Starting phenix.real_space_refine on Mon Nov 18 22:53:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d21_27139/11_2024/8d21_27139.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d21_27139/11_2024/8d21_27139.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d21_27139/11_2024/8d21_27139.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d21_27139/11_2024/8d21_27139.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d21_27139/11_2024/8d21_27139.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d21_27139/11_2024/8d21_27139.cif" } resolution = 3.96 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= 0.014 sd= 0.086 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 78 5.16 5 C 11019 2.51 5 N 2991 2.21 5 O 3453 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 17541 Number of models: 1 Model: "" Number of chains: 18 Chain: "B" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1396 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 1, 'TRANS': 171} Chain: "A" Number of atoms: 2536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2536 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 20, 'TRANS': 302} Chain: "H" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 950 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "L" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 100} Chain: "C" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1396 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 1, 'TRANS': 171} Chain: "D" Number of atoms: 2536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2536 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 20, 'TRANS': 302} Chain: "E" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 950 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "F" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 100} Chain: "G" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1396 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 1, 'TRANS': 171} Chain: "I" Number of atoms: 2536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2536 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 20, 'TRANS': 302} Chain: "J" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 950 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "K" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 100} Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "D" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "I" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 10.96, per 1000 atoms: 0.62 Number of scatterers: 17541 At special positions: 0 Unit cell: (136.395, 132.065, 162.375, 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 78 16.00 O 3453 8.00 N 2991 7.00 C 11019 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS B 47 " - pdb=" SG CYS I 30 " distance=2.04 Simple disulfide: pdb=" SG CYS B 137 " - pdb=" SG CYS A 14 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS C 47 " distance=2.04 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 137 " - pdb=" SG CYS D 14 " distance=2.03 Simple disulfide: pdb=" SG CYS C 144 " - pdb=" SG CYS C 148 " distance=2.03 Simple disulfide: pdb=" SG CYS D 30 " - pdb=" SG CYS G 47 " distance=2.04 Simple disulfide: pdb=" SG CYS D 52 " - pdb=" SG CYS D 277 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 76 " distance=2.03 Simple disulfide: pdb=" SG CYS D 97 " - pdb=" SG CYS D 139 " distance=2.03 Simple disulfide: pdb=" SG CYS D 281 " - pdb=" SG CYS D 305 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 137 " - pdb=" SG CYS I 14 " distance=2.03 Simple disulfide: pdb=" SG CYS G 144 " - pdb=" SG CYS G 148 " distance=2.03 Simple disulfide: pdb=" SG CYS I 52 " - pdb=" SG CYS I 277 " distance=2.03 Simple disulfide: pdb=" SG CYS I 64 " - pdb=" SG CYS I 76 " distance=2.03 Simple disulfide: pdb=" SG CYS I 97 " - pdb=" SG CYS I 139 " distance=2.03 Simple disulfide: pdb=" SG CYS I 281 " - pdb=" SG CYS I 305 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A 401 " - " ASN A 21 " " NAG A 402 " - " ASN A 129 " " NAG A 403 " - " ASN A 94 " " NAG A 404 " - " ASN A 33 " " NAG A 405 " - " ASN A 289 " " NAG A 406 " - " ASN A 63 " " NAG A 407 " - " ASN A 163 " " NAG D 401 " - " ASN D 21 " " NAG D 402 " - " ASN D 129 " " NAG D 403 " - " ASN D 94 " " NAG D 404 " - " ASN D 33 " " NAG D 405 " - " ASN D 289 " " NAG D 406 " - " ASN D 63 " " NAG D 407 " - " ASN D 163 " " NAG I 401 " - " ASN I 21 " " NAG I 402 " - " ASN I 129 " " NAG I 403 " - " ASN I 94 " " NAG I 404 " - " ASN I 33 " " NAG I 405 " - " ASN I 289 " " NAG I 406 " - " ASN I 63 " " NAG I 407 " - " ASN I 163 " " NAG M 1 " - " ASN B 154 " " NAG N 1 " - " ASN C 154 " " NAG O 1 " - " ASN G 154 " Time building additional restraints: 4.80 Conformation dependent library (CDL) restraints added in 2.5 seconds 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4002 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 51 sheets defined 19.5% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.59 Creating SS