Starting phenix.real_space_refine on Tue Mar 19 08:31:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgg_22869/03_2024/7kgg_22869_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgg_22869/03_2024/7kgg_22869.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgg_22869/03_2024/7kgg_22869_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgg_22869/03_2024/7kgg_22869_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgg_22869/03_2024/7kgg_22869_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgg_22869/03_2024/7kgg_22869.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgg_22869/03_2024/7kgg_22869.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgg_22869/03_2024/7kgg_22869_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kgg_22869/03_2024/7kgg_22869_updated.pdb" } resolution = 2.97 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.211 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 135 5.16 5 C 15374 2.51 5 N 3807 2.21 5 O 4355 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 7": "NH1" <-> "NH2" Residue "A ARG 8": "NH1" <-> "NH2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "A ARG 123": "NH1" <-> "NH2" Residue "A ARG 160": "NH1" <-> "NH2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A ARG 168": "NH1" <-> "NH2" Residue "A ARG 185": "NH1" <-> "NH2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A ARG 218": "NH1" <-> "NH2" Residue "A GLU 269": "OE1" <-> "OE2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A ARG 418": "NH1" <-> "NH2" Residue "A ARG 583": "NH1" <-> "NH2" Residue "A GLU 592": "OE1" <-> "OE2" Residue "A ARG 632": "NH1" <-> "NH2" Residue "A GLU 665": "OE1" <-> "OE2" Residue "A ARG 675": "NH1" <-> "NH2" Residue "A ARG 679": "NH1" <-> "NH2" Residue "A ARG 758": "NH1" <-> "NH2" Residue "A ARG 771": "NH1" <-> "NH2" Residue "A ARG 809": "NH1" <-> "NH2" Residue "A ARG 833": "NH1" <-> "NH2" Residue "A GLU 834": "OE1" <-> "OE2" Residue "A GLU 836": "OE1" <-> "OE2" Residue "A ARG 910": "NH1" <-> "NH2" Residue "A ARG 961": "NH1" <-> "NH2" Residue "A ARG 963": "NH1" <-> "NH2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "B ARG 7": "NH1" <-> "NH2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B GLU 66": "OE1" <-> "OE2" Residue "B GLU 101": "OE1" <-> "OE2" Residue "B ARG 123": "NH1" <-> "NH2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 160": "NH1" <-> "NH2" Residue "B ARG 168": "NH1" <-> "NH2" Residue "B ARG 185": "NH1" <-> "NH2" Residue "B ARG 208": "NH1" <-> "NH2" Residue "B ARG 218": "NH1" <-> "NH2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B ARG 418": "NH1" <-> "NH2" Residue "B GLU 525": "OE1" <-> "OE2" Residue "B PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 583": "NH1" <-> "NH2" Residue "B ARG 585": "NH1" <-> "NH2" Residue "B GLU 592": "OE1" <-> "OE2" Residue "B GLU 665": "OE1" <-> "OE2" Residue "B ARG 675": "NH1" <-> "NH2" Residue "B ARG 679": "NH1" <-> "NH2" Residue "B GLU 693": "OE1" <-> "OE2" Residue "B ARG 724": "NH1" <-> "NH2" Residue "B ARG 758": "NH1" <-> "NH2" Residue "B ARG 771": "NH1" <-> "NH2" Residue "B ARG 809": "NH1" <-> "NH2" Residue "B ARG 833": "NH1" <-> "NH2" Residue "B GLU 834": "OE1" <-> "OE2" Residue "B ARG 910": "NH1" <-> "NH2" Residue "B ARG 961": "NH1" <-> "NH2" Residue "B ARG 963": "NH1" <-> "NH2" Residue "C ARG 7": "NH1" <-> "NH2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C ARG 123": "NH1" <-> "NH2" Residue "C PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 160": "NH1" <-> "NH2" Residue "C GLU 165": "OE1" <-> "OE2" Residue "C ARG 168": "NH1" <-> "NH2" Residue "C ARG 185": "NH1" <-> "NH2" Residue "C ARG 208": "NH1" <-> "NH2" Residue "C GLU 213": "OE1" <-> "OE2" Residue "C ARG 218": "NH1" <-> "NH2" Residue "C GLU 244": "OE1" <-> "OE2" Residue "C ARG 307": "NH1" <-> "NH2" Residue "C PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C ARG 363": "NH1" <-> "NH2" Residue "C GLU 414": "OE1" <-> "OE2" Residue "C GLU 423": "OE1" <-> "OE2" Residue "C TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 563": "OE1" <-> "OE2" Residue "C GLU 564": "OE1" <-> "OE2" Residue "C ARG 583": "NH1" <-> "NH2" Residue "C ARG 585": "NH1" <-> "NH2" Residue "C ARG 632": "NH1" <-> "NH2" Residue "C ARG 679": "NH1" <-> "NH2" Residue "C GLU 693": "OE1" <-> "OE2" Residue "C ARG 724": "NH1" <-> "NH2" Residue "C ARG 758": "NH1" <-> "NH2" Residue "C GLU 767": "OE1" <-> "OE2" Residue "C ARG 771": "NH1" <-> "NH2" Residue "C ARG 809": "NH1" <-> "NH2" Residue "C ARG 813": "NH1" <-> "NH2" Residue "C PHE 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 836": "OE1" <-> "OE2" Residue "C ARG 910": "NH1" <-> "NH2" Residue "C GLU 938": "OE1" <-> "OE2" Residue "C ARG 961": "NH1" <-> "NH2" Residue "C ARG 963": "NH1" <-> "NH2" Residue "C GLU 988": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23677 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7785 Classifications: {'peptide': 1020} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 973} Chain breaks: 1 Chain: "B" Number of atoms: 7784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7784 Classifications: {'peptide': 1020} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 973} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 7785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7785 Classifications: {'peptide': 1020} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 973} Chain breaks: 1 Chain: "A" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 81 Unusual residues: {'PTY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'PTY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "C" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 153 Unusual residues: {' ET': 3, 'PTY': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Time building chain proxies: 12.44, per 1000 atoms: 0.53 Number of scatterers: 23677 At special positions: 0 Unit cell: (119.88, 114.48, 141.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 135 16.00 P 6 15.00 O 4355 8.00 N 3807 7.00 C 15374 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: 8.71 Conformation dependent library (CDL) restraints added in 4.4 seconds 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5706 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 108 helices and 27 sheets defined 55.0% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.43 Creating SS restraints... Processing helix chain 'A' and resid 2 through 6 Processing helix chain 'A' and resid 9 through 29 Proline residue: A 28 - end of helix Processing helix chain 'A' and resid 54 through 60 Processing helix chain 'A' and resid 62 through 71 removed outlier: 3.954A pdb=" N GLU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 69 " --> pdb=" O ILE A 65 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N SER A 70 " --> pdb=" O GLU A 66 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N GLY A 71 " --> pdb=" O ARG A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 115 removed outlier: 4.446A pdb=" N ALA A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N VAL A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU A 115 " --> pdb=" O ILE A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 151 through 161 Processing helix chain 'A' and resid 163 through 168 removed outlier: 3.676A pdb=" N ARG A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 196 removed outlier: 3.537A pdb=" N TYR A 196 " --> pdb=" O LYS A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 210 Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 262 through 265 No H-bonds generated for 'chain 'A' and resid 262 through 265' Processing helix chain 'A' and resid 299 through 316 removed outlier: 3.925A pdb=" N ASN A 316 " --> pdb=" O GLU A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 359 Processing helix chain 'A' and resid 362 through 386 Proline residue: A 368 - end of helix removed outlier: 4.108A pdb=" N VAL A 371 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA A 372 " --> pdb=" O PRO A 368 " (cutoff:3.500A) Proline residue: A 373 - end of helix Processing helix chain 'A' and resid 392 through 404 removed outlier: 4.400A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 422 Processing helix chain 'A' and resid 427 through 458 removed outlier: 5.428A pdb=" N SER A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) Proline residue: A 441 - end of helix removed outlier: 4.061A pdb=" N PHE A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Proline residue: A 455 - end of helix removed outlier: 4.026A pdb=" N PHE A 458 " --> pdb=" O LEU A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 486 removed outlier: 3.733A pdb=" N GLN A 469 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A 477 " --> pdb=" O THR A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 495 Processing helix chain 'A' and resid 509 through 533 Processing helix chain 'A' and resid 535 through 555 Processing helix chain 'A' and resid 581 through 595 Processing helix chain 'A' and resid 636 through 650 removed outlier: 4.013A pdb=" N ASN A 649 " --> pdb=" O SER A 645 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER A 650 " --> pdb=" O SER A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 700 removed outlier: 3.800A pdb=" N LYS A 700 " --> pdb=" O ALA