Starting phenix.real_space_refine on Sun Jul 21 06:22:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp4_41466/07_2024/8tp4_41466.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp4_41466/07_2024/8tp4_41466.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp4_41466/07_2024/8tp4_41466.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp4_41466/07_2024/8tp4_41466.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp4_41466/07_2024/8tp4_41466.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tp4_41466/07_2024/8tp4_41466.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 8427 2.51 5 N 2299 2.21 5 O 2666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 398": "OE1" <-> "OE2" Residue "C PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 398": "OE1" <-> "OE2" Residue "A PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 13472 Number of models: 1 Model: "" Number of chains: 11 Chain: "C" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3821 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 19, 'TRANS': 462} Chain breaks: 1 Chain: "H" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1008 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "L" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 835 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "A" Number of atoms: 3808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3808 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 19, 'TRANS': 460} Chain breaks: 1 Chain: "B" Number of atoms: 3748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3748 Classifications: {'peptide': 474} Link IDs: {'PTRANS': 18, 'TRANS': 455} Chain breaks: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 7.73, per 1000 atoms: 0.57 Number of scatterers: 13472 At special positions: 0 Unit cell: (103.5, 101.2, 170.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 2666 8.00 N 2299 7.00 C 8427 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 466 " distance=2.02 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.04 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.02 Simple disulfide: pdb=" SG CYS C 473 " - pdb=" SG CYS C 477 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS A 466 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.04 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.02 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 477 " distance=2.04 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 466 " distance=2.03 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 277 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 76 " distance=2.03 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 139 " distance=2.04 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 305 " distance=2.02 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 477 " distance=2.06 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 501 " - " ASN A 21 " " NAG A 502 " - " ASN A 33 " " NAG A 503 " - " ASN A 289 " " NAG A 504 " - " ASN A 483 " " NAG B 501 " - " ASN B 21 " " NAG B 502 " - " ASN B 33 " " NAG B 503 " - " ASN B 289 " " NAG B 504 " - " ASN B 483 " " NAG C 501 " - " ASN C 21 " " NAG C 502 " - " ASN C 33 " " NAG C 503 " - " ASN C 289 " " NAG C 504 " - " ASN C 483 " " NAG D 1 " - " ASN C 169 " " NAG E 1 " - " ASN A 169 " " NAG F 1 " - " ASN B 169 " Time building additional restraints: 5.18 Conformation dependent library (CDL) restraints added in 2.2 seconds 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3050 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 40 sheets defined 22.5% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 3.928A pdb=" N ASP C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ARG C 78 " --> pdb=" O GLU C 75 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU C 80 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 113 through 115 No H-bonds generated for 'chain 'C' and resid 113 through 115' Processing helix chain 'C' and resid 125 through 127 removed outlier: 3.840A pdb=" N TRP C 127 " --> pdb=" O LYS C 125a" (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'C' and resid 366 through 386 Processing helix chain 'C' and resid 403 through 456 removed outlier: 3.721A pdb=" N LEU C 409 " --> pdb=" O ARG C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 482 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.901A pdb=" N ASP A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ARG A 78 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 125 through 127 Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 366 through 386 Processing helix chain 'A' and resid 403 through 456 Processing helix chain 'A' and resid 474 through 484 Processing helix chain 'B' and resid 65 through 72 Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 125 through 127 