLU cc_start: 0.8101 (mp0) cc_final: 0.7692 (mt-10) REVERT: C 247 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7830 (mm-30) REVERT: C 481 MET cc_start: 0.7824 (tpt) cc_final: 0.7387 (tpp) REVERT: C 679 TRP cc_start: 0.8295 (OUTLIER) cc_final: 0.7486 (p90) REVERT: C 743 ASP cc_start: 0.7929 (m-30) cc_final: 0.7649 (m-30) REVERT: D 111 TYR cc_start: 0.6962 (m-80) cc_final: 0.6751 (m-80) REVERT: D 190 ASP cc_start: 0.8464 (t0) cc_final: 0.8188 (t0) REVERT: D 487 GLU cc_start: 0.4271 (tm-30) cc_final: 0.3966 (tm-30) REVERT: D 516 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8817 (tt) REVERT: D 547 TRP cc_start: 0.8475 (t60) cc_final: 0.7555 (t60) REVERT: D 671 ARG cc_start: 0.7674 (tpt170) cc_final: 0.7283 (tpm170) REVERT: B 132 GLU cc_start: 0.7574 (tt0) cc_final: 0.7330 (tt0) REVERT: B 311 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8147 (mt0) REVERT: B 321 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8187 (tm) REVERT: B 326 TRP cc_start: 0.8088 (m100) cc_final: 0.7833 (m100) REVERT: B 599 TYR cc_start: 0.8522 (m-80) cc_final: 0.8181 (m-80) outliers start: 59 outliers final: 44 residues processed: 281 average time/residue: 0.3166 time to fit residues: 138.1667 Evaluate side-chains 281 residues out of total 2234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 230 time to evaluate : 2.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG 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 472 SER Chi-restraints excluded: chain A residue 479 TRP Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 540 LEU 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 456 GLU 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 265 VAL Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 539 MET 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 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 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 149 optimal weight: 10.0000 chunk 241 optimal weight: 20.0000 chunk 147 optimal weight: 1.9990 chunk 114 optimal weight: 0.1980 chunk 167 optimal weight: 20.0000 chunk 253 optimal weight: 6.9990 chunk 232 optimal weight: 6.9990 chunk 201 optimal weight: 0.7980 chunk 20 optimal weight: 20.0000 chunk 155 optimal weight: 6.9990 chunk 123 optimal weight: 10.0000 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2349 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= 0.210 Angle : 0.541 8.994 28613 Z= 0.289 Chirality : 0.042 0.180 3071 Planarity : 0.004 0.049 3649 Dihedral : 4.114 18.458 2837 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.75 % Allowed : 18.73 % Favored : 78.52 % 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: -1.26 (0.17), residues: 2483 helix: 0.65 (0.24), residues: 510 sheet: -0.26 (0.19), residues: 831 loop : -1.99 (0.17), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 338 HIS 0.002 0.001 HIS A 50 PHE 0.022 0.001 PHE B 5 TYR 0.016 0.001 TYR A 426 ARG 0.007 0.000 ARG D 681 ********************** 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 289 residues out of total 2234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 228 time to evaluate : 2.567 Fit side-chains REVERT: A 17 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7342 (ptm-80) REVERT: A 338 TRP cc_start: 0.6506 (t60) cc_final: 0.6226 (t-100) REVERT: A 505 TYR cc_start: 0.7117 (OUTLIER) cc_final: 0.5885 (p90) REVERT: A 733 MET cc_start: 0.8916 (mtm) cc_final: 0.8648 (ttm) REVERT: C 103 PHE cc_start: 0.7902 (OUTLIER) cc_final: 0.7156 (p90) REVERT: C 189 MET cc_start: 0.8658 (ptm) cc_final: 0.8408 (ttp) REVERT: C 203 GLU cc_start: 0.8700 (pm20) cc_final: 0.8265 (pm20) REVERT: C 229 GLU cc_start: 0.8122 (mp0) cc_final: 0.7654 (mt-10) REVERT: C 481 MET cc_start: 0.7801 (tpt) cc_final: 0.7355 (tpp) REVERT: C 679 TRP cc_start: 0.8314 (OUTLIER) cc_final: 0.7506 (p90) REVERT: C 743 ASP cc_start: 0.7925 (m-30) cc_final: 0.7665 (m-30) REVERT: D 111 TYR cc_start: 0.6936 (m-80) cc_final: 0.6724 (m-80) REVERT: D 190 ASP cc_start: 0.8477 (t0) cc_final: 0.8184 (t0) REVERT: D 516 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8842 (tt) REVERT: D 547 TRP cc_start: 0.8496 (t60) cc_final: 0.7532 (t60) REVERT: D 671 ARG cc_start: 0.7685 (tpt170) cc_final: 0.7306 (tpm170) REVERT: B 132 GLU cc_start: 0.7563 (tt0) cc_final: 0.7307 (tt0) REVERT: B 203 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7969 (mp0) REVERT: B 311 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8155 (mt0) REVERT: B 321 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8184 (tm) REVERT: B 326 TRP cc_start: 0.8098 (m100) cc_final: 0.7852 (m100) REVERT: B 599 TYR cc_start: 0.8526 (m-80) cc_final: 0.8186 (m-80) outliers start: 61 outliers final: 53 residues processed: 272 average time/residue: 0.3191 time to fit residues: 134.7159 Evaluate side-chains 284 residues out of total 2234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 224 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 75 GLN 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 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 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 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 456 GLU 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 457 VAL Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 539 MET 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 9 THR 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 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 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 160 optimal weight: 10.0000 chunk 214 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 chunk 185 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 201 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 37 optimal weight: 50.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- 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 = 0.3397 r_free = 0.3397 target = 0.110885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.082655 restraints weight = 35782.710| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.07 r_work: 0.2811 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21196 Z= 0.252 Angle : 0.558 8.313 28613 Z= 0.298 Chirality : 0.043 0.163 3071 Planarity : 0.004 0.048 3649 Dihedral : 4.210 19.340 2837 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.98 % Allowed : 18.68 % Favored : 78.34 % 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: -1.28 (0.17), residues: 2483 helix: 0.67 (0.24), residues: 510 sheet: -0.31 (0.19), residues: 842 loop : -2.02 (0.17), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 338 HIS 0.003 0.001 HIS D 219 PHE 0.030 0.001 PHE C 751 TYR 0.016 0.001 TYR A 426 ARG 0.007 0.000 ARG D 681 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4003.86 seconds wall clock time: 72 minutes 30.45 seconds (4350.45 seconds total)