restraints... Processing helix chain 'B' and resid 1 through 7 removed outlier: 3.551A pdb=" N ILE B 6 " --> pdb=" O LEU B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 58 removed outlier: 3.814A pdb=" N GLN B 42 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N CYS B 47 " --> pdb=" O ASN B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 126 removed outlier: 3.784A pdb=" N GLU B 78 " --> pdb=" O GLU B 74 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG B 106 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 154 removed outlier: 3.777A pdb=" N SER B 151 " --> pdb=" O GLU B 147 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL B 152 " --> pdb=" O CYS B 148 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS B 153 " --> pdb=" O MET B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 173 removed outlier: 3.565A pdb=" N TYR B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU B 168 " --> pdb=" O GLU B 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 71 Processing helix chain 'A' and resid 104 through 113 Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'H' and resid 52A through 55 removed outlier: 3.712A pdb=" N LEU H 55 " --> pdb=" O GLY H 52A" (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 52A through 55' Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 37 through 58 removed outlier: 3.859A pdb=" N GLN C 42 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASN C 43 " --> pdb=" O LYS C 39 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN C 46 " --> pdb=" O GLN C 42 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N CYS C 47 " --> pdb=" O ASN C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 126 removed outlier: 3.777A pdb=" N GLU C 78 " --> pdb=" O GLU C 74 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 126 " --> pdb=" O VAL C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 154 removed outlier: 3.921A pdb=" N SER C 151 " --> pdb=" O GLU C 147 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL C 152 " --> pdb=" O CYS C 148 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS C 153 " --> pdb=" O MET C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 173 removed outlier: 3.598A pdb=" N TYR C 162 " --> pdb=" O ASP C 158 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU C 164 " --> pdb=" O PRO C 160 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLU C 165 " --> pdb=" O LYS C 161 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU C 168 " --> pdb=" O GLU C 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 71 Processing helix chain 'D' and resid 76 through 80 removed outlier: 3.923A pdb=" N LEU D 79 " --> pdb=" O CYS D 76 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE D 80 " --> pdb=" O GLU D 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 76 through 80' Processing helix chain 'D' and resid 104 through 112 Processing helix chain 'D' and resid 187 through 196 Processing helix chain 'E' and resid 52A through 55 removed outlier: 3.708A pdb=" N LEU E 55 " --> pdb=" O GLY E 52A" (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 52A through 55' Processing helix chain 'G' and resid 2 through 7 Processing helix chain 'G' and resid 37 through 58 removed outlier: 3.639A pdb=" N GLN G 42 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN G 43 " --> pdb=" O LYS G 39 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN G 46 " --> pdb=" O GLN G 42 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N CYS G 47 " --> pdb=" O ASN G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 73 No H-bonds generated for 'chain 'G' and resid 71 through 73' Processing helix chain 'G' and resid 74 through 126 removed outlier: 3.724A pdb=" N GLU G 78 " --> pdb=" O GLU G 74 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU G 105 " --> pdb=" O LEU G 101 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG G 106 " --> pdb=" O LEU G 102 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU G 126 " --> pdb=" O VAL G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 154 removed outlier: 3.747A pdb=" N SER G 151 " --> pdb=" O GLU G 147 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL G 152 " --> pdb=" O CYS G 148 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS G 153 " --> pdb=" O MET G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 173 removed outlier: 3.646A pdb=" N TYR G 162 " --> pdb=" O ASP G 158 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU G 164 " --> pdb=" O PRO G 160 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLU G 165 " --> pdb=" O LYS G 161 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU G 168 " --> pdb=" O GLU G 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 71 Processing helix chain 'I' and resid 104 through 112 Processing helix chain 'I' and resid 187 through 196 Processing helix chain 'J' and resid 52A through 55 removed outlier: 3.713A pdb=" N LEU J 55 " --> pdb=" O GLY J 