removed outlier: 3.912A pdb=" N TRP B 127 " --> pdb=" O LYS B 125a" (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 196 Processing helix chain 'B' and resid 366 through 386 Processing helix chain 'B' and resid 403 through 454 removed outlier: 3.557A pdb=" N LEU B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL B 444 " --> pdb=" O HIS B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 483 Processing sheet with id=AA1, first strand: chain 'C' and resid 342 through 343 removed outlier: 7.988A pdb=" N TRP C 343 " --> pdb=" O ILE C 15 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TYR C 17 " --> pdb=" O TRP C 343 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 342 through 343 removed outlier: 7.988A pdb=" N TRP C 343 " --> pdb=" O ILE C 15 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TYR C 17 " --> pdb=" O TRP C 343 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 24 through 26 removed outlier: 4.422A pdb=" N GLU C 24 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AA5, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AA6, first strand: chain 'C' and resid 51 through 54 removed outlier: 6.178A pdb=" N LEU C 51 " --> pdb=" O GLU C 275 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N CYS C 277 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 59 through 62 removed outlier: 6.105A pdb=" N LEU C 59 " --> pdb=" O MET C 88 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE C 87 " --> pdb=" O MET C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.729A pdb=" N SER C 101 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N TRP C 234 " --> pdb=" O SER C 101 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.729A pdb=" N SER C 101 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N TRP C 234 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 136 through 141 removed outlier: 7.496A pdb=" N ALA C 138 " --> pdb=" O ASN C 144 " (cutoff:3.500A) removed outlier: 9.442A pdb=" N ASN C 144 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AB3, first strand: chain 'C' and resid 286 through 287 removed outlier: 3.812A pdb=" N GLY C 303 " --> pdb=" O GLU C 393 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AB5, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.065A pdb=" N SER H 33 " --> pdb=" O ASP H 95 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.736A pdb=" N HIS H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLY H 96 " --> pdb=" O PHE H 100M" (cutoff:3.500A) removed outlier: 7.325A pdb=" N PHE H 100M" --> pdb=" O GLY H 96 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.692A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.692A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AC1, first strand: chain 'A' and resid 364 through 365 Processing sheet with id=AC2, first strand: chain 'A' and resid 24 through 26 removed outlier: 4.437A pdb=" N GLU A 24 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AC4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AC5, first strand: chain 'A' and resid 51 through 54 removed outlier: 6.104A pdb=" N LEU A 51 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N CYS A 277 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 59 through 62 removed outlier: 6.082A pdb=" N LEU A 59 " --> pdb=" O MET A 88 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE A 87 " --> pdb=" O MET A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.633A pdb=" N SER A 101 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N TRP A 234 " --> pdb=" O SER A 101 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.633A pdb=" N SER A 101 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N TRP A 234 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.434A pdb=" N ALA A 138 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 9.568A pdb=" N ASN A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AD2, first strand: chain 'A' and resid 286 through 287 Processing sheet with id=AD3, first strand: chain 'B' and resid 364 through 365 Processing sheet with id=AD4, first strand: chain 'B' and resid 24 through 26 removed outlier: 4.412A pdb=" N GLU B 24 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AD6, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AD7, first strand: chain 'B' and resid 51 through 54 removed outlier: 6.203A pdb=" N LEU B 51 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N CYS B 277 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 59 through 62 removed outlier: 6.134A pdb=" N LEU B 59 " --> pdb=" O MET B 88 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE B 87 " --> pdb=" O MET B 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'B' and resid 100 through 102 removed outlier: 6.749A pdb=" N SER B 101 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N TRP B 234 " --> pdb=" O SER B 101 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 100 through 102 removed outlier: 6.749A pdb=" N SER B 101 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N TRP B 234 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 136 through 141 removed outlier: 7.461A pdb=" N ALA B 138 " --> pdb=" O ASN B 144 " (cutoff:3.500A) removed outlier: 9.561A pdb=" N ASN B 144 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 164 through 168 Processing sheet with id=AE4, first strand: chain 'B' and resid 286 through 287 542 hydrogen bonds defined for protein. 