Starting phenix.real_space_refine on Fri Feb 16 05:50:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhk_33831/02_2024/7yhk_33831.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhk_33831/02_2024/7yhk_33831.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhk_33831/02_2024/7yhk_33831.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhk_33831/02_2024/7yhk_33831.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhk_33831/02_2024/7yhk_33831.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhk_33831/02_2024/7yhk_33831.pdb" } resolution = 3.14 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= 0.025 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 60 5.16 5 C 9153 2.51 5 N 2439 2.21 5 O 2850 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F ARG 67": "NH1" <-> "NH2" Residue "H GLU 97": "OE1" <-> "OE2" Residue "A GLU 25": "OE1" <-> "OE2" Residue "A GLU 124": "OE1" <-> "OE2" Residue "A GLU 173": "OE1" <-> "OE2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A GLU 427": "OE1" <-> "OE2" Residue "C ARG 67": "NH1" <-> "NH2" Residue "D GLU 97": "OE1" <-> "OE2" Residue "E GLU 25": "OE1" <-> "OE2" Residue "E GLU 124": "OE1" <-> "OE2" Residue "E GLU 173": "OE1" <-> "OE2" Residue "E GLU 198": "OE1" <-> "OE2" Residue "E GLU 427": "OE1" <-> "OE2" Residue "I ARG 67": "NH1" <-> "NH2" Residue "J GLU 97": "OE1" <-> "OE2" Residue "K GLU 25": "OE1" <-> "OE2" Residue "K GLU 124": "OE1" <-> "OE2" Residue "K GLU 173": "OE1" <-> "OE2" Residue "K GLU 198": "OE1" <-> "OE2" Residue "K GLU 427": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14502 Number of models: 1 Model: "" Number of chains: 15 Chain: "F" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 906 Classifications: {'peptide': 116} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 110} Chain: "H" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 847 Classifications: {'peptide': 111} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 4, 'TRANS': 102} Chain: "A" Number of atoms: 2997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2997 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 18, 'TRANS': 358} Chain breaks: 1 Chain: "B" 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: "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: "C" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 906 Classifications: {'peptide': 116} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 110} Chain: "D" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 847 Classifications: {'peptide': 111} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 4, 'TRANS': 102} Chain: "E" Number of atoms: 2997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2997 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 18, 'TRANS': 358} Chain breaks: 1 Chain: "G" 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: 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: "I" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 906 Classifications: {'peptide': 116} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 110} Chain: "J" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 847 Classifications: {'peptide': 111} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 4, 'TRANS': 102} Chain: "K" Number of atoms: 2997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2997 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 18, 'TRANS': 358} Chain breaks: 1 Chain: "L" 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: "K" 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: 7.49, per 1000 atoms: 0.52 Number of scatterers: 14502 At special positions: 0 Unit cell: (142.374, 147.042, 124.48, 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 60 16.00 O 2850 8.00 N 2439 7.00 C 9153 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 71 " distance=2.03 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 306 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 92 " distance=2.04 Simple disulfide: pdb=" SG CYS E 46 " - pdb=" SG CYS E 278 " distance=2.03 Simple disulfide: pdb=" SG CYS E 59 " - pdb=" SG CYS E 71 " distance=2.03 Simple disulfide: pdb=" SG CYS E 94 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 282 " - pdb=" SG CYS E 306 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS K 46 " - pdb=" SG CYS K 278 " distance=2.03 Simple disulfide: pdb=" SG CYS K 59 " - pdb=" SG CYS K 71 " distance=2.03 Simple disulfide: pdb=" SG CYS K 94 " - pdb=" SG CYS K 139 " distance=2.03 Simple disulfide: pdb=" SG CYS K 282 " - pdb=" SG CYS K 306 " distance=2.02 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 B 1 " - " NAG B 2 " " NAG G 1 " - " NAG G 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A 601 " - " ASN A 58 " " NAG A 602 " - " ASN A 27 " " NAG A 603 " - " ASN A 163 " " NAG A 604 " - " ASN A 290 " " NAG B 1 " - " ASN A 91 " " NAG E 601 " - " ASN E 58 " " NAG E 602 " - " ASN E 27 " " NAG E 603 " - " ASN E 163 " " NAG E 604 " - " ASN E 290 " " NAG G 1 " - " ASN E 91 " " NAG K 601 " - " ASN K 58 " " NAG K 602 " - " ASN K 27 " " NAG K 603 " - " ASN K 163 " " NAG K 604 " - " ASN K 290 " " NAG L 1 " - " ASN K 91 " Time building additional restraints: 5.49 Conformation dependent library (CDL) restraints added in 2.6 seconds 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3354 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 45 sheets defined 14.6% alpha, 29.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'F' and resid 62 through 65 removed outlier: 3.519A pdb=" N LYS F 65 " --> pdb=" O ASP F 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 62 through 65' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.727A pdb=" N ASP H 86 " --> pdb=" O GLU H 83 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA H 87 " --> pdb=" O GLU H 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 83 through 87' Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 71 through 75 removed outlier: 3.749A pdb=" N LEU A 74 " --> pdb=" O CYS A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 109 removed outlier: 3.586A pdb=" N GLU A 107 " --> pdb=" O GLU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 removed outlier: 3.522A pdb=" N GLN A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.961A pdb=" N LYS A 388 " --> pdb=" O SER A 384 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASN A 390 " --> pdb=" O ILE A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 442 removed outlier: 3.504A pdb=" N ASP A 420 " --> pdb=" O ASP A 416 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU A 435 " --> pdb=" O LEU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 448 removed outlier: 3.608A pdb=" N ASN A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 removed outlier: 3.520A pdb=" N LYS C 65 " --> pdb=" O ASP C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 65' Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.728A pdb=" N ASP D 86 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA D 87 " --> pdb=" O GLU D 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 83 through 87' Processing helix chain 'E' and resid 61 through 66 Processing helix chain 'E' and resid 71 through 75 removed outlier: 3.749A pdb=" N LEU E 74 " --> pdb=" O CYS E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 109 removed outlier: 3.586A pdb=" N GLU E 107 " --> pdb=" O GLU E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 195 removed outlier: 3.522A pdb=" N GLN E 191 " --> pdb=" O ASN E 187 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA E 193 " --> pdb=" O GLY E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 390 removed outlier: 3.961A pdb=" N LYS E 388 " --> pdb=" O SER E 384 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASN E 390 " --> pdb=" O ILE