A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 730 Processing helix chain 'A' and resid 734 through 742 Processing helix chain 'A' and resid 768 through 770 No H-bonds generated for 'chain 'A' and resid 768 through 770' Processing helix chain 'A' and resid 774 through 778 Processing helix chain 'A' and resid 792 through 795 No H-bonds generated for 'chain 'A' and resid 792 through 795' Processing helix chain 'A' and resid 828 through 841 removed outlier: 3.739A pdb=" N LYS A 841 " --> pdb=" O GLN A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 883 removed outlier: 4.799A pdb=" N ALA A 865 " --> pdb=" O GLU A 861 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N PHE A 866 " --> pdb=" O SER A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 892 Processing helix chain 'A' and resid 896 through 910 Processing helix chain 'A' and resid 916 through 947 removed outlier: 3.831A pdb=" N ILE A 936 " --> pdb=" O ASN A 932 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N PHE A 939 " --> pdb=" O LEU A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 980 removed outlier: 5.006A pdb=" N ARG A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Proline residue: A 964 - end of helix Proline residue: A 978 - end of helix Processing helix chain 'A' and resid 987 through 1026 removed outlier: 4.273A pdb=" N GLY A 996 " --> pdb=" O ALA A 992 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL A 997 " --> pdb=" O LEU A 993 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N PHE A1010 " --> pdb=" O ILE A1006 " (cutoff:3.500A) Proline residue: A1013 - end of helix Processing helix chain 'B' and resid 9 through 29 WARNING: missing atoms! Proline residue: B 28 - end of helix Processing helix chain 'B' and resid 54 through 60 Processing helix chain 'B' and resid 62 through 69 removed outlier: 4.013A pdb=" N GLU B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 114 removed outlier: 4.100A pdb=" N ALA B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N VAL B 114 " --> pdb=" O LYS B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 151 through 161 Processing helix chain 'B' and resid 163 through 167 Processing helix chain 'B' and resid 190 through 195 removed outlier: 3.766A pdb=" N VAL B 194 " --> pdb=" O PRO B 190 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER B 195 " --> pdb=" O ASN B 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 190 through 195' Processing helix chain 'B' and resid 200 through 210 Processing helix chain 'B' and resid 243 through 247 Processing helix chain 'B' and resid 262 through 265 No H-bonds generated for 'chain 'B' and resid 262 through 265' Processing helix chain 'B' and resid 299 through 315 removed outlier: 4.146A pdb=" N LEU B 315 " --> pdb=" O GLU B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 359 removed outlier: 3.752A pdb=" N LYS B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 386 Proline residue: B 368 - end of helix removed outlier: 4.630A pdb=" N VAL B 371 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA B 372 " --> pdb=" O PRO B 368 " (cutoff:3.500A) Proline residue: B 373 - end of helix Processing helix chain 'B' and resid 392 through 423 removed outlier: 4.416A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP B 407 " --> pdb=" O GLY B 403 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASP B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ALA B 409 " --> pdb=" O ILE B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 451 removed outlier: 5.800A pdb=" N SER B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) Proline residue: B 441 - end of helix Processing helix chain 'B' and resid 455 through 458 Processing helix chain 'B' and resid 461 through 495 removed outlier: 3.584A pdb=" N GLN B 469 " --> pdb=" O VAL B 465 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER B 477 " --> pdb=" O THR B 473 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N THR B 489 " --> pdb=" O ALA B 485 " (cutoff:3.500A) Proline residue: B 490 - end of helix Processing helix chain 'B' and resid 509 through 533 removed outlier: 3.989A pdb=" N LYS B 533 " --> pdb=" O LEU B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 555 Processing helix chain 'B' and resid 581 through 595 Processing helix chain 'B' and resid 636 through 649 removed outlier: 3.797A pdb=" N ASN B 649 " --> pdb=" O SER B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 700 removed outlier: 3.761A pdb=" N LYS B 700 " --> pdb=" O ALA B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 730 Processing helix chain 'B' and resid 734 through 742 Processing helix chain 'B' and resid 768 through 770 No H-bonds generated for 'chain 'B' and resid 768 through 770' Processing helix chain 'B' and resid 774 through 779 Processing helix chain 'B' and resid 792 through 795 No H-bonds generated for 'chain 'B' and resid 792 through 795' Processing helix chain 'B' and resid 828 through 841 removed outlier: 3.676A pdb=" N LYS B 841 " --> pdb=" O GLN B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 862 Processing helix chain 'B' and resid 864 through 883 Processing helix chain 'B' and resid 888 through 894 removed outlier: 3.590A pdb=" N LEU B 894 " --> pdb=" O LEU B 890 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 909 removed outlier: 4.749A pdb=" N GLY B 902 " --> pdb=" O LEU B 898 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE B 905 " --> pdb=" O PHE B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 946 removed outlier: 3.835A pdb=" N ILE B 936 " --> pdb=" O ASN B 932 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE B 939 " --> pdb=" O LEU B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 980 removed outlier: 5.093A pdb=" N ARG B 963 " --> pdb=" O LYS B 959 " (cutoff:3.500A) Proline residue: B 964 - end of helix Proline residue: B 978 - end of helix Processing helix chain 'B' and resid 987 through 1026 removed outlier: 4.477A pdb=" N GLY B 996 " --> pdb=" O ALA B 992 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL B 997 " --> pdb=" O LEU B 993 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE B1009 " --> pdb=" O THR B1005 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N PHE B1010 " --> pdb=" O ILE B1006 " (cutoff:3.500A) Proline residue: B1013 - end of helix Processing helix chain 'C' and resid 3 through 6 No H-bonds generated for 'chain 'C' and resid 3 through 6' Processing helix chain 'C' and resid 9 through 29 Proline residue: C 28 - end of helix Processing helix chain 'C' and resid 54 through 60 Processing helix chain 'C' and resid 62 through 71 removed outlier: 3.908A pdb=" N GLU C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLY C 71 " --> pdb=" O ARG C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 114 removed outlier: 3.886A pdb=" N ALA C 113 " --> pdb=" O ASN C 109 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL C 114 " --> pdb=" O LYS C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 151 through 161 Processing helix chain 'C' and resid 163 through 167 Processing helix chain 'C' and resid 190 through 195 Processing helix chain 'C' and resid 200 through 210 Processing helix chain 'C' and resid 243 through 247 Processing helix chain 'C' and resid 262 through 265 No H-bonds generated for 'chain 'C' and resid 262 through 265' Processing helix chain 'C' and resid 299 through 315 removed outlier: 3.828A pdb=" N LEU C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 359 removed outlier: 3.659A pdb=" N THR C 343 " --> pdb=" O LYS C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 386 Proline residue: C 368 - end of helix removed outlier: 4.304A pdb=" N ALA C 372 " --> pdb=" O ALA C 369 " (cutoff:3.500A) Proline residue: C 373 - end of helix Processing helix chain 'C' and resid 392 through 423 removed outlier: 4.379A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL C 411 " --> pdb=" O ASP C 407 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL C 412 " --> pdb=" O ASP C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 457 removed outlier: 5.619A pdb=" N SER C 440 " --> pdb=" O LYS C 436 " (cutoff:3.500A) Proline residue: C 441 - end of helix Proline residue: C 455 - end of helix Processing helix chain 'C' and resid 462 through 495 removed outlier: 3.657A pdb=" N PHE C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR C 473 " --> pdb=" O GLN C 469 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N THR C 489 " --> pdb=" O ALA C 485 " (cutoff:3.500A) Proline residue: C 490 - end of helix Processing helix chain 'C' and resid 509 through 533 Processing helix chain 'C' and resid 536 through 555 Processing helix chain 'C' and resid 581 through 596 Processing helix chain 'C' and resid 636 through 646 Processing helix chain 'C' and resid 684 through 700 removed outlier: 3.858A pdb=" N LYS C 700 " --> pdb=" O ALA C 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 730 Processing helix chain 'C' and resid 734 through 745 Processing helix chain 'C' and resid 768 through 770 No H-bonds generated for 'chain 'C' and resid 768 through 770' Processing helix chain 'C' and resid 774 through 779 Processing helix chain 'C' and resid 792 through 795 No H-bonds generated for 'chain 'C' and resid 792 through 