1440 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: 4.63 Time building geometry restraints manager: 5.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2733 1.32 - 1.45: 4321 1.45 - 1.59: 6585 1.59 - 1.72: 17 1.72 - 1.86: 116 Bond restraints: 13772 Sorted by residual: bond pdb=" CA SER H 31 " pdb=" CB SER H 31 " ideal model delta sigma weight residual 1.528 1.432 0.095 1.35e-02 5.49e+03 4.99e+01 bond pdb=" CB ASN C 433 " pdb=" CG ASN C 433 " ideal model delta sigma weight residual 1.516 1.369 0.147 2.50e-02 1.60e+03 3.45e+01 bond pdb=" CB LEU L 107 " pdb=" CG LEU L 107 " ideal model delta sigma weight residual 1.530 1.647 -0.117 2.00e-02 2.50e+03 3.42e+01 bond pdb=" CB PHE H 55 " pdb=" CG PHE H 55 " ideal model delta sigma weight residual 1.502 1.369 0.133 2.30e-02 1.89e+03 3.35e+01 bond pdb=" CB ASN A 433 " pdb=" CG ASN A 433 " ideal model delta sigma weight residual 1.516 1.393 0.123 2.50e-02 1.60e+03 2.43e+01 ... (remaining 13767 not shown) Histogram of bond angle deviations from ideal: 92.15 - 100.61: 26 100.61 - 109.06: 2130 109.06 - 117.52: 8021 117.52 - 125.97: 8192 125.97 - 134.42: 270 Bond angle restraints: 18639 Sorted by residual: angle pdb=" N LEU L 30 " pdb=" CA LEU L 30 " pdb=" C LEU L 30 " ideal model delta sigma weight residual 114.04 99.24 14.80 1.24e+00 6.50e-01 1.42e+02 angle pdb=" C HIS C 184 " pdb=" N PRO C 185 " pdb=" CA PRO C 185 " ideal model delta sigma weight residual 119.92 129.41 -9.49 1.07e+00 8.73e-01 7.87e+01 angle pdb=" C HIS C 354 " pdb=" CA HIS C 354 " pdb=" CB HIS C 354 " ideal model delta sigma weight residual 109.38 92.15 17.23 2.03e+00 2.43e-01 7.20e+01 angle pdb=" CA PHE C 118 " pdb=" CB PHE C 118 " pdb=" CG PHE C 118 " ideal model delta sigma weight residual 113.80 122.02 -8.22 1.00e+00 1.00e+00 6.76e+01 angle pdb=" C PRO C 57 " pdb=" N PRO C 58 " pdb=" CA PRO C 58 " ideal model delta sigma weight residual 120.52 128.65 -8.13 9.90e-01 1.02e+00 6.75e+01 ... (remaining 18634 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 8107 17.96 - 35.91: 254 35.91 - 53.87: 53 53.87 - 71.82: 26 71.82 - 89.78: 10 Dihedral angle restraints: 8450 sinusoidal: 3662 harmonic: 4788 Sorted by residual: dihedral pdb=" C HIS C 354 " pdb=" N HIS C 354 " pdb=" CA HIS C 354 " pdb=" CB HIS C 354 " ideal model delta harmonic sigma weight residual -122.60 -99.23 -23.37 0 2.50e+00 1.60e-01 8.74e+01 dihedral pdb=" CB CYS B 473 " pdb=" SG CYS B 473 " pdb=" SG CYS B 477 " pdb=" CB CYS B 477 " ideal model delta sinusoidal sigma weight residual -86.00 -15.99 -70.01 1 1.00e+01 1.00e-02 6.32e+01 dihedral pdb=" C HIS C 18 " pdb=" N HIS C 18 " pdb=" CA HIS C 18 " pdb=" CB HIS C 18 " ideal model delta harmonic sigma weight residual -122.60 -106.17 -16.43 0 2.50e+00 1.60e-01 4.32e+01 ... (remaining 8447 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.209: 1987 0.209 - 0.417: 54 0.417 - 0.626: 5 0.626 - 0.835: 0 0.835 - 1.043: 2 Chirality restraints: 2048 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 9.21e+01 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.36e+01 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN B 169 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.36 -1.04 2.00e-01 2.50e+01 2.72e+01 ... (remaining 2045 not shown) Planarity restraints: 2416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 504 " 0.322 2.00e-02 2.50e+03 2.77e-01 9.60e+02 pdb=" C7 NAG A 504 " -0.074 2.00e-02 2.50e+03 pdb=" C8 NAG A 504 " 0.015 2.00e-02 2.50e+03 pdb=" N2 NAG A 504 " -0.478 2.00e-02 2.50e+03 pdb=" O7 NAG A 504 " 0.214 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 503 " 0.302 2.00e-02 2.50e+03 2.62e-01 8.59e+02 pdb=" C7 NAG C 503 " -0.066 2.00e-02 2.50e+03 pdb=" C8 NAG C 503 " 0.150 2.00e-02 2.50e+03 pdb=" N2 NAG C 503 " -0.468 2.00e-02 2.50e+03 pdb=" O7 NAG C 503 " 0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 504 " -0.303 2.00e-02 2.50e+03 2.55e-01 8.14e+02 pdb=" C7 NAG B 504 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG B 504 " -0.189 2.00e-02 2.50e+03 pdb=" N2 NAG B 504 " 0.437 2.00e-02 2.50e+03 pdb=" O7 NAG B 504 " -0.023 2.00e-02 2.50e+03 ... (remaining 2413 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2487 2.76 - 3.29: 