E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 442 removed outlier: 3.505A pdb=" N ASP E 420 " --> pdb=" O ASP E 416 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR E 423 " --> pdb=" O LEU E 419 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU E 435 " --> pdb=" O LEU E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 443 through 448 removed outlier: 3.608A pdb=" N ASN E 447 " --> pdb=" O SER E 443 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 65 removed outlier: 3.518A pdb=" N LYS I 65 " --> pdb=" O ASP I 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 62 through 65' Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.726A pdb=" N ASP J 86 " --> pdb=" O GLU J 83 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA J 87 " --> pdb=" O GLU J 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 83 through 87' Processing helix chain 'K' and resid 61 through 66 Processing helix chain 'K' and resid 71 through 75 removed outlier: 3.749A pdb=" N LEU K 74 " --> pdb=" O CYS K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 109 removed outlier: 3.586A pdb=" N GLU K 107 " --> pdb=" O GLU K 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 187 through 195 removed outlier: 3.523A pdb=" N GLN K 191 " --> pdb=" O ASN K 187 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA K 193 " --> pdb=" O GLY K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 383 through 390 removed outlier: 3.962A pdb=" N LYS K 388 " --> pdb=" O SER K 384 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASN K 390 " --> pdb=" O ILE K 386 " (cutoff:3.500A) Processing helix chain 'K' and resid 407 through 442 removed outlier: 3.504A pdb=" N ASP K 420 " --> pdb=" O ASP K 416 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR K 423 " --> pdb=" O LEU K 419 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU K 435 " --> pdb=" O LEU K 431 " (cutoff:3.500A) Processing helix chain 'K' and resid 443 through 448 removed outlier: 3.608A pdb=" N ASN K 447 " --> pdb=" O SER K 443 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'F' and resid 3 through 6 removed outlier: 3.760A pdb=" N VAL F 18 " --> pdb=" O ILE F 83 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.275A pdb=" N GLU F 10 " --> pdb=" O THR F 114 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N TRP F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA F 40 " --> pdb=" O GLY F 44 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.732A pdb=" N ASP H 74 " --> pdb=" O SER H 71 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'H' and resid 10 through 13 removed outlier: 3.870A pdb=" N GLU H 109 " --> pdb=" O LEU H 11 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'H' and resid 30 through 31 Processing sheet with id= 6, first strand: chain 'H' and resid 57 through 58 removed outlier: 3.569A pdb=" N ASN H 57 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LEU H 50 " --> pdb=" O GLN H 41 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLN H 41 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE H 52 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR H 101 " --> pdb=" O GLN H 94 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 19 through 20 Processing sheet with id= 8, first strand: chain 'A' and resid 33 through 35 Processing sheet with id= 9, first strand: chain 'A' and resid 37 through 38 Processing sheet with id= 10, first strand: chain 'A' and resid 54 through 57 removed outlier: 6.839A pdb=" N LEU A 54 " --> pdb=" O VAL A 84 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'A' and resid 112 through 114 removed outlier: 6.983A pdb=" N SER A 261 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE A 258 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'A' and resid 117 through 119 removed outlier: 6.537A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE A 258 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.589A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'A' and resid 164 through 169 removed outlier: 3.616A pdb=" N ALA A 247 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'A' and resid 282 through 284 removed outlier: 3.823A pdb=" N CYS A 282 " --> pdb=" O ILE A 289 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE A 289 " --> pdb=" O CYS A 282 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.761A pdb=" N VAL C 18 " --> pdb=" O ILE C 83 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.274A pdb=" N GLU C 10 " --> pdb=" O THR C 114 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N MET C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N TRP C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA C 40 " --> pdb=" O GLY C 44 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.733A pdb=" N ASP D 74 " --> pdb=" O SER D 71 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.869A pdb=" N GLU D 109 " --> pdb=" O LEU D 11 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'D' and resid 30 through 31 Processing sheet with id= 21, first strand: chain 'D' and resid 57 through 58 removed outlier: 3.569A pdb=" N ASN D 57 " --> pdb=" O TYR D 53 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LEU D 50 " --> pdb=" O GLN D 41 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLN D 41 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE D 52 " --> pdb=" O TRP D 39 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N THR D 101 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'E' and resid 19 through 20 Processing sheet with id= 23, first strand: chain 'E' and resid 33 through 35 Processing sheet with id= 24, first strand: chain 'E' and resid 37 through 38 Processing sheet with id= 25, first strand: chain 'E' and resid 54 through 57 removed outlier: 6.839A pdb=" N LEU E 54 " --> pdb=" O VAL E 84 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'E' and resid 112 through 114 removed outlier: 6.984A pdb=" N SER E 261 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TYR E 256 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LEU E 179 " --> pdb=" O TYR E 256 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE E 258 " --> pdb=" O LEU E 177 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU E 175 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LEU E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'E' and resid 117 through 119 removed outlier: 6.537A pdb=" N TYR E 256 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LEU E 179 " --> pdb=" O TYR E 256 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE E 258 " --> pdb=" O LEU E 177 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU E 175 " --> pdb=" O LEU E 260 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'E' and resid 136 through 141 removed outlier: 4.588A pdb=" N CYS E 139 " --> pdb=" O SER E 146 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'E' and resid 164 through 169 removed outlier: 3.616A pdb=" N ALA E 247 " --> pdb=" O LEU E 164 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'E' and resid 282 through 284 removed outlier: 3.823A pdb=" N CYS E 282 " --> pdb=" O ILE E 289 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE E 289 " --> pdb=" O CYS E 282 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'I' and resid 3 through 6 removed outlier: 3.760A pdb=" N VAL I 18 " --> pdb=" O ILE I 83 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.275A pdb=" N GLU I 10 " --> pdb=" O THR I 114 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N TRP I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA I 40 " --> pdb=" O GLY I 44 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.732A pdb=" N ASP J 74 " --> pdb=" O SER J 71 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.870A pdb=" N