795' Processing helix chain 'C' and resid 828 through 840 Processing helix chain 'C' and resid 852 through 860 Processing helix chain 'C' and resid 863 through 883 Processing helix chain 'C' and resid 888 through 910 removed outlier: 4.148A pdb=" N VAL C 892 " --> pdb=" O ILE C 888 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL C 895 " --> pdb=" O SER C 891 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N VAL C 896 " --> pdb=" O VAL C 892 " (cutoff:3.500A) Proline residue: C 897 - end of helix removed outlier: 3.808A pdb=" N ILE C 900 " --> pdb=" O VAL C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 946 removed outlier: 3.558A pdb=" N PHE C 939 " --> pdb=" O LEU C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 950 through 980 removed outlier: 4.731A pdb=" N ARG C 963 " --> pdb=" O LYS C 959 " (cutoff:3.500A) Proline residue: C 964 - end of helix Proline residue: C 978 - end of helix Processing helix chain 'C' and resid 987 through 1026 removed outlier: 4.395A pdb=" N GLY C 996 " --> pdb=" O ALA C 992 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL C 997 " --> pdb=" O LEU C 993 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE C1009 " --> pdb=" O THR C1005 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N PHE C1010 " --> pdb=" O ILE C1006 " (cutoff:3.500A) Proline residue: C1013 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 128 through 131 Processing sheet with id= B, first strand: chain 'A' and resid 322 through 324 Processing sheet with id= C, first strand: chain 'A' and resid 266 through 272 Processing sheet with id= D, first strand: chain 'A' and resid 250 through 252 Processing sheet with id= E, first strand: chain 'A' and resid 278 through 280 removed outlier: 6.874A pdb=" N THR A 625 " --> pdb=" O LYS A 602 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ASN A 604 " --> pdb=" O PHE A 623 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE A 623 " --> pdb=" O ASN A 604 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ALA A 606 " --> pdb=" O VAL A 621 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL A 621 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU A 608 " --> pdb=" O VAL A 619 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N VAL A 619 " --> pdb=" O LEU A 608 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 846 through 850 removed outlier: 3.682A pdb=" N MET A 706 " --> pdb=" O ILE A 821 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 715 through 722 Processing sheet with id= H, first strand: chain 'A' and resid 752 through 755 Processing sheet with id= I, first strand: chain 'A' and resid 781 through 783 Processing sheet with id= J, first strand: chain 'B' and resid 128 through 131 Processing sheet with id= K, first strand: chain 'B' and resid 322 through 324 removed outlier: 3.577A pdb=" N MET B 138 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 266 through 272 removed outlier: 8.084A pdb=" N LYS B 182 " --> pdb=" O MET B 759 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N GLN B 761 " --> pdb=" O LYS B 182 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASN B 751 " --> pdb=" O VAL B 762 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL B 764 " --> pdb=" O TYR B 749 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N TYR B 749 " --> pdb=" O VAL B 764 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 217 through 219 Processing sheet with id= N, first strand: chain 'B' and resid 250 through 252 Processing sheet with id= O, first strand: chain 'B' and resid 284 through 286 removed outlier: 4.016A pdb=" N ILE B 279 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N THR B 625 " --> pdb=" O LYS B 602 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ASN B 604 " --> pdb=" O PHE B 623 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N PHE B 623 " --> pdb=" O ASN B 604 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ALA B 606 " --> pdb=" O VAL B 621 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL B 621 " --> pdb=" O ALA B 606 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N LEU B 608 " --> pdb=" O VAL B 619 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N VAL B 619 " --> pdb=" O LEU B 608 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 846 through 850 removed outlier: 3.592A pdb=" N MET B 706 " --> pdb=" O ILE B 821 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 715 through 722 Processing sheet with id= R, first strand: chain 'B' and resid 781 through 783 Processing sheet with id= S, first strand: chain 'C' and resid 128 through 131 removed outlier: 4.564A pdb=" N THR C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP C 83 " --> pdb=" O THR C 87 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 322 through 324 removed outlier: 6.795A pdb=" N ILE C 291 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU C 139 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA C 289 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLY C 141 " --> pdb=" O THR C 287 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N THR C 287 " --> pdb=" O GLY C 141 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA C 288 " --> pdb=" O PHE C 178 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 266 through 272 removed outlier: 8.115A pdb=" N LYS C 182 " --> pdb=" O MET C 759 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLN C 761 " --> pdb=" O LYS C 182 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN C 751 " --> pdb=" O VAL C 762 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL C 764 " --> pdb=" O TYR C 749 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N TYR C 749 " --> pdb=" O VAL C 764 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 217 through 219 Processing sheet with id= W, first strand: chain 'C' and resid 250 through 252 Processing sheet with id= X, first strand: chain 'C' and resid 278 through 281 removed outlier: 6.895A pdb=" N THR C 625 " --> pdb=" O LYS C 602 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ASN C 604 " --> pdb=" O PHE C 623 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N PHE C 623 " --> pdb=" O ASN C 604 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ALA C 606 " --> pdb=" O VAL C 621 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL C 621 " --> pdb=" O ALA C 606 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N LEU C 608 " --> pdb=" O VAL C 619 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N VAL C 619 " --> pdb=" O LEU C 608 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 846 through 850 removed outlier: 4.177A pdb=" N SER C 817 " --> pdb=" O GLU C 710 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 715 through 722 Processing sheet with id= AA, first strand: chain 'C' and resid 781 through 783 1367 hydrogen bonds defined for protein. 3945 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: 9.79 Time building geometry restraints manager: 9.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.24: 3221 1.24 - 1.38: 5348 1.38 - 1.53: 11556 1.53 - 1.67: 3717 1.67 - 1.81: 264 Bond restraints: 24106 Sorted by residual: bond pdb=" C PHE B 22 " pdb=" O PHE B 22 " ideal model delta sigma weight residual 1.236 1.097 0.140 1.15e-02 7.56e+03 1.48e+02 bond pdb=" C PHE B 480 " pdb=" O PHE B 480 " ideal model delta sigma weight residual 1.237 1.098 0.138 1.17e-02 7.31e+03 1.40e+02 bond pdb=" C SER B 738 " pdb=" O SER B 738 " ideal model delta sigma weight residual 1.236 1.102 0.135 1.15e-02 7.56e+03 1.37e+02 bond pdb=" C LEU C 674 " pdb=" O LEU C 674 " ideal model delta sigma weight residual 1.234 1.097 0.137 1.26e-02 6.30e+03 1.18e+02 bond pdb=" C MET A 639 " pdb=" O MET A 639 " ideal model delta sigma weight residual 1.237 1.114 0.123 1.19e-02 7.06e+03 1.07e+02 ... (remaining 24101 not shown) Histogram of bond angle deviations from ideal: 99.49 - 106.39: 696 106.39 - 113.29: 13500 113.29 - 120.19: 8254 120.19 - 127.10: 9980 127.10 - 134.00: 210 Bond angle restraints: 32640 Sorted by residual: angle pdb=" CA PHE B 22 " pdb=" C PHE B 22 " pdb=" O PHE B 22 " ideal model delta sigma weight residual 120.82 105.15 15.67 1.05e+00 9.07e-01 2.23e+02 angle pdb=" CA PHE B 22 " pdb=" C PHE B 22 " pdb=" N GLY B 23 " ideal model delta sigma weight residual 117.07 129.37 -12.30 1.14e+00 7.69e-01 1.16e+02 angle pdb=" CA PHE B 480 " pdb=" C PHE B 480 " pdb=" O PHE B 480 " ideal model delta sigma weight residual 120.55 110.25 10.30 1.06e+00 8.90e-01 9.44e+01 angle pdb=" CA SER B 738 " pdb=" C SER B 738 " pdb=" O SER B 738 " ideal model delta sigma weight residual 120.82 110.88 9.94 1.05e+00 9.07e-01 8.97e+01 angle pdb=" CA TYR B 364 " pdb=" C TYR B 364 " pdb=" O TYR B 364 " ideal model delta sigma weight residual 120.90 111.23 9.67 1.07e+00 8.73e-01 8.17e+01 ... (remaining 32635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.62: 14218 31.62 - 63.23: 357 63.23 - 94.85: 34 94.85 - 126.46: 4 126.46 - 158.08: 2 Dihedral angle restraints: 14615 sinusoidal: 5798 harmonic: 8817 Sorted by residual: dihedral pdb=" C ASN B 751 " pdb=" N ASN B 751 " pdb=" CA ASN B 751 " pdb=" CB ASN B 751 " ideal model delta harmonic sigma weight residual -122.60 -111.25 -11.35 0 2.50e+00 1.60e-01 2.06e+01 dihedral pdb=" C3 PTY C1102 " pdb=" O11 