12321 3.29 - 3.83: 22345 3.83 - 4.36: 28523 4.36 - 4.90: 46480 Nonbonded interactions: 112156 Sorted by model distance: nonbonded pdb=" O CYS B 477 " pdb=" N SER B 480 " model vdw 2.221 2.520 nonbonded pdb=" O HIS C 355 " pdb=" O SER C 361 " model vdw 2.281 3.040 nonbonded pdb=" N ASP B 457 " pdb=" O ASP B 457 " model vdw 2.294 2.496 nonbonded pdb=" N LEU L 30 " pdb=" N GLY L 30A" model vdw 2.313 2.560 nonbonded pdb=" N GLN B 454 " pdb=" O GLN B 454 " model vdw 2.346 2.496 ... (remaining 112151 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 11 through 487 or resid 501 through 504)) selection = (chain 'B' and (resid 11 through 334 or resid 337 through 487 or resid 501 throu \ gh 504)) selection = (chain 'C' and (resid 11 through 334 or resid 337 through 487 or resid 501 throu \ gh 504)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 37.940 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 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 : 0.020 0.147 13772 Z= 1.336 Angle : 1.766 17.226 18639 Z= 1.190 Chirality : 0.099 1.043 2048 Planarity : 0.017 0.277 2401 Dihedral : 10.273 89.776 5340 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.46 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.19), residues: 1662 helix: 0.66 (0.26), residues: 329 sheet: 1.71 (0.25), residues: 370 loop : -0.07 (0.19), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.006 TRP B 153 HIS 0.022 0.003 HIS C 354 PHE 0.041 0.006 PHE C 118 TYR 0.054 0.008 TYR C 17 ARG 0.008 0.001 ARG C 229 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 307 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 456 ARG cc_start: 0.7268 (mtt180) cc_final: 0.6815 (mtp-110) REVERT: A 268 MET cc_start: 0.8576 (ttm) cc_final: 0.8366 (ttm) REVERT: A 279 THR cc_start: 0.8324 (t) cc_final: 0.8122 (t) REVERT: B 367 LYS cc_start: 0.8567 (mmtt) cc_final: 0.8078 (mmtm) REVERT: B 371 GLN cc_start: 0.7963 (tp40) cc_final: 0.7561 (tp40) outliers start: 0 outliers final: 0 residues processed: 307 average time/residue: 0.3084 time to fit residues: 128.8140 Evaluate side-chains 162 residues out of total 1459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 141 optimal weight: 0.9980 chunk 126 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 151 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 HIS H 102 HIS L 37 GLN A 129 GLN A 354 HIS ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 HIS B 471 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13772 Z= 0.228 Angle : 0.652 10.179 18639 Z= 0.345 Chirality : 0.046 0.431 2048 Planarity : 0.004 0.034 2401 Dihedral : 6.530 55.876 2180 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.26 % Allowed : 6.44 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.20), residues: 1662 helix: 2.06 (0.28), residues: 328 sheet: 1.37 (0.26), residues: 360 loop : -0.39 (0.19), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 343 HIS 0.010 0.001 HIS B 471 PHE 0.022 0.002 PHE A 118 TYR 0.012 0.002 TYR A 353 ARG 0.004 0.001 ARG B 149 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 197 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 26 VAL cc_start: 0.8722 (t) cc_final: 0.8238 (m) REVERT: C 388 MET cc_start: 0.8106 (mmm) cc_final: 0.7859 (mmm) REVERT: C 485 THR cc_start: 0.8239 (m) cc_final: 0.7937 (p) REVERT: A 268 MET cc_start: 0.8385 (ttm) cc_final: 0.8071 (ttm) outliers start: 33 outliers final: 25 residues processed: 218 average time/residue: 0.2780 time to fit residues: 85.2880 Evaluate side-chains 166 residues out of total 1459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 141 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 449 ASP Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 343 TRP Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 412 LYS Chi-restraints excluded: chain B residue 427 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 84 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 126 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 164 optimal weight: 0.3980 chunk 135 optimal weight: 4.9990 chunk 150 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 244 ASN ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 100EHIS L 37 GLN A 244 ASN B 92 ASN B 471 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 13772 Z= 0.301 Angle : 0.598 8.286 18639 Z= 0.315 Chirality : 0.045 0.222 2048 Planarity : 0.004 0.035 2401 Dihedral : 6.003 52.657 2180 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.88 % Allowed : 7.54 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.20), residues: 1662 helix: 2.14 (0.27), residues: 334 sheet: 0.78 (0.26), residues: 367 loop : -0.62 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 343 HIS 0.007 0.002 HIS H 102 PHE 0.022 0.002 PHE A 439 TYR 0.026 0.002 TYR L 49 ARG 0.009 0.001 