GLU J 109 " --> pdb=" O LEU J 11 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'J' and resid 30 through 31 Processing sheet with id= 36, first strand: chain 'J' and resid 57 through 58 removed outlier: 3.569A pdb=" N ASN J 57 " --> pdb=" O TYR J 53 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N LEU J 50 " --> pdb=" O GLN J 41 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLN J 41 " --> pdb=" O LEU J 50 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE J 52 " --> pdb=" O TRP J 39 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR J 101 " --> pdb=" O GLN J 94 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'K' and resid 19 through 20 Processing sheet with id= 38, first strand: chain 'K' and resid 33 through 35 Processing sheet with id= 39, first strand: chain 'K' and resid 37 through 38 Processing sheet with id= 40, first strand: chain 'K' and resid 54 through 57 removed outlier: 6.840A pdb=" N LEU K 54 " --> pdb=" O VAL K 84 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'K' and resid 112 through 114 removed outlier: 6.984A pdb=" N SER K 261 " --> pdb=" O SER K 113 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TYR K 256 " --> pdb=" O LEU K 179 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LEU K 179 " --> pdb=" O TYR K 256 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE K 258 " --> pdb=" O LEU K 177 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU K 175 " --> pdb=" O LEU K 260 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LEU K 179 " --> pdb=" O PRO K 254 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'K' and resid 117 through 119 removed outlier: 6.537A pdb=" N TYR K 256 " --> pdb=" O LEU K 179 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LEU K 179 " --> pdb=" O TYR K 256 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE K 258 " --> pdb=" O LEU K 177 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU K 175 " --> pdb=" O LEU K 260 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'K' and resid 136 through 141 removed outlier: 4.589A pdb=" N CYS K 139 " --> pdb=" O SER K 146 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'K' and resid 164 through 169 removed outlier: 3.616A pdb=" N ALA K 247 " --> pdb=" O LEU K 164 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'K' and resid 282 through 284 removed outlier: 3.824A pdb=" N CYS K 282 " --> pdb=" O ILE K 289 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE K 289 " --> pdb=" O CYS K 282 " (cutoff:3.500A) 444 hydrogen bonds defined for protein. 1197 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: 4.51 Time building geometry restraints manager: 5.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2461 1.32 - 1.45: 4221 1.45 - 1.58: 8075 1.58 - 1.71: 0 1.71 - 1.84: 84 Bond restraints: 14841 Sorted by residual: bond pdb=" CA LYS E 123 " pdb=" C LYS E 123 " ideal model delta sigma weight residual 1.527 1.456 0.071 1.35e-02 5.49e+03 2.74e+01 bond pdb=" CA LYS A 123 " pdb=" C LYS A 123 " ideal model delta sigma weight residual 1.527 1.456 0.071 1.35e-02 5.49e+03 2.73e+01 bond pdb=" CA LYS K 123 " pdb=" C LYS K 123 " ideal model delta sigma weight residual 1.527 1.456 0.071 1.35e-02 5.49e+03 2.73e+01 bond pdb=" CA SER E 125 " pdb=" C SER E 125 " ideal model delta sigma weight residual 1.523 1.462 0.061 1.34e-02 5.57e+03 2.10e+01 bond pdb=" CA SER A 125 " pdb=" C SER A 125 " ideal model delta sigma weight residual 1.523 1.462 0.061 1.34e-02 5.57e+03 2.08e+01 ... (remaining 14836 not shown) Histogram of bond angle deviations from ideal: 98.32 - 105.64: 353 105.64 - 112.96: 7908 112.96 - 120.29: 5460 120.29 - 127.61: 6247 127.61 - 134.93: 183 Bond angle restraints: 20151 Sorted by residual: angle pdb=" N GLU A 90 " pdb=" CA GLU A 90 " pdb=" C GLU A 90 " ideal model delta sigma weight residual 111.36 124.73 -13.37 1.09e+00 8.42e-01 1.50e+02 angle pdb=" N GLU E 90 " pdb=" CA GLU E 90 " pdb=" C GLU E 90 " ideal model delta sigma weight residual 111.36 124.71 -13.35 1.09e+00 8.42e-01 1.50e+02 angle pdb=" N GLU K 90 " pdb=" CA GLU K 90 " pdb=" C GLU K 90 " ideal model delta sigma weight residual 111.36 124.70 -13.34 1.09e+00 8.42e-01 1.50e+02 angle pdb=" N ALA C 76 " pdb=" CA ALA C 76 " pdb=" C ALA C 76 " ideal model delta sigma weight residual 109.96 99.51 10.45 1.58e+00 4.01e-01 4.37e+01 angle pdb=" N ALA I 76 " pdb=" CA ALA I 76 " pdb=" C ALA I 76 " ideal model delta sigma weight residual 109.96 99.54 10.42 1.58e+00 4.01e-01 4.35e+01 ... (remaining 20146 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 8176 17.70 - 35.40: 725 35.40 - 53.09: 138 53.09 - 70.79: 21 70.79 - 88.49: 18 Dihedral angle restraints: 9078 sinusoidal: 3846 harmonic: 5232 Sorted by residual: dihedral pdb=" CB CYS K 46 " pdb=" SG CYS K 46 " pdb=" SG CYS K 278 " pdb=" CB CYS K 278 " ideal model delta sinusoidal sigma weight residual -86.00 -23.50 -62.50 1 1.00e+01 1.00e-02 5.17e+01 dihedral pdb=" CB CYS A 46 " pdb=" SG CYS A 46 " pdb=" SG CYS A 278 " pdb=" CB CYS A 278 " ideal model delta sinusoidal sigma weight residual -86.00 -23.51 -62.49 1 1.00e+01 1.00e-02 5.17e+01 dihedral pdb=" CB CYS E 46 " pdb=" SG CYS E 46 " pdb=" SG CYS E 278 " pdb=" CB CYS E 278 " ideal model delta sinusoidal sigma weight residual -86.00 -23.54 -62.46 1 1.00e+01 1.00e-02 5.16e+01 ... (remaining 9075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 2078 0.105 - 0.209: 148 0.209 - 0.314: 9 0.314 - 0.419: 3 0.419 - 0.523: 3 Chirality restraints: 2241 Sorted by residual: chirality pdb=" CA GLU E 90 " pdb=" N GLU E 90 " pdb=" C GLU E 90 " pdb=" CB GLU E 90 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.85e+00 chirality pdb=" CA GLU A 90 " pdb=" N GLU A 90 " pdb=" C GLU A 90 " pdb=" CB GLU A 90 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.82e+00 chirality pdb=" CA GLU K 90 " pdb=" N GLU K 90 " pdb=" C GLU K 90 " pdb=" CB GLU K 90 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.78e+00 ... (remaining 2238 not shown) Planarity restraints: 2607 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 602 " 0.086 2.00e-02 2.50e+03 7.10e-02 6.31e+01 pdb=" C7 NAG K 602 " -0.024 2.00e-02 2.50e+03 pdb=" C8 NAG K 602 " 0.065 2.00e-02 2.50e+03 pdb=" N2 NAG K 602 " -0.113 2.00e-02 2.50e+03 pdb=" O7 NAG K 602 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 602 " -0.086 2.00e-02 2.50e+03 7.10e-02 6.30e+01 pdb=" C7 NAG E 602 " 0.024 2.00e-02 2.50e+03 pdb=" C8 NAG E 602 " -0.065 2.00e-02 2.50e+03 pdb=" N2 NAG E 602 " 0.113 2.00e-02 2.50e+03 pdb=" O7 NAG E 602 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 602 " 0.086 2.00e-02 2.50e+03 7.10e-02 6.30e+01 pdb=" C7 NAG A 602 " -0.024 2.00e-02 2.50e+03 pdb=" C8 NAG A 602 " 0.065 2.00e-02 2.50e+03 pdb=" N2 NAG A 602 " -0.113 2.00e-02 2.50e+03 pdb=" O7 NAG A 602 " -0.015 2.00e-02 2.50e+03 ... (remaining 2604 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 3994 2.81 - 3.33: 11086 3.33 - 3.85: 23582 3.85 - 4.38: 27950 4.38 - 4.90: 49806 Nonbonded interactions: 116418 Sorted by model distance: nonbonded pdb=" OG1 THR E 284 " pdb=" O GLY E 287 " model vdw 2.283 2.440 nonbonded pdb=" OG1 THR A 284 " pdb=" O GLY A 287 " model vdw 2.284 2.440 nonbonded pdb=" OG1 THR K 284 " pdb=" O GLY K 287 " model vdw 2.284 2.440 nonbonded pdb=" OG SER J 28 " pdb=" OD1 ASP J 30 " model vdw 2.294 2.440 nonbonded pdb=" OG SER H 28 " pdb=" OD1 ASP H 30 " model vdw 2.294 2.440 ... (remaining 116413 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' selection = chain 'E' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'J' } 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: 6.170 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: 0.010 Extract box with map and model: 18.750 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 39.310 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 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 : 0.007 0.071 14841 Z= 0.454 Angle : 0.995 13.371 20151 Z= 0.577 Chirality : 0.059 0.523 2241 Planarity : 0.008 0.071 2592 Dihedral : 14.130 88.488 5670 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.03 % Favored : 94.80 % Rotamer: Outliers : 0.76 % Allowed : 3.63 % Favored : 95.