PTY C1102 " pdb=" P1 PTY C1102 " pdb=" O12 PTY C1102 " ideal model delta sinusoidal sigma weight residual -59.77 98.31 -158.08 1 3.00e+01 1.11e-03 2.06e+01 dihedral pdb=" C3 PTY C1101 " pdb=" O11 PTY C1101 " pdb=" P1 PTY C1101 " pdb=" O12 PTY C1101 " ideal model delta sinusoidal sigma weight residual -59.77 72.97 -132.74 1 3.00e+01 1.11e-03 1.79e+01 ... (remaining 14612 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 3660 0.093 - 0.185: 195 0.185 - 0.278: 15 0.278 - 0.371: 4 0.371 - 0.464: 2 Chirality restraints: 3876 Sorted by residual: chirality pdb=" CB ILE C 777 " pdb=" CA ILE C 777 " pdb=" CG1 ILE C 777 " pdb=" CG2 ILE C 777 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.46 2.00e-01 2.50e+01 5.37e+00 chirality pdb=" CA GLN C 292 " pdb=" N GLN C 292 " pdb=" C GLN C 292 " pdb=" CB GLN C 292 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CA ARG B 363 " pdb=" N ARG B 363 " pdb=" C ARG B 363 " pdb=" CB ARG B 363 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 3873 not shown) Planarity restraints: 4073 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C 46 " 0.021 2.00e-02 2.50e+03 4.47e-02 2.00e+01 pdb=" C SER C 46 " -0.077 2.00e-02 2.50e+03 pdb=" O SER C 46 " 0.029 2.00e-02 2.50e+03 pdb=" N ALA C 47 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 77 " 0.021 2.00e-02 2.50e+03 4.44e-02 1.98e+01 pdb=" C TYR C 77 " -0.077 2.00e-02 2.50e+03 pdb=" O TYR C 77 " 0.028 2.00e-02 2.50e+03 pdb=" N TYR C 78 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 590 " 0.021 2.00e-02 2.50e+03 4.36e-02 1.90e+01 pdb=" C GLN A 590 " -0.075 2.00e-02 2.50e+03 pdb=" O GLN A 590 " 0.028 2.00e-02 2.50e+03 pdb=" N PHE A 591 " 0.026 2.00e-02 2.50e+03 ... (remaining 4070 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 273 2.67 - 3.22: 22735 3.22 - 3.78: 36874 3.78 - 4.34: 51494 4.34 - 4.90: 84703 Nonbonded interactions: 196079 Sorted by model distance: nonbonded pdb=" OG SER B 786 " pdb=" OE1 GLN B 788 " model vdw 2.108 2.440 nonbonded pdb=" OE2 GLU B 213 " pdb=" NE2 GLN B 239 " model vdw 2.111 2.520 nonbonded pdb=" O LYS B 941 " pdb=" OE1 GLU B 945 " model vdw 2.174 3.040 nonbonded pdb=" O ALA B 308 " pdb=" OE1 GLU B 312 " model vdw 2.180 3.040 nonbonded pdb=" OD1 ASP B 716 " pdb=" NZ LYS B 802 " model vdw 2.196 2.520 ... (remaining 196074 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 14 or (resid 15 and (name N or name CA or name C \ or name CB or name CG1 or name CG2 or name CD1)) or resid 16 through 1027 or (r \ esid 1101 and (name C1 or name C11 or name C12 or name C13 or name C14 or name C \ 15 or name C16 or name C17 or name C18 or name C19 or name C2 or name C20 or nam \ e C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or \ name C36 or name C37 or name C38 or name C39 or name C5 or name C6 or name C8 or \ name N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 \ or name O4 or name O7 or name P1 )) or (resid 1102 and (name C1 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C19 or name C2 or name C20 or name C21 or name C22 or name C3 or name C \ 30 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or na \ me C37 or name C38 or name C39 or name C40 or name C41 or name C5 or name C6 or \ name C8 or name N1 or name O10 or name O11 or name O12 or name O13 or name O14 o \ r name O30 or name O4 or name O7 or name P1 )))) selection = (chain 'B' and (resid 1 through 1027 or (resid 1101 and (name C1 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C19 or name C2 or name C20 or name C3 or name C30 or name C31 or name C \ 32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or na \ me C39 or name C5 or name C6 or name C8 or name N1 or name O10 or name O11 or na \ me O12 or name O13 or name O14 or name O30 or name O4 or name O7 or name P1 )) o \ r (resid 1102 and (name C1 or name C11 or name C12 or name C13 or name C14 or na \ me C15 or name C16 or name C17 or name C18 or name C19 or name C2 or name C20 or \ name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C3 \ or name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C5 or name C6 or name C8 or name N1 or name O10 or name \ O11 or name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or na \ me P1 )))) selection = (chain 'C' and (resid 1 through 14 or (resid 15 and (name N or name CA or name C \ or name CB or name CG1 or name CG2 or name CD1)) or resid 16 through 1027 or (r \ esid 1101 and (name C1 or name C11 or name C12 or name C13 or name C14 or name C \ 15 or name C16 or name C17 or name C18 or name C19 or name C2 or name C20 or nam \ e C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or \ name C36 or name C37 or name C38 or name C39 or name C5 or name C6 or name C8 or \ name N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 \ or name O4 or name O7 or name P1 )) or resid 1102)) } 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: 0.010 Normalize map: mean=0, sd=1: 0.210 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: 2.040 Check model and map are aligned: 0.360 Set scattering table: 0.210 Process input model: 65.440 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.120 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:15.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 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 0.140 24106 Z= 0.387 Angle : 0.919 16.768 32640 Z= 0.575 Chirality : 0.046 0.464 3876 Planarity : 0.006 0.090 4073 Dihedral : 14.142 158.079 8909 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.09 % Allowed : 1.13 % Favored : 97.78 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.17 % 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: 2.20 (0.15), residues: 3048 helix: 2.38 (0.13), residues: 1684 sheet: 0.44 (0.21), residues: 529 loop : 0.33 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 568 HIS 0.002 0.000 HIS C 342 PHE 0.058 0.002 PHE B 569 TYR 0.047 0.002 TYR C 77 ARG 0.012 0.001 ARG C 724 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 637 time to evaluate : 2.718 Fit side-chains revert: symmetry clash REVERT: A 112 LYS cc_start: 0.7249 (mmmt) cc_final: 0.6934 (mmtt) REVERT: A 321 MET cc_start: 0.8174 (mtt) cc_final: 0.7846 (mtt) REVERT: A 366 LEU cc_start: 0.8200 (mt) cc_final: 0.7945 (mt) REVERT: A 639 MET cc_start: 0.8618 (mtp) cc_final: 0.8116 (mtm) REVERT: A 706 MET cc_start: 0.7509 (mtp) cc_final: 0.7094 (mtp) REVERT: A 884 GLU cc_start: 0.8246 (tp30) cc_final: 0.7763 (tp30) REVERT: A 893 MET cc_start: 0.8513 (mmm) cc_final: 0.8202 (mmm) REVERT: B 68 GLU cc_start: 0.6863 (mm-30) cc_final: 0.6521 (mm-30) REVERT: B 293 LEU cc_start: 0.8106 (mt) cc_final: 0.7892 (tp) REVERT: B 402 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8786 (mm) REVERT: B 545 ILE cc_start: 0.9068 (mt) cc_final: 0.8842 (mt) REVERT: B 553 MET cc_start: 0.8472 (mmm) cc_final: 0.8234 (mmm) REVERT: B 697 MET cc_start: 0.8614 (mtm) cc_final: 0.8295 (mtt) REVERT: B 706 MET cc_start: 0.8275 (mtp) cc_final: 0.8036 (mtp) REVERT: B 799 GLN cc_start: 0.7427 (tt0) cc_final: 0.7212 (mt0) REVERT: B 913 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8418 (mpp) REVERT: B 931 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8343 (ttpt) REVERT: C 8 ARG cc_start: 0.8375 (mtt-85) cc_final: 0.8006 (mtp180) REVERT: C 66 GLU cc_start: 0.7631 (tt0) cc_final: 0.7242 (tt0) REVERT: C 292 GLN cc_start: 0.7453 (OUTLIER) cc_final: 0.7243 (mp10) REVERT: C 352 PHE cc_start: 0.7175 (m-10) cc_final: 0.6798 (t80) REVERT: C 407 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7873 (t0) REVERT: C 592 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6990 (mm-30) REVERT: C 612 PHE cc_start: 0.6603 (m-80) cc_final: 0.5283 (m-80) REVERT: C 745 MET cc_start: 0.7598 (mmt) cc_final: 0.7372 (mmt) REVERT: C 931 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8305 (mttt) outliers start: 28 outliers final: 7 residues processed: 655 average time/residue: 1.2235 time to fit residues: 925.0510 Evaluate side-chains 532 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 518 time to evaluate : 2.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 793 SER Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 538 MET Chi-restraints excluded: chain B residue 738 SER Chi-restraints excluded: chain B residue 913 MET Chi-restraints excluded: chain B residue 931 LYS Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 931 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 4.9990 chunk 231 optimal weight: 10.0000 chunk 128 optimal weight: 0.1980 chunk 79 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 239 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 145 optimal weight: 3.9990 chunk 178 optimal weight: 20.0000 chunk 277 optimal weight: 3.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN A 147 ASN A 298 ASN ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN B 691 GLN B 799 GLN C 124 GLN C 205 ASN C 239 GLN C 282 ASN C 298 ASN C 594 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24106 Z= 0.234 Angle : 0.545 7.162 32640 Z= 0.285 Chirality : 0.042 0.192 3876 Planarity : 0.005 0.053 4073 Dihedral : 9.942 177.890 3440 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 3.00 % Allowed : 12.05 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 2.10 (0.15), residues: 3048 helix: 2.27 (0.13), residues: 1688 sheet: 0.49 (0.21), residues: 535 loop : 0.27 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 800 HIS 0.002 0.001 HIS B 360 PHE 0.017 0.002 PHE B 672 TYR 0.012 0.001 TYR B 883 ARG 0.007 0.000 ARG B 7 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 543 time to evaluate : 2.