ARG H 76 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 162 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 363 TYR cc_start: 0.8147 (OUTLIER) cc_final: 0.5838 (t80) REVERT: H 66 ARG cc_start: 0.7722 (mtp85) cc_final: 0.7361 (mtp-110) REVERT: L 91 TYR cc_start: 0.8674 (t80) cc_final: 0.8399 (t80) REVERT: A 357 ASN cc_start: 0.6166 (p0) cc_final: 0.5708 (p0) REVERT: B 144 ASN cc_start: 0.8334 (m-40) cc_final: 0.8044 (m-40) outliers start: 42 outliers final: 30 residues processed: 191 average time/residue: 0.2538 time to fit residues: 70.6665 Evaluate side-chains 176 residues out of total 1459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 145 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 363 TYR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 343 TRP Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 412 LYS Chi-restraints excluded: chain B residue 427 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 150 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 152 optimal weight: 0.4980 chunk 161 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN A 18 HIS B 471 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13772 Z= 0.195 Angle : 0.529 7.663 18639 Z= 0.276 Chirality : 0.043 0.232 2048 Planarity : 0.003 0.038 2401 Dihedral : 5.815 59.435 2180 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.60 % Allowed : 8.98 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.20), residues: 1662 helix: 2.53 (0.27), residues: 334 sheet: 0.76 (0.26), residues: 378 loop : -0.65 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 343 HIS 0.009 0.001 HIS A 18 PHE 0.016 0.001 PHE A 439 TYR 0.024 0.001 TYR L 49 ARG 0.003 0.000 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 163 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 363 TYR cc_start: 0.8093 (OUTLIER) cc_final: 0.5828 (t80) REVERT: H 66 ARG cc_start: 0.7603 (mtp85) cc_final: 0.7010 (mtp85) REVERT: L 91 TYR cc_start: 0.8642 (t80) cc_final: 0.8411 (t80) outliers start: 38 outliers final: 27 residues processed: 184 average time/residue: 0.2554 time to fit residues: 68.7279 Evaluate side-chains 174 residues out of total 1459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 146 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 363 TYR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 483 ASN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 343 TRP Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 412 LYS Chi-restraints excluded: chain B residue 458 ASN Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 471 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 134 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 38 GLN A 18 HIS A 355 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.110 13772 Z= 0.426 Angle : 0.637 8.428 18639 Z= 0.333 Chirality : 0.047 0.315 2048 Planarity : 0.004 0.041 2401 Dihedral : 6.334 57.450 2180 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.08 % Allowed : 10.01 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.20), residues: 1662 helix: 2.25 (0.27), residues: 334 sheet: 0.28 (0.26), residues: 395 loop : -0.83 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 343 HIS 0.026 0.002 HIS B 471 PHE 0.026 0.002 PHE B 439 TYR 0.025 0.002 TYR L 49 ARG 0.009 0.001 ARG H 76 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 152 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 348 ASP cc_start: 0.7286 (OUTLIER) cc_final: 0.6950 (p0) outliers start: 45 outliers final: 33 residues processed: 184 average time/residue: 0.2686 time to fit residues: 71.7460 Evaluate side-chains 173 residues out of total 1459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 139 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 483 ASN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 412 LYS Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 458 ASN Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 481 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 54 optimal weight: 5.9990 chunk 145 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 chunk 134 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 10 GLN A 18 HIS B 471 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13772 Z= 0.192 Angle : 0.525 7.551 18639 Z= 0.274 Chirality : 0.042 0.266 2048 Planarity : 0.003 0.033 2401 Dihedral : 6.083 59.001 2180 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.40 % Allowed : 12.20 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.20), residues: 1662 helix: 2.63 (0.27), residues: 334 sheet: 0.54 (0.27), residues: 385 loop : -0.81 (0.19), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP H 36 HIS 0.010 0.001 HIS A 18 PHE 0.014 0.001 PHE A 439 TYR 0.028 0.001 TYR L 49 ARG 0.009 0.000 ARG H 76 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 151 time to evaluate : 1.