52A" (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 52A through 55' Processing helix chain 'J' and resid 61 through 64 removed outlier: 3.571A pdb=" N LYS J 64 " --> pdb=" O ASP J 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 61 through 64' Processing sheet with id=AA1, first strand: chain 'B' and resid 35 through 36 removed outlier: 3.568A pdb=" N GLY A 16 " --> pdb=" O GLY B 23 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS A 14 " --> pdb=" O HIS B 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 53 removed outlier: 5.329A pdb=" N LEU A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N CYS A 277 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 59 through 60 removed outlier: 7.015A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ILE A 87 " --> pdb=" O ILE A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.544A pdb=" N GLU A 119 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.544A pdb=" N GLU A 119 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL A 176 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL A 178 " --> pdb=" O THR A 235 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 141 removed outlier: 5.187A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER A 146 " --> pdb=" O CYS A 139 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB2, first strand: chain 'A' and resid 287 through 288 removed outlier: 3.744A pdb=" N ILE A 288 " --> pdb=" O CYS A 281 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE A 302 " --> pdb=" O GLN A 282 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.583A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE H 107 " --> pdb=" O PHE H 90 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL H 109 " --> pdb=" O ALA H 88 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL H 37 " --> pdb=" O TYR H 91 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N SER H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 17 through 19 removed outlier: 3.604A pdb=" N LEU H 18 " --> pdb=" O MET H 82 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET H 82 " --> pdb=" O LEU H 18 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.742A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.579A pdb=" N THR L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N THR L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 62 through 67 removed outlier: 3.594A pdb=" N THR L 74 " --> pdb=" O SER L 63 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER L 65 " --> pdb=" O THR L 72 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 22 through 24 removed outlier: 3.680A pdb=" N GLY D 16 " --> pdb=" O GLY C 23 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 25 through 26 removed outlier: 3.616A pdb=" N VAL D 34 " --> pdb=" O VAL D 26 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 39 through 41 Processing sheet with id=AC3, first strand: chain 'D' and resid 43 through 44 removed outlier: 3.524A pdb=" N GLN D 295 " --> pdb=" O LYS D 307 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 51 through 53 removed outlier: 5.360A pdb=" N LEU D 51 " --> pdb=" O ASP D 275 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N CYS D 277 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 59 through 60 removed outlier: 6.984A pdb=" N LEU D 59 " --> pdb=" O VAL D 88 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ILE D 87 " --> pdb=" O ILE D 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 118 through 119 removed outlier: 7.921A pdb=" N LEU D 179 " --> pdb=" O PRO D 254 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 118 through 119 removed outlier: 3.828A pdb=" N VAL D 178 " --> pdb=" O THR D 235 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 136 through 141 removed outlier: 5.223A pdb=" N CYS D 139 " --> pdb=" O SER D 146 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER D 146 " --> pdb=" O CYS D 139 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 164 through 169 removed outlier: 3.559A pdb=" N ARG D 211 " --> pdb=" O VAL D 204 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR D 209 " --> pdb=" O SER D 206 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 286 through 288 removed outlier: 3.624A pdb=" N ILE D 288 " --> pdb=" O CYS D 281 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N CYS D 281 " --> pdb=" O ILE D 288 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE D 302 " --> pdb=" O GLN D 282 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.584A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU E 5 " --> pdb=" O LYS E 23 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.584A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU E 5 " --> pdb=" O LYS E 23 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER E 70 " --> pdb=" O TYR E 79 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.545A pdb=" N GLY E 10 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE E 107 " --> pdb=" O PHE E 90 