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.7645 (mtmt) cc_final: 0.7341 (pttp) REVERT: A 149 TYR cc_start: 0.7747 (m-80) cc_final: 0.7488 (m-80) REVERT: A 247 LYS cc_start: 0.8077 (mttt) cc_final: 0.7657 (mtpp) REVERT: A 321 MET cc_start: 0.8211 (mtt) cc_final: 0.7929 (mtt) REVERT: A 346 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7913 (mt-10) REVERT: A 366 LEU cc_start: 0.8258 (mt) cc_final: 0.7969 (mt) REVERT: A 383 MET cc_start: 0.8779 (mtp) cc_final: 0.8339 (mtp) REVERT: A 415 ASN cc_start: 0.7920 (m-40) cc_final: 0.7520 (m110) REVERT: A 639 MET cc_start: 0.8441 (mtp) cc_final: 0.7895 (mtm) REVERT: A 677 GLN cc_start: 0.8700 (mt0) cc_final: 0.8471 (mt0) REVERT: A 697 MET cc_start: 0.7843 (mtm) cc_final: 0.7638 (mtm) REVERT: A 893 MET cc_start: 0.8534 (mmm) cc_final: 0.8248 (mmm) REVERT: B 68 GLU cc_start: 0.7000 (mm-30) cc_final: 0.6697 (mm-30) REVERT: B 69 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7902 (mm) REVERT: B 312 GLU cc_start: 0.6697 (mp0) cc_final: 0.6261 (mp0) REVERT: B 325 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.7976 (mm) REVERT: B 402 ILE cc_start: 0.9214 (OUTLIER) cc_final: 0.8857 (mm) REVERT: B 553 MET cc_start: 0.8535 (mmm) cc_final: 0.8329 (mmm) REVERT: B 799 GLN cc_start: 0.7395 (tt0) cc_final: 0.7176 (mt0) REVERT: B 913 MET cc_start: 0.8762 (mpm) cc_final: 0.8480 (mpp) REVERT: B 942 MET cc_start: 0.7281 (tmt) cc_final: 0.7026 (tmm) REVERT: B 945 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6546 (mp0) REVERT: C 176 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7156 (tt0) REVERT: C 264 ASP cc_start: 0.6800 (m-30) cc_final: 0.6583 (m-30) REVERT: C 339 LYS cc_start: 0.7068 (OUTLIER) cc_final: 0.6472 (mmtp) REVERT: C 352 PHE cc_start: 0.7271 (m-10) cc_final: 0.6845 (t80) REVERT: C 356 TYR cc_start: 0.8428 (t80) cc_final: 0.8133 (t80) REVERT: C 589 ASN cc_start: 0.7859 (m110) cc_final: 0.7506 (m110) REVERT: C 592 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6579 (mm-30) REVERT: C 612 PHE cc_start: 0.6571 (m-80) cc_final: 0.5448 (m-80) REVERT: C 692 ASP cc_start: 0.8052 (m-30) cc_final: 0.7765 (m-30) REVERT: C 697 MET cc_start: 0.8621 (mtt) cc_final: 0.8375 (mtt) REVERT: C 799 GLN cc_start: 0.7923 (tt0) cc_final: 0.7379 (tt0) outliers start: 77 outliers final: 31 residues processed: 582 average time/residue: 1.2781 time to fit residues: 856.9358 Evaluate side-chains 546 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 508 time to evaluate : 2.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 793 SER Chi-restraints excluded: chain A residue 799 GLN Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 862 SER Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 945 GLU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 339 LYS Chi-restraints excluded: chain C residue 495 THR Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 594 ASN Chi-restraints excluded: chain C residue 709 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 231 optimal weight: 10.0000 chunk 189 optimal weight: 8.9990 chunk 76 optimal weight: 0.2980 chunk 278 optimal weight: 4.9990 chunk 300 optimal weight: 0.9980 chunk 247 optimal weight: 3.9990 chunk 276 optimal weight: 20.0000 chunk 94 optimal weight: 20.0000 chunk 223 optimal weight: 7.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN A 298 ASN ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 805 GLN A 863 GLN A 914 ASN B 109 ASN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 GLN B 779 ASN C 108 GLN C 124 GLN C 205 ASN ** C 859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24106 Z= 0.176 Angle : 0.495 7.188 32640 Z= 0.258 Chirality : 0.039 0.194 3876 Planarity : 0.004 0.053 4073 Dihedral : 9.331 170.516 3412 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.73 % Allowed : 13.49 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 2.07 (0.15), residues: 3048 helix: 2.26 (0.13), residues: 1691 sheet: 0.43 (0.21), residues: 535 loop : 0.24 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 800 HIS 0.001 0.000 HIS B 360 PHE 0.017 0.001 PHE B 509 TYR 0.010 0.001 TYR A 49 ARG 0.009 0.000 ARG B 7 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 543 time to evaluate : 2.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5763 (OUTLIER) cc_final: 0.5477 (ttt) REVERT: A 73 LYS cc_start: 0.7700 (mtmt) cc_final: 0.7359 (pttp) REVERT: A 89 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.6675 (tm-30) REVERT: A 247 LYS cc_start: 0.8041 (mttt) cc_final: 0.7674 (mtpp) REVERT: A 321 MET cc_start: 0.8209 (mtt) cc_final: 0.7976 (mtt) REVERT: A 346 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7899 (mt-10) REVERT: A 366 LEU cc_start: 0.8231 (mt) cc_final: 0.7959 (mt) REVERT: A 605 THR cc_start: 0.8686 (m) cc_final: 0.8364 (m) REVERT: A 639 MET cc_start: 0.8442 (mtp) cc_final: 0.7873 (mtm) REVERT: A 677 GLN cc_start: 0.8684 (mt0) cc_final: 0.8475 (mt0) REVERT: A 802 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7986 (mtpp) REVERT: A 893 MET cc_start: 0.8534 (mmm) cc_final: 0.8187 (mmm) REVERT: A 946 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.5672 (mp0) REVERT: A 1018 PHE cc_start: 0.8102 (t80) cc_final: 0.7865 (t80) REVERT: B 68 GLU cc_start: 0.7062 (mm-30) cc_final: 0.6762 (mm-30) REVERT: B 69 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7738 (mm) REVERT: B 312 GLU cc_start: 0.6710 (mp0) cc_final: 0.6285 (mp0) REVERT: B 325 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.7974 (mm) REVERT: B 402 ILE cc_start: 0.9238 (OUTLIER) cc_final: 0.8843 (mm) REVERT: B 561 MET cc_start: 0.7693 (mtp) cc_final: 0.7228 (mtm) REVERT: B 779 ASN cc_start: 0.8032 (OUTLIER) cc_final: 0.7735 (t160) REVERT: B 799 GLN cc_start: 0.7438 (tt0) cc_final: 0.7191 (mt0) REVERT: B 913 MET cc_start: 0.8741 (mpm) cc_final: 0.8508 (mpp) REVERT: B 942 MET cc_start: 0.7242 (tmt) cc_final: 0.7006 (tmm) REVERT: B 945 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6573 (mp0) REVERT: C 8 ARG cc_start: 0.8459 (mtt-85) cc_final: 0.7992 (mtt180) REVERT: C 176 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.7229 (tt0) REVERT: C 339 LYS cc_start: 0.7104 (OUTLIER) cc_final: 0.6546 (mmtp) REVERT: C 352 PHE cc_start: 0.7244 (m-10) cc_final: 0.6876 (t80) REVERT: C 356 TYR cc_start: 0.8406 (t80) cc_final: 0.8067 (t80) REVERT: C 561 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8018 (ttm) REVERT: C 589 ASN cc_start: 0.7847 (m110) cc_final: 0.7492 (m110) REVERT: C 592 GLU cc_start: 0.6754 (OUTLIER) cc_final: 0.6452 (tt0) REVERT: C 612 PHE cc_start: 0.6586 (m-80) cc_final: 0.5480 (m-80) REVERT: C 697 MET cc_start: 0.8623 (mtt) cc_final: 0.8234 (mtt) REVERT: C 799 GLN cc_start: 0.8001 (tt0) cc_final: 0.7470 (tt0) outliers start: 70 outliers final: 31 residues processed: 577 average time/residue: 1.2752 time to fit residues: 859.7070 Evaluate side-chains 569 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 525 time to evaluate : 2.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 779 ASN Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 945 GLU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain B residue 983 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 339 LYS Chi-restraints excluded: chain C residue 495 THR Chi-restraints excluded: chain C residue 561 MET Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 759 MET Chi-restraints excluded: chain C residue 770 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 30.0000 chunk 209 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 186 optimal weight: 10.0000 chunk 279 optimal weight: 20.0000 chunk 295 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 264 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN B 109 ASN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 GLN C 124 GLN C 205 ASN C 298 ASN ** C 859 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 24106 Z= 0.293 Angle : 0.569 8.535 32640 Z= 0.297 Chirality : 0.042 0.217 3876 Planarity : 0.005 0.055 4073 Dihedral : 9.444 166.533 3411 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.27 % Allowed : 14.11 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.69 (0.15), residues: 3048 helix: 1.98 (0.13), residues: 1700 sheet: 0.15 (0.21), residues: 555 loop : 0.09 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 610 HIS 0.003 0.001 HIS B 360 PHE 0.019 0.002 PHE B 672 TYR 0.020 0.002 TYR A 49 ARG 0.007 0.001 ARG B 7 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 547 time to evaluate : 2.