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.35 % 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: -3.95 (0.16), residues: 1788 helix: -4.60 (0.12), residues: 213 sheet: -1.95 (0.20), residues: 549 loop : -2.62 (0.15), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 64 HIS 0.009 0.001 HIS J 80 PHE 0.022 0.002 PHE E 115 TYR 0.016 0.002 TYR H 36 ARG 0.011 0.001 ARG K 220 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 270 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.7955 (tp30) cc_final: 0.7631 (tp30) REVERT: A 44 LYS cc_start: 0.6915 (mtmt) cc_final: 0.6602 (mttm) REVERT: A 55 GLN cc_start: 0.8549 (tt0) cc_final: 0.8339 (mt0) REVERT: A 88 ASN cc_start: 0.7597 (m110) cc_final: 0.7117 (p0) REVERT: A 188 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7619 (tp) REVERT: A 192 ARG cc_start: 0.7131 (mtt180) cc_final: 0.6925 (mtt180) REVERT: A 219 LYS cc_start: 0.8285 (tttm) cc_final: 0.7758 (ttmt) REVERT: A 316 ARG cc_start: 0.7963 (mtp85) cc_final: 0.7697 (mtt90) REVERT: A 317 MET cc_start: 0.8330 (mtp) cc_final: 0.7919 (mtp) REVERT: A 383 ASN cc_start: 0.7029 (t0) cc_final: 0.6627 (t0) REVERT: A 407 MET cc_start: 0.6683 (ttp) cc_final: 0.6453 (ttp) REVERT: C 13 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7168 (mmtm) REVERT: E 38 GLU cc_start: 0.7918 (tp30) cc_final: 0.7713 (tp30) REVERT: E 88 ASN cc_start: 0.7637 (m110) cc_final: 0.7099 (p0) REVERT: E 188 ILE cc_start: 0.7746 (OUTLIER) cc_final: 0.7545 (tp) REVERT: E 219 LYS cc_start: 0.8255 (tttm) cc_final: 0.7718 (ttmt) REVERT: E 281 LYS cc_start: 0.7073 (mmtt) cc_final: 0.6865 (mmtt) REVERT: E 316 ARG cc_start: 0.7881 (mtp85) cc_final: 0.7429 (mtt90) REVERT: E 398 LYS cc_start: 0.8281 (mttm) cc_final: 0.7900 (mttp) REVERT: E 407 MET cc_start: 0.6750 (ttp) cc_final: 0.6398 (ttp) REVERT: I 54 TYR cc_start: 0.7431 (t80) cc_final: 0.7186 (t80) REVERT: K 38 GLU cc_start: 0.8036 (tp30) cc_final: 0.7692 (tp30) REVERT: K 44 LYS cc_start: 0.6884 (mtmt) cc_final: 0.6409 (mtmt) REVERT: K 55 GLN cc_start: 0.8570 (tt0) cc_final: 0.8355 (mt0) REVERT: K 72 GLU cc_start: 0.7669 (tt0) cc_final: 0.7432 (mt-10) REVERT: K 88 ASN cc_start: 0.7613 (m110) cc_final: 0.7169 (p0) REVERT: K 188 ILE cc_start: 0.7784 (OUTLIER) cc_final: 0.7557 (tp) REVERT: K 192 ARG cc_start: 0.7078 (mtt180) cc_final: 0.6868 (mtt180) REVERT: K 219 LYS cc_start: 0.8330 (tttm) cc_final: 0.7775 (ttmt) REVERT: K 275 MET cc_start: 0.8076 (tpt) cc_final: 0.7513 (tpt) REVERT: K 276 ASN cc_start: 0.7168 (t0) cc_final: 0.6841 (t0) REVERT: K 316 ARG cc_start: 0.7929 (mtp85) cc_final: 0.7682 (mtt90) REVERT: K 317 MET cc_start: 0.8443 (mtp) cc_final: 0.8012 (mtp) REVERT: K 383 ASN cc_start: 0.7032 (t0) cc_final: 0.6642 (t0) outliers start: 12 outliers final: 1 residues processed: 280 average time/residue: 0.2627 time to fit residues: 106.9701 Evaluate side-chains 213 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 208 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain K residue 188 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 0.0970 chunk 134 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 71 optimal weight: 10.0000 chunk 138 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 160 optimal weight: 0.5980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 6 GLN F 39 GLN F 82 GLN F 84 ASN F 109 GLN H 35 ASN H 41 GLN H 78 ASN A 88 ASN A 130 HIS A 184 HIS A 191 GLN A 196 HIS A 199 ASN A 226 GLN A 231 ASN A 250 ASN A 286 GLN ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 ASN C 39 GLN C 82 GLN C 84 ASN C 109 GLN D 41 GLN D 78 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 ASN E 130 HIS ** E 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 HIS E 191 GLN E 199 ASN E 231 ASN E 250 ASN E 297 ASN E 409 ASN I 6 GLN I 39 GLN I 82 GLN I 84 ASN I 109 GLN J 35 ASN J 41 GLN K 88 ASN K 130 HIS ** K 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 184 HIS K 191 GLN K 231 ASN K 250 ASN ** K 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 409 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14841 Z= 0.191 Angle : 0.596 8.190 20151 Z= 0.310 Chirality : 0.042 0.139 2241 Planarity : 0.005 0.044 2592 Dihedral : 5.798 52.800 2333 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.27 % Allowed : 8.46 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.35 % 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: -3.01 (0.17), residues: 1788 helix: -2.34 (0.26), residues: 225 sheet: -1.58 (0.19), residues: 588 loop : -2.19 (0.17), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 422 HIS 0.002 0.001 HIS E 130 PHE 0.017 0.001 PHE K 440 TYR 0.009 0.001 TYR C 60 ARG 0.004 0.000 ARG A 436 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 229 time to evaluate : 1.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2 ILE cc_start: 0.8153 (mm) cc_final: 0.7885 (mm) REVERT: F 87 LYS cc_start: 0.6102 (mttm) cc_final: 0.5861 (mttt) REVERT: A 88 ASN cc_start: 0.7735 (m-40) cc_final: 0.6906 (p0) REVERT: A 90 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7299 (mm-30) REVERT: A 219 LYS cc_start: 0.8218 (tttm) cc_final: 0.7719 (ttmt) REVERT: A 275 MET cc_start: 0.7940 (tpt) cc_final: 0.7527 (tpt) REVERT: A 316 ARG cc_start: 0.7892 (mtp85) cc_final: 0.7611 (mtt90) REVERT: A 317 MET cc_start: 0.7859 (mtp) cc_final: 0.7399 (tpp) REVERT: A 383 ASN cc_start: 0.6648 (t0) cc_final: 0.6257 (t0) REVERT: A 398 LYS cc_start: 0.8332 (mttm) cc_final: 0.8113 (mttm) REVERT: A 402 LYS cc_start: 0.7493 (mmtm) cc_final: 0.7133 (mmmt) REVERT: A 407 MET cc_start: 0.6627 (ttp) cc_final: 0.6280 (ttp) REVERT: E 88 ASN cc_start: 0.7670 (m-40) cc_final: 0.6841 (p0) REVERT: E 90 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7295 (mm-30) REVERT: E 156 GLU cc_start: 0.8125 (pt0) cc_final: 0.7858 (pt0) REVERT: E 219 LYS cc_start: 0.8240 (tttm) cc_final: 0.7729 (ttmt) REVERT: E 276 ASN cc_start: 0.7335 (t0) cc_final: 0.7113 (t0) REVERT: E 297 ASN cc_start: 0.6966 (m110) cc_final: 0.6616 (m110) REVERT: E 402 LYS cc_start: 0.7352 (mmpt) cc_final: 0.7060 (mtpt) REVERT: E 407 MET cc_start: 0.6689 (ttp) cc_final: 0.6375 (ttp) REVERT: I 54 TYR cc_start: 0.7331 (t80) cc_final: 0.7060 (t80) REVERT: I 104 MET cc_start: 0.7920 (mtm) cc_final: 0.7476 (mtt) REVERT: K 88 ASN cc_start: 0.7691 (m-40) cc_final: 0.6953 (p0) REVERT: K 90 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7409 (mm-30) REVERT: K 156 GLU cc_start: 0.8041 (pt0) cc_final: 0.7717 (pt0) REVERT: K 219 LYS cc_start: 0.8311 (tttm) cc_final: 0.7804 (ttmt) REVERT: K 275 MET cc_start: 0.8069 (tpt) cc_final: 0.7541 (tpt) REVERT: K 276 ASN cc_start: 0.7126 (t0) cc_final: 0.6587 (t0) REVERT: K 316 ARG cc_start: 0.7866 (mtp85) cc_final: 0.7609 (mtt90) REVERT: K 317 MET cc_start: 0.7948 (mtp) cc_final: 0.7720 (mtp) REVERT: K 383 ASN cc_start: 0.6684 (t0) cc_final: 0.6250 (t0) outliers start: 20 outliers final: 18 residues processed: 240 average time/residue: 0.2856 time to fit residues: 98.6524 Evaluate side-chains 230 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 212 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 109 GLN Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain I residue 109 GLN Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain K residue 81 SER Chi-restraints excluded: chain K residue 160 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 