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL E 109 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU E 34 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N SER E 50 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 4 through 6 removed outlier: 3.984A pdb=" N THR F 5 " --> pdb=" O ARG F 24 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 10 through 11 removed outlier: 3.508A pdb=" N LEU F 11 " --> pdb=" O ARG F 103 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR F 102 " --> pdb=" O TYR F 86 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR F 53 " --> pdb=" O TYR F 49 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 62 through 67 removed outlier: 3.660A pdb=" N THR F 74 " --> pdb=" O SER F 63 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER F 65 " --> pdb=" O THR F 72 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 22 through 24 removed outlier: 3.721A pdb=" N GLY I 16 " --> pdb=" O GLY G 23 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 131 through 132 Processing sheet with id=AE1, first strand: chain 'I' and resid 25 through 26 removed outlier: 3.562A pdb=" N VAL I 34 " --> pdb=" O VAL I 26 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 39 through 41 Processing sheet with id=AE3, first strand: chain 'I' and resid 43 through 44 Processing sheet with id=AE4, first strand: chain 'I' and resid 51 through 53 removed outlier: 5.323A pdb=" N LEU I 51 " --> pdb=" O ASP I 275 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N CYS I 277 " --> pdb=" O LEU I 51 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 59 through 60 removed outlier: 6.986A pdb=" N LEU I 59 " --> pdb=" O VAL I 88 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ILE I 87 " --> pdb=" O ILE I 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'I' and resid 136 through 141 removed outlier: 5.242A pdb=" N CYS I 139 " --> pdb=" O SER I 146 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER I 146 " --> pdb=" O CYS I 139 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 151 through 153 removed outlier: 7.780A pdb=" N LEU I 179 " --> pdb=" O PRO I 254 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL I 178 " --> pdb=" O THR I 235 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG I 229 " --> pdb=" O HIS I 184 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 151 through 153 removed outlier: 7.780A pdb=" N LEU I 179 " --> pdb=" O PRO I 254 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 164 through 169 Processing sheet with id=AF1, first strand: chain 'I' and resid 281 through 282 removed outlier: 3.752A pdb=" N ILE I 302 " --> pdb=" O GLN I 282 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.614A pdb=" N LEU J 5 " --> pdb=" O LYS J 23 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU J 20 " --> pdb=" O LEU J 80 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER J 70 " --> pdb=" O TYR J 79 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.608A pdb=" N GLY J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE J 107 " --> pdb=" O PHE J 90 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL J 109 " --> pdb=" O ALA J 88 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL J 37 " --> pdb=" O TYR J 91 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 4 through 6 removed outlier: 3.754A pdb=" N THR K 5 " --> pdb=" O ARG K 24 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 53 through 54 removed outlier: 3.963A pdb=" N THR K 53 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR K 102 " --> pdb=" O TYR K 86 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 62 through 67 removed outlier: 3.605A pdb=" N THR K 74 " --> pdb=" O SER K 63 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER K 65 " --> pdb=" O THR K 72 " (cutoff:3.500A) 529 hydrogen bonds defined for protein. 1455 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: 6.05 Time building geometry restraints manager: 5.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5696 1.35 - 1.47: 4562 1.47 - 1.59: 7582 1.59 - 1.72: 1 1.72 - 1.84: 102 Bond restraints: 17943 Sorted by residual: bond pdb=" CB PRO D 306 " pdb=" CG PRO D 306 " ideal model delta sigma weight residual 1.492 1.619 -0.127 5.00e-02 4.00e+02 6.49e+00 bond pdb=" N GLY C 1 " pdb=" CA GLY C 1 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.39e+00 bond pdb=" N GLY B 1 " pdb=" CA GLY B 1 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.20e+00 bond pdb=" N GLY G 1 " pdb=" CA GLY G 1 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 6.06e+00 bond pdb=" N GLU L 81 " pdb=" CA GLU L 81 " ideal model delta sigma weight residual 1.459 1.484 -0.026 1.28e-02 6.10e+03 4.00e+00 ... (remaining 17938 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 23810 2.11 - 4.23: 468 4.23 - 6.34: 44 6.34 - 8.45: 6 8.45 - 10.57: 2 Bond angle restraints: 24330 Sorted by residual: angle pdb=" CA PRO D 306 " pdb=" N PRO D 306 " pdb=" CD PRO D 306 " ideal model delta sigma weight