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5625 (OUTLIER) cc_final: 0.5366 (ttt) REVERT: A 73 LYS cc_start: 0.7682 (mtmt) cc_final: 0.7393 (pttp) REVERT: A 89 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.6665 (tm-30) REVERT: A 247 LYS cc_start: 0.8091 (mttt) cc_final: 0.7716 (mtpp) REVERT: A 346 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7958 (mt-10) REVERT: A 366 LEU cc_start: 0.8304 (mt) cc_final: 0.7993 (mt) REVERT: A 605 THR cc_start: 0.8810 (m) cc_final: 0.8457 (m) REVERT: A 639 MET cc_start: 0.8542 (mtp) cc_final: 0.7909 (mtm) REVERT: A 642 ASP cc_start: 0.7774 (m-30) cc_final: 0.7536 (m-30) REVERT: A 677 GLN cc_start: 0.8739 (mt0) cc_final: 0.8530 (mt0) REVERT: A 695 MET cc_start: 0.9039 (mmp) cc_final: 0.8826 (mmp) REVERT: A 772 MET cc_start: 0.8832 (mmt) cc_final: 0.8253 (mmt) REVERT: A 802 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7996 (mtpp) REVERT: A 893 MET cc_start: 0.8551 (mmm) cc_final: 0.8264 (mmm) REVERT: A 1018 PHE cc_start: 0.8174 (t80) cc_final: 0.7926 (t80) REVERT: B 68 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6756 (mm-30) REVERT: B 69 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7771 (mm) REVERT: B 307 ARG cc_start: 0.7448 (ttm110) cc_final: 0.7172 (mtt-85) REVERT: B 312 GLU cc_start: 0.6704 (OUTLIER) cc_final: 0.6226 (mp0) REVERT: B 325 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8050 (mm) REVERT: B 945 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6529 (mp0) REVERT: C 8 ARG cc_start: 0.8474 (mtt-85) cc_final: 0.8020 (mtp180) REVERT: C 176 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.7385 (tt0) REVERT: C 221 ASP cc_start: 0.8246 (t70) cc_final: 0.7997 (t0) REVERT: C 339 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.6888 (tmtm) REVERT: C 352 PHE cc_start: 0.7266 (m-10) cc_final: 0.6872 (t80) REVERT: C 356 TYR cc_start: 0.8602 (t80) cc_final: 0.8146 (t80) REVERT: C 589 ASN cc_start: 0.7865 (m110) cc_final: 0.7486 (m110) REVERT: C 592 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.6410 (mm-30) REVERT: C 612 PHE cc_start: 0.6799 (m-80) cc_final: 0.5526 (m-80) REVERT: C 697 MET cc_start: 0.8604 (mtt) cc_final: 0.8286 (mtt) outliers start: 84 outliers final: 44 residues processed: 584 average time/residue: 1.2291 time to fit residues: 828.8697 Evaluate side-chains 581 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 527 time to evaluate : 2.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 799 GLN Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 862 SER Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 945 GLU Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 108 GLN Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 339 LYS Chi-restraints excluded: chain C residue 495 THR Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 745 MET Chi-restraints excluded: chain C residue 759 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 6.9990 chunk 167 optimal weight: 0.0870 chunk 4 optimal weight: 0.8980 chunk 220 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 252 optimal weight: 10.0000 chunk 204 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 151 optimal weight: 7.9990 chunk 265 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 overall best weight: 1.4962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN A 644 ASN A 649 ASN ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 GLN C 124 GLN C 566 GLN C 859 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 24106 Z= 0.154 Angle : 0.483 7.298 32640 Z= 0.251 Chirality : 0.039 0.199 3876 Planarity : 0.004 0.053 4073 Dihedral : 9.090 165.313 3411 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.77 % Allowed : 15.87 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.92 (0.15), residues: 3048 helix: 2.18 (0.13), residues: 1696 sheet: 0.30 (0.22), residues: 530 loop : 0.14 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 800 HIS 0.001 0.000 HIS B 360 PHE 0.020 0.001 PHE B 509 TYR 0.013 0.001 TYR A 49 ARG 0.007 0.000 ARG B 7 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 542 time to evaluate : 2.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.7676 (mtmt) cc_final: 0.7388 (pttp) REVERT: A 89 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.6567 (tm-30) REVERT: A 247 LYS cc_start: 0.8073 (mttt) cc_final: 0.7719 (mtpp) REVERT: A 254 LYS cc_start: 0.6657 (mmmm) cc_final: 0.6352 (mmpt) REVERT: A 346 GLU cc_start: 0.8342 (mt-10) cc_final: 0.7948 (mt-10) REVERT: A 605 THR cc_start: 0.8645 (m) cc_final: 0.8294 (m) REVERT: A 642 ASP cc_start: 0.7642 (m-30) cc_final: 0.7315 (m-30) REVERT: A 677 GLN cc_start: 0.8729 (mt0) cc_final: 0.8485 (mt0) REVERT: A 772 MET cc_start: 0.8861 (mmt) cc_final: 0.8107 (mmt) REVERT: A 802 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.8000 (mtpp) REVERT: A 893 MET cc_start: 0.8542 (mmm) cc_final: 0.8173 (mmm) REVERT: A 1018 PHE cc_start: 0.8124 (t80) cc_final: 0.7893 (t80) REVERT: B 1 MET cc_start: 0.5951 (ptm) cc_final: 0.5649 (ptp) REVERT: B 68 GLU cc_start: 0.6981 (mm-30) cc_final: 0.6723 (mm-30) REVERT: B 69 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7738 (mm) REVERT: B 273 GLN cc_start: 0.8052 (tp40) cc_final: 0.7197 (tt0) REVERT: B 312 GLU cc_start: 0.6665 (OUTLIER) cc_final: 0.6119 (mp0) REVERT: B 779 ASN cc_start: 0.8229 (t0) cc_final: 0.7664 (t160) REVERT: B 942 MET cc_start: 0.7218 (tpp) cc_final: 0.6810 (tmm) REVERT: B 945 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6544 (mp0) REVERT: C 8 ARG cc_start: 0.8377 (mtt-85) cc_final: 0.7926 (mtt180) REVERT: C 176 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.7335 (tt0) REVERT: C 221 ASP cc_start: 0.8212 (t70) cc_final: 0.7992 (t0) REVERT: C 339 LYS cc_start: 0.6902 (OUTLIER) cc_final: 0.6302 (mmtp) REVERT: C 352 PHE cc_start: 0.7127 (m-10) cc_final: 0.6867 (t80) REVERT: C 356 TYR cc_start: 0.8427 (t80) cc_final: 0.8037 (t80) REVERT: C 592 GLU cc_start: 0.6631 (OUTLIER) cc_final: 0.6393 (mm-30) REVERT: C 612 PHE cc_start: 0.6531 (m-80) cc_final: 0.5387 (m-80) REVERT: C 665 GLU cc_start: 0.6730 (mp0) cc_final: 0.6524 (mp0) REVERT: C 697 MET cc_start: 0.8554 (mtt) cc_final: 0.8107 (mtt) REVERT: C 779 ASN cc_start: 0.7505 (t0) cc_final: 0.7242 (t0) REVERT: C 799 GLN cc_start: 0.7989 (tt0) cc_final: 0.7513 (tt0) outliers start: 71 outliers final: 33 residues processed: 576 average time/residue: 1.2445 time to fit residues: 830.0299 Evaluate side-chains 554 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 513 time to evaluate : 2.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 862 SER Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 945 GLU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 339 LYS Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 977 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 5.9990 chunk 266 optimal weight: 20.0000 chunk 58 optimal weight: 8.9990 chunk 173 optimal weight: 30.0000 chunk 73 optimal weight: 9.9990 chunk 296 optimal weight: 3.9990 chunk 245 optimal weight: 6.9990 chunk 137 optimal weight: 9.9990 chunk 24 optimal weight: 0.4980 chunk 97 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN A 593 ASN ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 ASN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 GLN C 108 GLN C 124 GLN C 298 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24106 Z= 0.268 Angle : 0.548 8.758 32640 Z= 0.284 Chirality : 0.042 0.202 3876 Planarity : 0.005 0.054 4073 Dihedral : 9.188 167.129 3411 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.92 % Allowed : 16.80 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.70 (0.15), residues: 3048 helix: 2.00 (0.13), residues: 1699 sheet: 0.20 (0.21), residues: 530 loop : 0.05 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 610 HIS 0.002 0.001 HIS B 360 PHE 0.018 0.002 PHE B 672 TYR 0.021 0.002 TYR A 49 ARG 0.008 0.000 ARG B 7 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 535 time to evaluate : 2.709 Fit side-chains revert: symmetry clash REVERT: A 73 LYS cc_start: 0.7696 (mtmt) cc_final: 0.7413 (pttp) REVERT: A 89 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.6583 (tm-30) REVERT: A 247 LYS cc_start: 0.8105 (mttt) cc_final: 0.7723 (mtpp) REVERT: A 254 LYS cc_start: 0.6690 (mmmm) cc_final: 0.6374 (mmpt) REVERT: A 346 GLU cc_start: 0.8400 (mt-10) cc_final: 0.7956 (mt-10) REVERT: A 366 LEU cc_start: 0.8307 (mt) cc_final: 0.7988 (mt) REVERT: A 605 THR cc_start: 0.8800 (m) cc_final: 0.8460 (m) REVERT: A 772 MET cc_start: 0.8861 (mmt) cc_final: 0.8277 (mmt) REVERT: A 802 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.8014 (mtpp) REVERT: A 893 MET cc_start: 0.8553 (mmm) cc_final: 0.8167 (mmm) REVERT: A 1018 PHE cc_start: 0.8152 (t80) cc_final: 0.7888 (t80) REVERT: B 68 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6805 (mm-30) REVERT: B 69 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7735 (mm) REVERT: B 312 GLU cc_start: 0.6665 (OUTLIER) cc_final: 0.6298 (mp0) REVERT: B 325 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8056 (mm) REVERT: B 518 ASP cc_start: 0.7154 (OUTLIER) cc_final: 0.6879 (m-30) REVERT: B 779 ASN cc_start: 0.8355 (t0) cc_final: 0.7774 (t160) REVERT: B 945 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6519 (mp0) REVERT: C 8 ARG cc_start: 0.8409 (mtt-85) cc_final: 0.7933 (mtp180) REVERT: C 176 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.7333 (tt0) REVERT: C 221 ASP cc_start: 0.8268 (t70) cc_final: 0.8047 (t0) REVERT: C 339 LYS cc_start: 0.7065 (OUTLIER) cc_final: 0.6416 (mmtp) REVERT: C 352 PHE cc_start: 0.7172 (m-10) cc_final: 0.6849 (t80) REVERT: C 356 TYR cc_start: 0.8552 (t80) cc_final: 0.8102 (t80) REVERT: C 554 LYS cc_start: 0.8050 (tttt) cc_final: 0.7744 (tppt) REVERT: C 561 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8307 (mtm) REVERT: C 592 GLU cc_start: 0.6695 (OUTLIER) cc_final: 0.6421 (mm-30) REVERT: C 612 PHE cc_start: 0.6632 (m-80) cc_final: 0.5452 (m-80) REVERT: C 697 MET cc_start: 0.8617 (mtt) cc_final: 0.8398 (mtt) REVERT: C 779 ASN cc_start: 0.7424 (t0) cc_final: 0.7008 (t160) REVERT: C 844 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7833 (tmmt) outliers start: 75 outliers final: 42 residues processed: 571 average time/residue: 1.2414 time to fit residues: 818.6880 Evaluate side-chains 578 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 524 time to evaluate : 2.