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 363 TYR cc_start: 0.8171 (OUTLIER) cc_final: 0.5869 (t80) REVERT: L 27 SER cc_start: 0.8735 (p) cc_final: 0.8385 (t) REVERT: A 476 GLU cc_start: 0.7340 (tp30) cc_final: 0.7051 (tp30) REVERT: B 239 MET cc_start: 0.7046 (mtp) cc_final: 0.6807 (mtp) outliers start: 35 outliers final: 23 residues processed: 171 average time/residue: 0.2535 time to fit residues: 63.6314 Evaluate side-chains 165 residues out of total 1459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 141 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain C residue 363 TYR Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 483 ASN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 412 LYS Chi-restraints excluded: chain B residue 458 ASN Chi-restraints excluded: chain B residue 459 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 155 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 160 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 10 GLN A 18 HIS B 471 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13772 Z= 0.205 Angle : 0.516 7.554 18639 Z= 0.269 Chirality : 0.042 0.257 2048 Planarity : 0.003 0.031 2401 Dihedral : 5.873 57.820 2180 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.13 % Favored : 96.81 % Rotamer: Outliers : 2.54 % Allowed : 12.20 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.20), residues: 1662 helix: 2.69 (0.27), residues: 334 sheet: 0.48 (0.26), residues: 390 loop : -0.77 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 343 HIS 0.010 0.001 HIS A 18 PHE 0.016 0.001 PHE A 439 TYR 0.027 0.001 TYR L 49 ARG 0.009 0.000 ARG H 76 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 150 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 363 TYR cc_start: 0.8146 (OUTLIER) cc_final: 0.5837 (t80) REVERT: L 27 SER cc_start: 0.8742 (p) cc_final: 0.8394 (t) outliers start: 37 outliers final: 30 residues processed: 173 average time/residue: 0.2608 time to fit residues: 65.8251 Evaluate side-chains 175 residues out of total 1459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 144 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain C residue 363 TYR Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 483 ASN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 412 LYS Chi-restraints excluded: chain B residue 458 ASN Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 471 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 99 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 96 optimal weight: 0.5980 chunk 48 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 109 optimal weight: 0.4980 chunk 79 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 126 optimal weight: 0.0770 chunk 146 optimal weight: 0.2980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 10 GLN A 18 HIS B 471 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13772 Z= 0.146 Angle : 0.493 7.274 18639 Z= 0.257 Chirality : 0.041 0.244 2048 Planarity : 0.003 0.031 2401 Dihedral : 5.692 58.009 2180 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.59 % Favored : 97.35 % Rotamer: Outliers : 2.33 % Allowed : 12.75 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.20), residues: 1662 helix: 2.85 (0.27), residues: 334 sheet: 0.65 (0.27), residues: 376 loop : -0.75 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 343 HIS 0.015 0.001 HIS B 471 PHE 0.012 0.001 PHE A 439 TYR 0.027 0.001 TYR L 49 ARG 0.008 0.000 ARG H 76 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 156 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 363 TYR cc_start: 0.8049 (OUTLIER) cc_final: 0.5869 (t80) REVERT: L 27 SER cc_start: 0.8717 (p) cc_final: 0.8366 (t) REVERT: A 239 MET cc_start: 0.8070 (mmt) cc_final: 0.7344 (mmt) REVERT: B 26 VAL cc_start: 0.9014 (t) cc_final: 0.8810 (m) outliers start: 34 outliers final: 25 residues processed: 177 average time/residue: 0.2551 time to fit residues: 66.1284 Evaluate side-chains 173 residues out of total 1459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 147 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain C residue 363 TYR Chi-restraints excluded: chain C residue 483 ASN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 343 TRP Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 412 LYS Chi-restraints excluded: chain B residue 458 ASN Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 471 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 154 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 141 optimal weight: 0.0970 chunk 98 optimal weight: 5.9990 chunk 158 optimal weight: 1.