133 optimal weight: 0.0770 chunk 109 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 161 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 159 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 109 GLN C 109 GLN D 78 ASN ** E 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 ASN I 109 GLN ** K 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 226 GLN ** K 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14841 Z= 0.231 Angle : 0.577 9.600 20151 Z= 0.294 Chirality : 0.041 0.136 2241 Planarity : 0.004 0.044 2592 Dihedral : 5.182 27.289 2322 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.35 % Allowed : 10.37 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.35 % 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: -2.47 (0.18), residues: 1788 helix: -1.00 (0.33), residues: 225 sheet: -1.27 (0.20), residues: 552 loop : -2.03 (0.17), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 107 HIS 0.004 0.001 HIS E 184 PHE 0.021 0.001 PHE A 440 TYR 0.010 0.001 TYR C 60 ARG 0.004 0.000 ARG K 436 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 217 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 2 ILE cc_start: 0.8149 (mm) cc_final: 0.7885 (mm) REVERT: F 87 LYS cc_start: 0.6028 (mttm) cc_final: 0.5800 (mttt) REVERT: F 109 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.7267 (pp30) REVERT: A 44 LYS cc_start: 0.6757 (mtmt) cc_final: 0.6295 (mtpt) REVERT: A 88 ASN cc_start: 0.7749 (m-40) cc_final: 0.6967 (p0) REVERT: A 90 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7384 (mm-30) REVERT: A 115 PHE cc_start: 0.8005 (OUTLIER) cc_final: 0.7319 (m-10) REVERT: A 219 LYS cc_start: 0.8191 (tttm) cc_final: 0.7682 (ttmt) REVERT: A 316 ARG cc_start: 0.7900 (mtp85) cc_final: 0.7535 (ttt90) REVERT: A 317 MET cc_start: 0.7928 (mtp) cc_final: 0.7453 (mtp) REVERT: A 383 ASN cc_start: 0.6605 (t0) cc_final: 0.6214 (t0) REVERT: A 402 LYS cc_start: 0.7375 (mmtm) cc_final: 0.7066 (mmmt) REVERT: A 407 MET cc_start: 0.6592 (ttp) cc_final: 0.6388 (ttp) REVERT: C 104 MET cc_start: 0.8127 (mtm) cc_final: 0.7897 (mtm) REVERT: E 37 LEU cc_start: 0.7630 (mt) cc_final: 0.7395 (mt) REVERT: E 88 ASN cc_start: 0.7721 (m-40) cc_final: 0.7224 (p0) REVERT: E 90 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7368 (mm-30) REVERT: E 115 PHE cc_start: 0.7904 (OUTLIER) cc_final: 0.7318 (m-10) REVERT: E 219 LYS cc_start: 0.8178 (tttm) cc_final: 0.7682 (ttmt) REVERT: E 402 LYS cc_start: 0.7295 (mmpt) cc_final: 0.7009 (mtpt) REVERT: E 407 MET cc_start: 0.6690 (ttp) cc_final: 0.6440 (ttp) REVERT: I 54 TYR cc_start: 0.7283 (t80) cc_final: 0.7033 (t80) REVERT: I 80 TYR cc_start: 0.7595 (m-80) cc_final: 0.7027 (m-80) REVERT: K 44 LYS cc_start: 0.6776 (mtmt) cc_final: 0.6283 (mtmt) REVERT: K 88 ASN cc_start: 0.7741 (m-40) cc_final: 0.6930 (p0) REVERT: K 90 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7513 (mm-30) REVERT: K 115 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.7264 (m-10) REVERT: K 156 GLU cc_start: 0.8050 (pt0) cc_final: 0.7761 (pt0) REVERT: K 219 LYS cc_start: 0.8291 (tttm) cc_final: 0.7736 (ttmm) REVERT: K 317 MET cc_start: 0.7940 (mtp) cc_final: 0.7718 (mtp) REVERT: K 383 ASN cc_start: 0.6714 (t0) cc_final: 0.6268 (t0) outliers start: 37 outliers final: 27 residues processed: 237 average time/residue: 0.2719 time to fit residues: 93.3276 Evaluate side-chains 240 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 209 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 109 GLN Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 115 PHE Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain I residue 109 GLN Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 81 SER Chi-restraints excluded: chain K residue 115 PHE Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 187 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 159 optimal weight: 0.6980 chunk 121 optimal weight: 0.9990 chunk 83 optimal weight: 0.3980 chunk 17 optimal weight: 0.0770 chunk 76 optimal weight: 3.9990 chunk 108 optimal weight: 0.1980 chunk 161 optimal weight: 2.9990 chunk 171 optimal weight: 0.9980 chunk 84 optimal weight: 0.3980 chunk 153 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 109 GLN C 109 GLN D 78 ASN ** E 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 HIS I 109 GLN ** K 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 226 GLN K 297 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14841 Z= 0.135 Angle : 0.524 8.728 20151 Z= 0.268 Chirality : 0.040 0.137 2241 Planarity : 0.003 0.039 2592 Dihedral : 4.864 29.098 2322 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.72 % Allowed : 11.45 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.35 % 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: -2.01 (0.18), residues: 1788 helix: -0.30 (0.36), residues: 222 sheet: -1.05 (0.20), residues: 588 loop : -1.76 (0.18), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 107 HIS 0.003 0.001 HIS E 196 PHE 0.023 0.001 PHE A 440 TYR 0.009 0.001 TYR C 60 ARG 0.004 0.000 ARG E 436 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 229 time to evaluate : 1.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2 ILE cc_start: 0.8133 (mm) cc_final: 0.7884 (mm) REVERT: F 109 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7522 (pp30) REVERT: A 44 LYS cc_start: 0.6744 (mtmt) cc_final: 0.6404 (mtpt) REVERT: A 88 ASN cc_start: 0.7769 (m-40) cc_final: 0.7279 (p0) REVERT: A 90 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7455 (mm-30) REVERT: A 115 PHE cc_start: 0.7816 (OUTLIER) cc_final: 0.7278 (m-10) REVERT: A 219 LYS cc_start: 0.8174 (tttm) cc_final: 0.7648 (ttmt) REVERT: A 316 ARG cc_start: 0.7868 (mtp85) cc_final: 0.7540 (ttt90) REVERT: A 317 MET cc_start: 0.7855 (mtp) cc_final: 0.7369 (tpp) REVERT: A 383 ASN cc_start: 0.6541 (t0) cc_final: 0.6124 (t0) REVERT: A 402 LYS cc_start: 0.7277 (mmtm) cc_final: 0.7048 (mtpt) REVERT: C 104 MET cc_start: 0.8016 (mtm) cc_final: 0.7807 (mtt) REVERT: C 109 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7087 (pp30) REVERT: E 44 LYS cc_start: 0.6579 (mtmt) cc_final: 0.6119 (mtpt) REVERT: E 88 ASN cc_start: 0.7748 (m-40) cc_final: 0.7228 (p0) REVERT: E 90 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7349 (mm-30) REVERT: E 115 PHE cc_start: 0.7714 (OUTLIER) cc_final: 0.7192 (m-10) REVERT: E 219 LYS cc_start: 0.8160 (tttm) cc_final: 0.7675 (ttmt) REVERT: E 281 LYS cc_start: 0.7014 (mmtt) cc_final: 0.6802 (mmtt) REVERT: E 407 MET cc_start: 0.6642 (ttp) cc_final: 0.6396 (ttp) REVERT: I 54 TYR cc_start: 0.7211 (t80) cc_final: 0.6948 (t80) REVERT: I 80 TYR cc_start: 0.7593 (m-80) cc_final: 0.7110 (m-80) REVERT: I 104 MET cc_start: 0.7937 (mtm) cc_final: 0.7568 (mtt) REVERT: K 44 LYS cc_start: 0.6659 (mtmt) cc_final: 0.6204 (mtpt) REVERT: K 88 ASN cc_start: 0.7753 (m-40) cc_final: 0.6903 (p0) REVERT: K 90 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7499 (mm-30) REVERT: K 115 PHE cc_start: 0.7754 (OUTLIER) cc_final: 0.7230 (m-10) REVERT: K 116 GLU cc_start: 0.7179 (tt0) cc_final: 0.6935 (tt0) REVERT: K 156 GLU cc_start: 0.8025 (pt0) cc_final: 0.7774 (pt0) REVERT: K 219 LYS cc_start: 0.8236 (tttm) cc_final: 0.7707 (ttmt) REVERT: K 292 SER cc_start: 0.8859 (t) cc_final: 0.8537 (p) REVERT: K 317 MET cc_start: 0.7864 (mtp) cc_final: 0.7572 (mtp) REVERT: K 383 ASN cc_start: 0.6614 (t0) cc_final: 0.6191 (t0) outliers start: 27 outliers final: 17 residues processed: 241 average time/residue: 0.2814 time to fit residues: 98.7488 Evaluate side-chains 241 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 219 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 109 GLN Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain E residue 115 