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 738 SER Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 945 GLU Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 339 LYS Chi-restraints excluded: chain C residue 495 THR Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 561 MET Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 759 MET Chi-restraints excluded: chain C residue 844 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 168 optimal weight: 8.9990 chunk 216 optimal weight: 6.9990 chunk 167 optimal weight: 0.0020 chunk 249 optimal weight: 9.9990 chunk 165 optimal weight: 6.9990 chunk 294 optimal weight: 9.9990 chunk 184 optimal weight: 8.9990 chunk 179 optimal weight: 8.9990 chunk 136 optimal weight: 4.9990 overall best weight: 5.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN A 586 ASN A 593 ASN A 644 ASN A 649 ASN A 677 GLN ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN B 109 ASN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 GLN C 104 GLN C 124 GLN C 801 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 24106 Z= 0.306 Angle : 0.571 9.220 32640 Z= 0.297 Chirality : 0.043 0.209 3876 Planarity : 0.005 0.055 4073 Dihedral : 9.294 168.851 3411 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.08 % Allowed : 17.58 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.50 (0.15), residues: 3048 helix: 1.84 (0.13), residues: 1698 sheet: 0.08 (0.21), residues: 543 loop : -0.01 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 610 HIS 0.003 0.001 HIS B 360 PHE 0.020 0.002 PHE B 509 TYR 0.027 0.002 TYR A 49 ARG 0.010 0.001 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 537 time to evaluate : 2.420 Fit side-chains revert: symmetry clash REVERT: A 73 LYS cc_start: 0.7686 (mtmt) cc_final: 0.7434 (pttp) REVERT: A 89 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.6633 (tm-30) REVERT: A 247 LYS cc_start: 0.8099 (mttt) cc_final: 0.7711 (mtpp) REVERT: A 254 LYS cc_start: 0.6701 (mmmm) cc_final: 0.6383 (mmpt) REVERT: A 276 ASN cc_start: 0.8100 (p0) cc_final: 0.7709 (p0) REVERT: A 346 GLU cc_start: 0.8413 (mt-10) cc_final: 0.7974 (mt-10) REVERT: A 366 LEU cc_start: 0.8279 (mt) cc_final: 0.7970 (mt) REVERT: A 605 THR cc_start: 0.8848 (m) cc_final: 0.8538 (m) REVERT: A 772 MET cc_start: 0.8850 (mmt) cc_final: 0.8257 (mmt) REVERT: A 802 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.8024 (mtpp) REVERT: A 893 MET cc_start: 0.8577 (mmm) cc_final: 0.8164 (mmm) REVERT: A 1018 PHE cc_start: 0.8143 (t80) cc_final: 0.7927 (t80) REVERT: B 1 MET cc_start: 0.6056 (ptm) cc_final: 0.5790 (ptp) REVERT: B 68 GLU cc_start: 0.7096 (mm-30) cc_final: 0.6778 (mm-30) REVERT: B 69 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7814 (mm) REVERT: B 312 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.6354 (mp0) REVERT: B 325 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8073 (mm) REVERT: B 518 ASP cc_start: 0.7194 (OUTLIER) cc_final: 0.6867 (m-30) REVERT: B 779 ASN cc_start: 0.8395 (t0) cc_final: 0.7806 (t160) REVERT: B 945 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6535 (mp0) REVERT: C 8 ARG cc_start: 0.8428 (mtt-85) cc_final: 0.7974 (mtt180) REVERT: C 176 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7307 (tt0) REVERT: C 221 ASP cc_start: 0.8265 (t70) cc_final: 0.8027 (t0) REVERT: C 352 PHE cc_start: 0.7174 (m-10) cc_final: 0.6823 (t80) REVERT: C 356 TYR cc_start: 0.8660 (t80) cc_final: 0.8154 (t80) REVERT: C 589 ASN cc_start: 0.7872 (m110) cc_final: 0.7488 (m110) REVERT: C 592 GLU cc_start: 0.6796 (OUTLIER) cc_final: 0.6498 (mm-30) REVERT: C 612 PHE cc_start: 0.6762 (m-80) cc_final: 0.5905 (m-80) REVERT: C 656 MET cc_start: 0.7387 (ttm) cc_final: 0.7180 (ttm) REVERT: C 779 ASN cc_start: 0.7409 (t0) cc_final: 0.6973 (t160) REVERT: C 799 GLN cc_start: 0.7945 (tt0) cc_final: 0.7624 (tt0) REVERT: C 844 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7878 (tmmt) outliers start: 79 outliers final: 52 residues processed: 574 average time/residue: 1.2083 time to fit residues: 805.8533 Evaluate side-chains 590 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 528 time to evaluate : 2.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 799 GLN Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 738 SER Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 945 GLU Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 339 LYS Chi-restraints excluded: chain C residue 495 THR Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 759 MET Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 983 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 176 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 187 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 145 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 231 optimal weight: 10.0000 chunk 268 optimal weight: 30.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN A 586 ASN A 649 ASN ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 GLN C 108 GLN C 124 GLN C 298 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24106 Z= 0.238 Angle : 0.542 8.314 32640 Z= 0.282 Chirality : 0.041 0.209 3876 Planarity : 0.005 0.055 4073 Dihedral : 9.160 172.056 3411 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.77 % Allowed : 18.48 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 (0.15), residues: 3048 helix: 1.88 (0.13), residues: 1700 sheet: 0.08 (0.21), residues: 543 loop : 0.02 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 610 HIS 0.002 0.001 HIS B 360 PHE 0.016 0.001 PHE B 672 TYR 0.023 0.001 TYR A 49 ARG 0.008 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 532 time to evaluate : 2.763 Fit side-chains revert: symmetry clash REVERT: A 73 LYS cc_start: 0.7720 (mtmt) cc_final: 0.7436 (pttp) REVERT: A 89 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.6580 (tm-30) REVERT: A 247 LYS cc_start: 0.8114 (mttt) cc_final: 0.7732 (mtpp) REVERT: A 276 ASN cc_start: 0.8084 (p0) cc_final: 0.7848 (p0) REVERT: A 346 GLU cc_start: 0.8377 (mt-10) cc_final: 0.7910 (mt-10) REVERT: A 605 THR cc_start: 0.8769 (m) cc_final: 0.8449 (m) REVERT: A 772 MET cc_start: 0.8849 (mmt) cc_final: 0.8278 (mmt) REVERT: A 802 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.8016 (mtpp) REVERT: A 893 MET cc_start: 0.8561 (mmm) cc_final: 0.8260 (mmm) REVERT: A 1018 PHE cc_start: 0.8157 (t80) cc_final: 0.7921 (t80) REVERT: B 68 GLU cc_start: 0.7076 (mm-30) cc_final: 0.6827 (mm-30) REVERT: B 69 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7810 (mm) REVERT: B 312 GLU cc_start: 0.6680 (OUTLIER) cc_final: 0.6319 (mp0) REVERT: B 325 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8064 (mm) REVERT: B 518 ASP cc_start: 0.7183 (OUTLIER) cc_final: 0.6856 (m-30) REVERT: B 779 ASN cc_start: 0.8396 (t0) cc_final: 0.7824 (t160) REVERT: B 945 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6484 (mp0) REVERT: C 8 ARG cc_start: 0.8438 (mtt-85) cc_final: 0.7971 (mtt180) REVERT: C 176 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7327 (tt0) REVERT: C 205 ASN cc_start: 0.7192 (OUTLIER) cc_final: 0.6913 (m110) REVERT: C 221 ASP cc_start: 0.8250 (t70) cc_final: 0.8022 (t0) REVERT: C 322 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.6545 (tt0) REVERT: C 352 PHE cc_start: 0.7144 (m-10) cc_final: 0.6841 (t80) REVERT: C 356 TYR cc_start: 0.8569 (t80) cc_final: 0.8067 (t80) REVERT: C 589 ASN cc_start: 0.7851 (m110) cc_final: 0.7476 (m110) REVERT: C 592 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.6503 (mm-30) REVERT: C 612 PHE cc_start: 0.6718 (m-80) cc_final: 0.5601 (m-80) REVERT: C 656 MET cc_start: 0.7345 (ttm) cc_final: 0.7095 (ttm) REVERT: C 779 ASN cc_start: 0.7294 (t0) cc_final: 0.6869 (t160) REVERT: C 844 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7874 (tmmt) outliers start: 71 outliers final: 45 residues processed: 562 average time/residue: 1.2606 time to fit residues: 818.4053 Evaluate side-chains 583 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 526 time to evaluate : 2.