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 HIS A 18 HIS ** B 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 13772 Z= 0.319 Angle : 0.558 7.044 18639 Z= 0.290 Chirality : 0.044 0.254 2048 Planarity : 0.004 0.032 2401 Dihedral : 5.895 56.335 2180 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.19 % Favored : 96.75 % Rotamer: Outliers : 2.54 % Allowed : 13.16 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.20), residues: 1662 helix: 2.66 (0.27), residues: 334 sheet: 0.36 (0.27), residues: 383 loop : -0.80 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 343 HIS 0.015 0.002 HIS B 471 PHE 0.020 0.002 PHE B 439 TYR 0.024 0.002 TYR L 49 ARG 0.012 0.001 ARG H 76 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 153 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 27 SER cc_start: 0.8876 (p) cc_final: 0.8578 (t) REVERT: A 239 MET cc_start: 0.8321 (mmt) cc_final: 0.7552 (mmt) REVERT: B 56 ILE cc_start: 0.8982 (mt) cc_final: 0.8729 (pt) REVERT: B 285 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8923 (mm) outliers start: 37 outliers final: 31 residues processed: 177 average time/residue: 0.2565 time to fit residues: 66.4515 Evaluate side-chains 178 residues out of total 1459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 146 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 483 ASN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain L residue 17 GLN Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 412 LYS Chi-restraints excluded: chain B residue 458 ASN Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 471 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 96 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 166 optimal weight: 0.0870 chunk 153 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 105 optimal weight: 0.9990 chunk 141 optimal weight: 0.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 18 HIS ** B 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13772 Z= 0.179 Angle : 0.508 6.791 18639 Z= 0.265 Chirality : 0.042 0.244 2048 Planarity : 0.003 0.031 2401 Dihedral : 5.814 56.024 2180 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.83 % Favored : 97.11 % Rotamer: Outliers : 2.19 % Allowed : 13.50 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.20), residues: 1662 helix: 2.81 (0.27), residues: 335 sheet: 0.51 (0.27), residues: 391 loop : -0.77 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP H 36 HIS 0.013 0.001 HIS A 18 PHE 0.014 0.001 PHE A 439 TYR 0.026 0.001 TYR L 49 ARG 0.008 0.000 ARG H 76 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 153 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 363 TYR cc_start: 0.8139 (OUTLIER) cc_final: 0.5811 (t80) REVERT: C 478 MET cc_start: 0.7691 (ttm) cc_final: 0.7388 (mtt) REVERT: L 27 SER cc_start: 0.8861 (p) cc_final: 0.8587 (t) REVERT: A 239 MET cc_start: 0.8177 (mmt) cc_final: 0.7433 (mmt) REVERT: B 26 VAL cc_start: 0.9035 (t) cc_final: 0.8830 (m) REVERT: B 56 ILE cc_start: 0.9007 (mt) cc_final: 0.8767 (pt) REVERT: B 285 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8933 (mm) outliers start: 32 outliers final: 23 residues processed: 174 average time/residue: 0.2561 time to fit residues: 65.6217 Evaluate side-chains 174 residues out of total 1459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 149 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain C residue 363 TYR Chi-restraints excluded: chain C residue 483 ASN Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 343 TRP Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 412 LYS Chi-restraints excluded: chain B residue 458 ASN Chi-restraints excluded: chain B residue 459 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 40 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 55 optimal weight: 0.0170 chunk 136 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 24 optimal weight: 0.0770 chunk 116 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN ** B 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.115235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.095085 restraints weight = 20019.703| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.95 r_work: 0.3022 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 13772 Z= 0.322 Angle : 0.564 6.962 18639 Z= 0.294 Chirality : 0.044 0.259 2048 Planarity : 0.004 0.032 2401 Dihedral : 6.056 54.442 2180 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.73 % Favored : 96.21 % Rotamer: Outliers : 2.26 % Allowed : 13.50 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.20), residues: 1662 helix: 2.60 (0.27), residues: 334 sheet: 0.29 (0.27), residues: 383 loop : -0.87 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP H 36 HIS 0.005 0.001 HIS B 18 PHE 0.020 0.002 PHE B 439 TYR 0.032 0.002 TYR L 49 ARG 0.006 0.001 ARG H 76 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2960.06 seconds wall clock time: 53 minutes 52.84 seconds (3232.84 seconds total)