PHE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain I residue 109 GLN Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain K residue 115 PHE Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 187 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 142 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 0 optimal weight: 0.6980 chunk 87 optimal weight: 0.5980 chunk 153 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 78 ASN ** E 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 226 GLN K 297 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14841 Z= 0.248 Angle : 0.559 10.214 20151 Z= 0.284 Chirality : 0.041 0.133 2241 Planarity : 0.004 0.041 2592 Dihedral : 4.862 26.180 2322 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.23 % Allowed : 11.77 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.35 % 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: -1.86 (0.19), residues: 1788 helix: -0.15 (0.35), residues: 222 sheet: -0.92 (0.20), residues: 588 loop : -1.70 (0.18), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 107 HIS 0.003 0.001 HIS K 184 PHE 0.027 0.001 PHE A 440 TYR 0.009 0.001 TYR C 60 ARG 0.005 0.000 ARG A 436 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 219 time to evaluate : 1.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2 ILE cc_start: 0.8136 (mm) cc_final: 0.7876 (mm) REVERT: F 109 GLN cc_start: 0.7995 (pp30) cc_final: 0.7754 (pm20) REVERT: A 88 ASN cc_start: 0.7759 (m-40) cc_final: 0.6989 (p0) REVERT: A 90 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7535 (mm-30) REVERT: A 115 PHE cc_start: 0.7882 (OUTLIER) cc_final: 0.7296 (m-10) REVERT: A 171 ASN cc_start: 0.6234 (m-40) cc_final: 0.5838 (p0) REVERT: A 219 LYS cc_start: 0.8204 (tttm) cc_final: 0.7699 (ttmt) REVERT: A 316 ARG cc_start: 0.7863 (mtp85) cc_final: 0.7544 (ttt90) REVERT: A 317 MET cc_start: 0.8008 (mtp) cc_final: 0.7757 (mtp) REVERT: A 383 ASN cc_start: 0.6576 (t0) cc_final: 0.6176 (t0) REVERT: A 402 LYS cc_start: 0.7227 (mmtm) cc_final: 0.6993 (mtpt) REVERT: C 104 MET cc_start: 0.8167 (mtm) cc_final: 0.7940 (mtt) REVERT: C 109 GLN cc_start: 0.7886 (pp30) cc_final: 0.7581 (pm20) REVERT: E 88 ASN cc_start: 0.7722 (m-40) cc_final: 0.7199 (p0) REVERT: E 90 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7458 (mm-30) REVERT: E 115 PHE cc_start: 0.7792 (OUTLIER) cc_final: 0.7226 (m-10) REVERT: E 171 ASN cc_start: 0.6465 (m-40) cc_final: 0.6143 (p0) REVERT: E 219 LYS cc_start: 0.8163 (tttm) cc_final: 0.7680 (ttmt) REVERT: I 80 TYR cc_start: 0.7634 (m-80) cc_final: 0.7128 (m-80) REVERT: I 104 MET cc_start: 0.8041 (mtm) cc_final: 0.7715 (mtt) REVERT: I 109 GLN cc_start: 0.8059 (pp30) cc_final: 0.7749 (pm20) REVERT: K 44 LYS cc_start: 0.6537 (mtmt) cc_final: 0.6089 (mtmt) REVERT: K 88 ASN cc_start: 0.7777 (m-40) cc_final: 0.6936 (p0) REVERT: K 90 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7585 (mm-30) REVERT: K 115 PHE cc_start: 0.7868 (OUTLIER) cc_final: 0.7255 (m-10) REVERT: K 156 GLU cc_start: 0.8048 (pt0) cc_final: 0.7782 (pt0) REVERT: K 171 ASN cc_start: 0.6301 (m-40) cc_final: 0.6073 (p0) REVERT: K 219 LYS cc_start: 0.8254 (tttm) cc_final: 0.7688 (ttmt) REVERT: K 252 ILE cc_start: 0.7689 (OUTLIER) cc_final: 0.7290 (mt) REVERT: K 292 SER cc_start: 0.8823 (t) cc_final: 0.8526 (p) REVERT: K 383 ASN cc_start: 0.6664 (t0) cc_final: 0.6239 (t0) outliers start: 35 outliers final: 25 residues processed: 239 average time/residue: 0.2730 time to fit residues: 95.8465 Evaluate side-chains 241 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 212 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain E residue 115 PHE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain K residue 115 PHE Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 179 LEU Chi-restraints excluded: chain K residue 187 ASN Chi-restraints excluded: chain K residue 252 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 57 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 42 optimal weight: 0.0060 chunk 171 optimal weight: 0.3980 chunk 142 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 109 GLN A 199 ASN C 109 GLN ** E 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 ASN I 109 GLN ** K 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 226 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14841 Z= 0.147 Angle : 0.503 8.821 20151 Z= 0.257 Chirality : 0.040 0.136 2241 Planarity : 0.003 0.040 2592 Dihedral : 4.559 25.025 2322 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.42 % Allowed : 12.60 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.35 % 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: -1.52 (0.19), residues: 1788 helix: 0.23 (0.36), residues: 222 sheet: -0.73 (0.21), residues: 588 loop : -1.48 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.002 0.001 HIS A 441 PHE 0.027 0.001 PHE A 440 TYR 0.008 0.001 TYR C 60 ARG 0.007 0.000 ARG A 436 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 223 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2 ILE cc_start: 0.8140 (mm) cc_final: 0.7896 (mm) REVERT: F 109 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.7615 (pm20) REVERT: A 88 ASN cc_start: 0.7829 (m-40) cc_final: 0.7049 (p0) REVERT: A 90 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7548 (mm-30) REVERT: A 115 PHE cc_start: 0.7715 (OUTLIER) cc_final: 0.7221 (m-10) REVERT: A 219 LYS cc_start: 0.8170 (tttm) cc_final: 0.7633 (ttmt) REVERT: A 281 LYS cc_start: 0.7007 (mmtt) cc_final: 0.6774 (mmtt) REVERT: A 316 ARG cc_start: 0.7841 (mtp85) cc_final: 0.7540 (ttt90) REVERT: A 317 MET cc_start: 0.7974 (mtp) cc_final: 0.7724 (mtp) REVERT: A 383 ASN cc_start: 0.6502 (t0) cc_final: 0.6094 (t0) REVERT: C 104 MET cc_start: 0.7977 (mtm) cc_final: 0.7774 (mtt) REVERT: C 109 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7387 (pm20) REVERT: E 88 ASN cc_start: 0.7734 (m-40) cc_final: 0.7242 (p0) REVERT: E 90 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7505 (mm-30) REVERT: E 115 PHE cc_start: 0.7645 (OUTLIER) cc_final: 0.7154 (m-10) REVERT: E 171 ASN cc_start: 0.6347 (m-40) cc_final: 0.6085 (p0) REVERT: E 219 LYS cc_start: 0.8155 (tttm) cc_final: 0.7677 (ttmt) REVERT: E 279 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.7325 (t0) REVERT: E 292 SER cc_start: 0.8824 (t) cc_final: 0.8593 (p) REVERT: E 442 ASP cc_start: 0.7501 (t70) cc_final: 0.7263 (t0) REVERT: I 80 TYR cc_start: 0.7636 (m-80) cc_final: 0.7053 (m-80) REVERT: I 104 MET cc_start: 0.7916 (mtm) cc_final: 0.7597 (mtt) REVERT: I 109 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7597 (pm20) REVERT: K 44 LYS cc_start: 0.6492 (mtmt) cc_final: 0.6062 (mtmt) REVERT: K 88 ASN cc_start: 0.7787 (m-40) cc_final: 0.6926 (p0) REVERT: K 90 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7550 (mm-30) REVERT: K 115 PHE cc_start: 0.7654 (OUTLIER) cc_final: 0.7149 (m-10) REVERT: K 116 GLU cc_start: 0.7119 (tt0) cc_final: 0.6915 (tt0) REVERT: K 219 LYS cc_start: 0.8229 (tttm) cc_final: 0.7685 (ttmt) REVERT: K 292 SER cc_start: 0.8795 (t) cc_final: 0.8542 (p) REVERT: K 383 ASN cc_start: 0.6592 (t0) cc_final: 0.6180 (t0) outliers start: 38 outliers final: 26 residues processed: 241 average time/residue: 0.2672 time to fit residues: 93.9939 Evaluate side-chains 248 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 215 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 109 GLN Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain E residue 115 PHE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 279 ASP Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain I residue 109 GLN Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain K residue 81 SER Chi-restraints excluded: chain K residue 115 PHE Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 