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 945 GLU Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 205 ASN Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain C residue 339 LYS Chi-restraints excluded: chain C residue 342 HIS Chi-restraints excluded: chain C residue 495 THR Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 759 MET Chi-restraints excluded: chain C residue 844 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 20.0000 chunk 257 optimal weight: 0.8980 chunk 274 optimal weight: 6.9990 chunk 165 optimal weight: 20.0000 chunk 119 optimal weight: 20.0000 chunk 215 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 248 optimal weight: 5.9990 chunk 259 optimal weight: 0.2980 chunk 273 optimal weight: 0.0470 chunk 180 optimal weight: 10.0000 overall best weight: 2.6482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN A 586 ASN A 644 ASN A 914 ASN B 691 GLN C 124 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24106 Z= 0.195 Angle : 0.521 8.512 32640 Z= 0.271 Chirality : 0.040 0.209 3876 Planarity : 0.005 0.055 4073 Dihedral : 8.998 175.635 3411 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.46 % Allowed : 19.42 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.64 (0.15), residues: 3048 helix: 1.95 (0.13), residues: 1701 sheet: 0.13 (0.22), residues: 530 loop : 0.02 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 800 HIS 0.002 0.000 HIS C 360 PHE 0.014 0.001 PHE B 672 TYR 0.019 0.001 TYR A 49 ARG 0.009 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 534 time to evaluate : 2.680 Fit side-chains revert: symmetry clash REVERT: A 73 LYS cc_start: 0.7779 (mtmt) cc_final: 0.7487 (pttp) REVERT: A 89 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.6575 (tm-30) REVERT: A 247 LYS cc_start: 0.8097 (mttt) cc_final: 0.7726 (mtpp) REVERT: A 346 GLU cc_start: 0.8376 (mt-10) cc_final: 0.7917 (mt-10) REVERT: A 414 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7207 (tt0) REVERT: A 605 THR cc_start: 0.8706 (m) cc_final: 0.8388 (m) REVERT: A 678 ASP cc_start: 0.8236 (t0) cc_final: 0.7799 (t70) REVERT: A 772 MET cc_start: 0.8872 (mmt) cc_final: 0.8291 (mmt) REVERT: A 802 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.8018 (mtpp) REVERT: A 893 MET cc_start: 0.8593 (mmm) cc_final: 0.8300 (mmm) REVERT: A 1018 PHE cc_start: 0.8157 (t80) cc_final: 0.7912 (t80) REVERT: B 68 GLU cc_start: 0.7053 (mm-30) cc_final: 0.6800 (mm-30) REVERT: B 69 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7825 (mm) REVERT: B 312 GLU cc_start: 0.6672 (OUTLIER) cc_final: 0.6320 (mp0) REVERT: B 325 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.8059 (mm) REVERT: B 518 ASP cc_start: 0.7165 (OUTLIER) cc_final: 0.6849 (m-30) REVERT: B 779 ASN cc_start: 0.8387 (t0) cc_final: 0.7815 (t160) REVERT: B 945 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6462 (mp0) REVERT: C 8 ARG cc_start: 0.8432 (mtt-85) cc_final: 0.7956 (mtt180) REVERT: C 176 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.7310 (tt0) REVERT: C 221 ASP cc_start: 0.8262 (t70) cc_final: 0.8044 (t0) REVERT: C 339 LYS cc_start: 0.7094 (OUTLIER) cc_final: 0.6429 (mmtp) REVERT: C 352 PHE cc_start: 0.7096 (m-10) cc_final: 0.6826 (t80) REVERT: C 356 TYR cc_start: 0.8539 (t80) cc_final: 0.8052 (t80) REVERT: C 589 ASN cc_start: 0.7843 (m110) cc_final: 0.7451 (m110) REVERT: C 612 PHE cc_start: 0.6701 (m-80) cc_final: 0.5523 (m-80) REVERT: C 656 MET cc_start: 0.7316 (ttm) cc_final: 0.7089 (ttm) REVERT: C 779 ASN cc_start: 0.7273 (t0) cc_final: 0.6868 (t160) REVERT: C 844 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7895 (tmmt) outliers start: 63 outliers final: 46 residues processed: 561 average time/residue: 1.2594 time to fit residues: 822.0499 Evaluate side-chains 580 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 524 time to evaluate : 2.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 945 GLU Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 339 LYS Chi-restraints excluded: chain C residue 342 HIS Chi-restraints excluded: chain C residue 495 THR Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 759 MET Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 983 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 9.9990 chunk 177 optimal weight: 20.0000 chunk 137 optimal weight: 9.9990 chunk 202 optimal weight: 2.9990 chunk 304 optimal weight: 0.9980 chunk 280 optimal weight: 9.9990 chunk 242 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 187 optimal weight: 0.9980 chunk 148 optimal weight: 4.9990 chunk 192 optimal weight: 9.9990 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 ASN A 298 ASN A 586 ASN ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 859 GLN A 914 ASN B 691 GLN C 124 GLN C 298 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24106 Z= 0.251 Angle : 0.558 8.868 32640 Z= 0.288 Chirality : 0.041 0.211 3876 Planarity : 0.005 0.055 4073 Dihedral : 8.974 177.803 3408 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.46 % Allowed : 19.49 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 (0.15), residues: 3048 helix: 1.87 (0.13), residues: 1704 sheet: 0.10 (0.22), residues: 530 loop : -0.00 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 800 HIS 0.002 0.001 HIS B 360 PHE 0.020 0.002 PHE B 509 TYR 0.025 0.002 TYR A 49 ARG 0.009 0.000 ARG A 123 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 529 time to evaluate : 2.783 Fit side-chains revert: symmetry clash REVERT: A 73 LYS cc_start: 0.7718 (mtmt) cc_final: 0.7442 (pttp) REVERT: A 89 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.6626 (tm-30) REVERT: A 149 TYR cc_start: 0.7986 (m-10) cc_final: 0.7473 (m-80) REVERT: A 247 LYS cc_start: 0.8129 (mttt) cc_final: 0.7743 (mtpp) REVERT: A 276 ASN cc_start: 0.8058 (p0) cc_final: 0.7842 (p0) REVERT: A 346 GLU cc_start: 0.8382 (mt-10) cc_final: 0.7911 (mt-10) REVERT: A 414 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7248 (tt0) REVERT: A 605 THR cc_start: 0.8768 (m) cc_final: 0.8446 (m) REVERT: A 678 ASP cc_start: 0.8251 (t0) cc_final: 0.7828 (t70) REVERT: A 772 MET cc_start: 0.8851 (mmt) cc_final: 0.8258 (mmt) REVERT: A 802 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.8011 (mtpp) REVERT: A 893 MET cc_start: 0.8574 (mmm) cc_final: 0.8265 (mmm) REVERT: A 1018 PHE cc_start: 0.8167 (t80) cc_final: 0.7925 (t80) REVERT: B 68 GLU cc_start: 0.7078 (mm-30) cc_final: 0.6823 (mm-30) REVERT: B 69 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7870 (mm) REVERT: B 312 GLU cc_start: 0.6686 (OUTLIER) cc_final: 0.6327 (mp0) REVERT: B 325 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.8074 (mm) REVERT: B 518 ASP cc_start: 0.7154 (OUTLIER) cc_final: 0.6829 (m-30) REVERT: B 779 ASN cc_start: 0.8404 (t0) cc_final: 0.7823 (t160) REVERT: B 945 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6449 (mp0) REVERT: C 8 ARG cc_start: 0.8450 (mtt-85) cc_final: 0.7973 (mtt180) REVERT: C 176 GLN cc_start: 0.7693 (OUTLIER) cc_final: 0.7328 (tt0) REVERT: C 221 ASP cc_start: 0.8279 (t70) cc_final: 0.8050 (t0) REVERT: C 339 LYS cc_start: 0.7142 (OUTLIER) cc_final: 0.6489 (mmtp) REVERT: C 352 PHE cc_start: 0.7100 (m-10) cc_final: 0.6824 (t80) REVERT: C 356 TYR cc_start: 0.8558 (t80) cc_final: 0.8032 (t80) REVERT: C 570 MET cc_start: 0.7829 (ttp) cc_final: 0.7560 (ttp) REVERT: C 589 ASN cc_start: 0.7844 (m110) cc_final: 0.7489 (m110) REVERT: C 612 PHE cc_start: 0.6648 (m-80) cc_final: 0.5400 (m-80) REVERT: C 656 MET cc_start: 0.7320 (ttm) cc_final: 0.7105 (ttm) REVERT: C 779 ASN cc_start: 0.7294 (t0) cc_final: 0.6887 (t160) REVERT: C 844 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7909 (tmmt) outliers start: 63 outliers final: 44 residues processed: 557 average time/residue: 1.2423 time to fit residues: 799.8362 Evaluate side-chains 579 residues out of total 2565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 525 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 799 GLN Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 518 ASP Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 738 SER Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 945 GLU Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 981 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 339 LYS Chi-restraints excluded: chain C residue 495 THR Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain C residue 639 MET Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 759 MET Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 983 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 223 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 243 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 249 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 213 optimal weight: 0.5980 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 ASN A 298 ASN A 586 ASN A 859 GLN B 691 GLN C 124 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.134520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.115203 restraints weight = 25348.394| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.13 r_work: 0.2961 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24106 Z= 0.197 Angle : 0.524 8.128 32640 Z= 0.272 Chirality : 0.040 0.210 3876 Planarity : 0.005 0.055 4073 Dihedral : 8.822 179.421 3408 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.30 % Allowed : 19.69 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.63 (0.15), residues: 3048 helix: 1.95 (0.13), residues: 1701 sheet: 0.08 (0.21), residues: 542 loop : 0.06 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 800 HIS 0.002 0.000 HIS C 360 PHE 0.016 0.001 PHE C 998 TYR 0.023 0.001 TYR A 149 ARG 0.009 0.000 ARG B 7 =============================================================================== Job complete usr+sys time: 11228.13 seconds wall clock time: 197 minutes 37.74 seconds (11857.74 seconds total)