187 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 165 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 144 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 170 optimal weight: 6.9990 chunk 106 optimal weight: 0.0770 chunk 104 optimal weight: 1.9990 chunk 78 optimal weight: 0.0770 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 109 GLN A 199 ASN C 109 GLN D 78 ASN ** E 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 ASN I 109 GLN ** K 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 196 HIS K 226 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14841 Z= 0.190 Angle : 0.521 9.406 20151 Z= 0.266 Chirality : 0.041 0.135 2241 Planarity : 0.003 0.039 2592 Dihedral : 4.540 24.873 2322 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.16 % Allowed : 13.68 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.35 % 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: -1.52 (0.19), residues: 1788 helix: 0.31 (0.36), residues: 222 sheet: -0.72 (0.20), residues: 600 loop : -1.51 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.003 0.001 HIS K 196 PHE 0.028 0.001 PHE A 440 TYR 0.008 0.001 TYR C 60 ARG 0.006 0.000 ARG K 436 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 212 time to evaluate : 1.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2 ILE cc_start: 0.8149 (mm) cc_final: 0.7900 (mm) REVERT: A 88 ASN cc_start: 0.7845 (m-40) cc_final: 0.7066 (p0) REVERT: A 90 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7555 (mm-30) REVERT: A 115 PHE cc_start: 0.7759 (OUTLIER) cc_final: 0.7275 (m-10) REVERT: A 219 LYS cc_start: 0.8195 (tttm) cc_final: 0.7644 (ttmt) REVERT: A 316 ARG cc_start: 0.7826 (mtp85) cc_final: 0.7524 (ttt90) REVERT: A 317 MET cc_start: 0.8049 (mtp) cc_final: 0.7794 (mtp) REVERT: A 383 ASN cc_start: 0.6525 (t0) cc_final: 0.6116 (t0) REVERT: E 88 ASN cc_start: 0.7767 (m-40) cc_final: 0.7283 (p0) REVERT: E 90 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7542 (mm-30) REVERT: E 115 PHE cc_start: 0.7669 (OUTLIER) cc_final: 0.7189 (m-10) REVERT: E 171 ASN cc_start: 0.6346 (m-40) cc_final: 0.6072 (p0) REVERT: E 219 LYS cc_start: 0.8153 (tttm) cc_final: 0.7681 (ttmt) REVERT: E 279 ASP cc_start: 0.7693 (OUTLIER) cc_final: 0.7389 (t0) REVERT: E 292 SER cc_start: 0.8836 (t) cc_final: 0.8614 (p) REVERT: E 442 ASP cc_start: 0.7466 (t70) cc_final: 0.7195 (t0) REVERT: I 80 TYR cc_start: 0.7656 (m-80) cc_final: 0.7061 (m-80) REVERT: I 104 MET cc_start: 0.7934 (mtm) cc_final: 0.7628 (mtt) REVERT: K 44 LYS cc_start: 0.6456 (mtmt) cc_final: 0.6019 (mtmt) REVERT: K 88 ASN cc_start: 0.7770 (m-40) cc_final: 0.6919 (p0) REVERT: K 90 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7549 (mm-30) REVERT: K 115 PHE cc_start: 0.7670 (OUTLIER) cc_final: 0.7181 (m-10) REVERT: K 219 LYS cc_start: 0.8227 (tttm) cc_final: 0.7679 (ttmt) REVERT: K 292 SER cc_start: 0.8770 (t) cc_final: 0.8508 (p) REVERT: K 383 ASN cc_start: 0.6567 (t0) cc_final: 0.6175 (t0) outliers start: 34 outliers final: 28 residues processed: 228 average time/residue: 0.2640 time to fit residues: 88.1501 Evaluate side-chains 242 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 210 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 109 GLN Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain E residue 115 PHE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 279 ASP Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain I residue 109 GLN Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 115 PHE Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 187 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 15 optimal weight: 0.0970 chunk 134 optimal weight: 4.9990 chunk 155 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 109 GLN A 199 ASN C 109 GLN ** E 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 ASN I 109 GLN J 6 GLN ** K 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14841 Z= 0.172 Angle : 0.514 9.389 20151 Z= 0.262 Chirality : 0.040 0.135 2241 Planarity : 0.003 0.037 2592 Dihedral : 4.489 24.905 2322 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.35 % Allowed : 13.80 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.19), residues: 1788 helix: 0.46 (0.36), residues: 222 sheet: -0.76 (0.20), residues: 612 loop : -1.40 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.002 0.001 HIS A 141 PHE 0.028 0.001 PHE A 440 TYR 0.008 0.001 TYR C 60 ARG 0.006 0.000 ARG E 436 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 211 time to evaluate : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2 ILE cc_start: 0.8143 (mm) cc_final: 0.7901 (mm) REVERT: A 88 ASN cc_start: 0.7851 (m-40) cc_final: 0.7070 (p0) REVERT: A 90 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7596 (mm-30) REVERT: A 115 PHE cc_start: 0.7732 (OUTLIER) cc_final: 0.7258 (m-10) REVERT: A 219 LYS cc_start: 0.8188 (tttm) cc_final: 0.7647 (ttmt) REVERT: A 276 ASN cc_start: 0.7165 (t0) cc_final: 0.6904 (t0) REVERT: A 316 ARG cc_start: 0.7815 (mtp85) cc_final: 0.7527 (ttt90) REVERT: A 317 MET cc_start: 0.8060 (mtp) cc_final: 0.7792 (mtp) REVERT: A 383 ASN cc_start: 0.6521 (t0) cc_final: 0.6123 (t0) REVERT: A 442 ASP cc_start: 0.7499 (t70) cc_final: 0.7225 (t0) REVERT: E 88 ASN cc_start: 0.7767 (m-40) cc_final: 0.7285 (p0) REVERT: E 90 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7586 (mm-30) REVERT: E 115 PHE cc_start: 0.7643 (OUTLIER) cc_final: 0.7175 (m-10) REVERT: E 171 ASN cc_start: 0.6303 (m-40) cc_final: 0.6059 (p0) REVERT: E 219 LYS cc_start: 0.8149 (tttm) cc_final: 0.7677 (ttmt) REVERT: E 279 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.7367 (t0) REVERT: E 292 SER cc_start: 0.8825 (t) cc_final: 0.8616 (p) REVERT: E 442 ASP cc_start: 0.7463 (t70) cc_final: 0.7202 (t0) REVERT: I 80 TYR cc_start: 0.7661 (m-80) cc_final: 0.7069 (m-80) REVERT: I 104 MET cc_start: 0.7961 (mtm) cc_final: 0.7665 (mtt) REVERT: K 44 LYS cc_start: 0.6435 (mtmt) cc_final: 0.6000 (mtmt) REVERT: K 88 ASN cc_start: 0.7768 (m-40) cc_final: 0.6939 (p0) REVERT: K 90 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7576 (mm-30) REVERT: K 115 PHE cc_start: 0.7670 (OUTLIER) cc_final: 0.7180 (m-10) REVERT: K 219 LYS cc_start: 0.8224 (tttm) cc_final: 0.7676 (ttmt) REVERT: K 292 SER cc_start: 0.8761 (t) cc_final: 0.8504 (p) REVERT: K 383 ASN cc_start: 0.6549 (t0) cc_final: 0.6134 (t0) outliers start: 37 outliers final: 31 residues processed: 228 average time/residue: 0.2711 time to fit residues: 90.4706 Evaluate side-chains 244 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 209 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 109 GLN Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain E residue 115 PHE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 279 ASP Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain I residue 109 GLN Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 81 SER Chi-restraints excluded: chain K residue 115 PHE Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 187 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 163 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 143 optimal weight: 3.9990 chunk 150 optimal weight: 0.7980 chunk 104 optimal weight: 0.0870 chunk 168 optimal weight: 0.9980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 109 GLN H 6 GLN C 109 GLN ** E 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 ASN I 109 GLN ** K 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14841 Z= 0.181 Angle : 0.517 9.495 20151 Z= 0.264 Chirality : 0.041 0.135 2241 Planarity : 0.003 0.038 2592 Dihedral : 4.474 24.783 2322 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.29 % Allowed : 13.87 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.19), residues: 1788 helix: 0.52 (0.36), residues: 222 sheet: -0.73 (0.20), residues: 612 loop : -1.37 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 64 HIS 0.002 0.001 HIS A 141 PHE 0.029 0.001 PHE A 440 TYR 0.008 0.001 TYR C 60 ARG 0.006 0.000 ARG K 436 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 213 time to evaluate : 1.901 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 2 ILE cc_start: 0.8146 (mm) cc_final: 0.7905 (mm) REVERT: A 88 ASN cc_start: 0.7850 (m-40) cc_final: 0.7104 (p0) REVERT: A 90 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7621 (mm-30) REVERT: A 115 PHE cc_start: 0.7717 (OUTLIER) cc_final: 0.7260 (m-10) REVERT: A 219 LYS cc_start: 0.8189 (tttm) cc_final: 0.7628 (ttmt) REVERT: A 276 ASN cc_start: 0.7180 (t0) cc_final: 0.6934 (t0) REVERT: A 292 SER cc_start: 0.8810 (t) cc_final: 0.8594 (p) REVERT: A 316 ARG cc_start: 0.7809 (mtp85) cc_final: 0.7529 (ttt90) REVERT: A 317 MET cc_start: 0.8075 (mtp) cc_final: 0.7799 (mtp) REVERT: A 383 ASN cc_start: 0.6527 (t0) cc_final: 0.6126 (t0) REVERT: A 442 ASP cc_start: 0.7507 (t70) cc_final: 0.7235 (t0) REVERT: E 88 ASN cc_start: 0.7792 (m-40) cc_final: 0.7313 (p0) REVERT: E 90 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7630 (mm-30) REVERT: E 115 PHE cc_start: 0.7631 (OUTLIER) cc_final: 0.7167 (m-10) REVERT: E 171 ASN cc_start: 0.6293 (m-40) cc_final: 0.6070 (p0) REVERT: E 219 LYS cc_start: 0.8156 (tttm) cc_final: 0.7684 (ttmt) REVERT: E 279 ASP cc_start: 0.7657 (OUTLIER) cc_final: 0.7356 (t0) REVERT: E 292 SER cc_start: 0.8777 (t) cc_final: 0.8570 (p) REVERT: E 442 ASP cc_start: 0.7466 (t70) cc_final: 0.7213 (t0) REVERT: I 80 TYR cc_start: 0.7646 (m-80) cc_final: 0.7054 (m-80) REVERT: I 104 MET cc_start: 0.7992 (mtm) cc_final: 0.7715 (mtt) REVERT: K 88 ASN cc_start: 0.7794 (m-40) cc_final: 0.7025 (p0) REVERT: K 90 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7576 (mm-30) REVERT: K 115 PHE cc_start: 0.7672 (OUTLIER) cc_final: 0.7193 (m-10) REVERT: K 219 LYS cc_start: 0.8207 (tttm) cc_final: 0.7660 (ttmt) REVERT: K 292 SER cc_start: 0.8750 (t) cc_final: 0.8499 (p) REVERT: K 383 ASN cc_start: 0.6612 (t0) cc_final: 0.6215 (t0) outliers start: 36 outliers final: 32 residues processed: 228 average time/residue: 0.2699 time to fit residues: 89.9264 Evaluate side-chains 245 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 209 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 109 GLN Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 115 PHE Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 279 ASP Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain I residue 109 GLN Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 81 SER Chi-restraints excluded: chain K residue 115 PHE Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 187 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 102 optimal weight: 0.5980 chunk 79 optimal weight: 0.0270 chunk 116 optimal weight: 0.8980 chunk 176 optimal weight: 7.9990 chunk 162 optimal weight: 1.9990 chunk 140 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 111 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.8640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 109 GLN A 199 ASN C 109 GLN D 6 GLN ** E 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 109 GLN ** K 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14841 Z= 0.210 Angle : 0.532 10.009 20151 Z= 0.271 Chirality : 0.041 0.135 2241 Planarity : 0.004 0.038 2592 Dihedral : 4.506 24.917 2322 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.42 % Allowed : 13.93 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.35 % 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: -1.40 (0.19), residues: 1788 helix: 0.54 (0.36), residues: 222 sheet: -0.74 (0.20), residues: 615 loop : -1.39 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 64 HIS 0.003 0.001 HIS A 141 PHE 0.030 0.001 PHE A 440 TYR 0.009 0.001 TYR C 60 ARG 0.006 0.000 ARG E 436 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 208 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 2 ILE cc_start: 0.8154 (mm) cc_final: 0.7913 (mm) REVERT: A 88 ASN cc_start: 0.7861 (m-40) cc_final: 0.7171 (p0) REVERT: A 90 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7634 (mm-30) REVERT: A 115 PHE cc_start: 0.7762 (OUTLIER) cc_final: 0.7248 (m-10) REVERT: A 219 LYS cc_start: 0.8209 (tttm) cc_final: 0.7649 (ttmt) REVERT: A 276 ASN cc_start: 0.7171 (t0) cc_final: 0.6936 (t0) REVERT: A 292 SER cc_start: 0.8801 (t) cc_final: 0.8582 (p) REVERT: A 316 ARG cc_start: 0.7801 (mtp85) cc_final: 0.7527 (ttt90) REVERT: A 317 MET cc_start: 0.8076 (mtp) cc_final: 0.7784 (mtp) REVERT: A 383 ASN cc_start: 0.6541 (t0) cc_final: 0.6134 (t0) REVERT: E 88 ASN cc_start: 0.7795 (m-40) cc_final: 0.7318 (p0) REVERT: E 90 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7659 (mm-30) REVERT: E 115 PHE cc_start: 0.7664 (OUTLIER) cc_final: 0.7208 (m-10) REVERT: E 171 ASN cc_start: 0.6271 (m-40) cc_final: 0.6062 (p0) REVERT: E 219 LYS cc_start: 0.8156 (tttm) cc_final: 0.7682 (ttmt) REVERT: E 279 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.7387 (t0) REVERT: E 292 SER cc_start: 0.8773 (t) cc_final: 0.8567 (p) REVERT: E 442 ASP cc_start: 0.7439 (t70) cc_final: 0.7188 (t0) REVERT: I 80 TYR cc_start: 0.7678 (m-80) cc_final: 0.7076 (m-80) REVERT: I 104 MET cc_start: 0.8018 (mtm) cc_final: 0.7738 (mtt) REVERT: K 88 ASN cc_start: 0.7816 (m-40) cc_final: 0.7111 (p0) REVERT: K 90 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7552 (mm-30) REVERT: K 115 PHE cc_start: 0.7672 (OUTLIER) cc_final: 0.7138 (m-10) REVERT: K 219 LYS cc_start: 0.8201 (tttm) cc_final: 0.7648 (ttmt) REVERT: K 292 SER cc_start: 0.8745 (t) cc_final: 0.8498 (p) REVERT: K 383 ASN cc_start: 0.6634 (t0) cc_final: 0.6233 (t0) outliers start: 38 outliers final: 32 residues processed: 224 average time/residue: 0.2737 time to fit residues: 89.3107 Evaluate side-chains 242 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 206 time to evaluate : 2.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 109 GLN Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 115 PHE Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 279 ASP Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain I residue 109 GLN Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 81 SER Chi-restraints excluded: chain K residue 115 PHE Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 187 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 43 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 0.4980 chunk 140 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 144 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 109 GLN A 199 ASN C 109 GLN ** E 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 109 GLN ** K 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.142457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.109922 restraints weight = 17776.249| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.29 r_work: 0.2968 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 14841 Z= 0.312 Angle : 0.804 59.183 20151 Z= 0.456 Chirality : 0.044 0.564 2241 Planarity : 0.006 0.122 2592 Dihedral : 4.583 38.729 2322 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.64 % Favored : 96.31 % Rotamer: Outliers : 2.16 % Allowed : 14.19 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.40 (0.19), residues: 1788 helix: 0.53 (0.36), residues: 222 sheet: -0.74 (0.20), residues: 615 loop : -1.40 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 64 HIS 0.003 0.001 HIS A 141 PHE 0.029 0.001 PHE A 440 TYR 0.008 0.001 TYR C 60 ARG 0.005 0.000 ARG K 436 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3510.63 seconds wall clock time: 64 minutes 23.24 seconds (3863.24 seconds total)