residual 112.00 101.63 10.37 1.40e+00 5.10e-01 5.48e+01 angle pdb=" CA PRO D 99 " pdb=" N PRO D 99 " pdb=" CD PRO D 99 " ideal model delta sigma weight residual 112.00 105.53 6.47 1.40e+00 5.10e-01 2.14e+01 angle pdb=" CA PRO I 128 " pdb=" N PRO I 128 " pdb=" CD PRO I 128 " ideal model delta sigma weight residual 112.00 106.31 5.69 1.40e+00 5.10e-01 1.65e+01 angle pdb=" N VAL H 100A" pdb=" CA VAL H 100A" pdb=" C VAL H 100A" ideal model delta sigma weight residual 108.88 100.87 8.01 2.16e+00 2.14e-01 1.38e+01 angle pdb=" N PRO A 306 " pdb=" CA PRO A 306 " pdb=" C PRO A 306 " ideal model delta sigma weight residual 110.40 115.62 -5.22 1.61e+00 3.86e-01 1.05e+01 ... (remaining 24325 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.52: 9846 21.52 - 43.03: 1006 43.03 - 64.55: 154 64.55 - 86.06: 54 86.06 - 107.58: 13 Dihedral angle restraints: 11073 sinusoidal: 4806 harmonic: 6267 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 177.56 -84.56 1 1.00e+01 1.00e-02 8.69e+01 dihedral pdb=" CA VAL H 100A" pdb=" C VAL H 100A" pdb=" N PRO H 100B" pdb=" CA PRO H 100B" ideal model delta harmonic sigma weight residual 180.00 -138.88 -41.12 0 5.00e+00 4.00e-02 6.76e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 92 " pdb=" CB CYS E 92 " ideal model delta sinusoidal sigma weight residual -86.00 -153.61 67.61 1 1.00e+01 1.00e-02 5.94e+01 ... (remaining 11070 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2265 0.054 - 0.108: 338 0.108 - 0.162: 96 0.162 - 0.216: 3 0.216 - 0.270: 4 Chirality restraints: 2706 Sorted by residual: chirality pdb=" C5 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" C6 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C5 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C6 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" C5 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C6 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 2703 not shown) Planarity restraints: 3141 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL H 100A" 0.102 5.00e-02 4.00e+02 1.54e-01 3.79e+01 pdb=" N PRO H 100B" -0.266 5.00e-02 4.00e+02 pdb=" CA PRO H 100B" 0.085 5.00e-02 4.00e+02 pdb=" CD PRO H 100B" 0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP I 127 " 0.090 5.00e-02 4.00e+02 1.33e-01 2.85e+01 pdb=" N PRO I 128 " -0.231 5.00e-02 4.00e+02 pdb=" CA PRO I 128 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO I 128 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 98 " -0.071 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO D 99 " 0.178 5.00e-02 4.00e+02 pdb=" CA PRO D 99 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO D 99 " -0.056 5.00e-02 4.00e+02 ... (remaining 3138 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 345 2.63 - 3.20: 15720 3.20 - 3.77: 25317 3.77 - 4.33: 34424 4.33 - 4.90: 57327 Nonbonded interactions: 133133 Sorted by model distance: nonbonded pdb=" OG SER J 35 " pdb=" OG SER J 50 " model vdw 2.068 3.040 nonbonded pdb=" OG SER E 35 " pdb=" OG SER E 50 " model vdw 2.078 3.040 nonbonded pdb=" OG SER H 35 " pdb=" OG SER H 50 " model vdw 2.107 3.040 nonbonded pdb=" O3 NAG M 1 " pdb=" O5 NAG M 2 " model vdw 2.116 3.040 nonbonded pdb=" O3 NAG O 1 " pdb=" O5 NAG O 2 " model vdw 2.119 3.040 ... (remaining 133128 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.750 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 41.670 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 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 : 0.004 0.127 17943 Z= 0.271 Angle : 0.687 10.566 24330 Z= 0.351 Chirality : 0.045 0.270 2706 Planarity : 0.007 0.154 3117 Dihedral : 17.327 107.581 6990 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.17 % Favored : 93.74 % Rotamer: Outliers : 0.64 % Allowed : 25.70 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.18), residues: 2157 helix: 0.87 (0.28), residues: 372 sheet: -0.67 (0.27), residues: 375 loop : -1.72 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 100E HIS 0.009 0.001 HIS G 25 PHE 0.024 0.001 PHE G 110 TYR 0.016 0.001 TYR D 98 ARG 0.009 0.001 ARG D 229 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 188 time to evaluate : 2.182 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: symmetry clash revert: symmetry clash REVERT: B 62 GLN cc_start: 0.9292 (tp40) cc_final: 0.8938 (mp10) REVERT: B 90 ASP cc_start: 0.9037 (m-30) cc_final: 0.8374 (m-30) REVERT: A 24 ASP cc_start: 0.9191 (m-30) cc_final: 0.8882 (t0) REVERT: H 13 ARG cc_start: 0.8900 (mtt90) cc_final: 0.8611 (mtt-85) REVERT: H 95 ASP cc_start: 0.8889 (t0) cc_final: 0.8325 (m-30) REVERT: L 32 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8600 (mt-10) REVERT: L 82 ASP cc_start: 0.7825 (m-30) cc_final: 0.6586 (m-30) REVERT: C 19 ASP cc_start: 0.9060 (m-30) cc_final: 0.8680 (p0) REVERT: C 62 GLN cc_start: 0.9371 (tp40) cc_final: 0.9082 (mp10) REVERT: C 149 MET cc_start: 0.9293 (tpp) cc_final: 0.8922 (tpp) REVERT: E 13 ARG cc_start: 0.9377 (mtp85) cc_final: 0.8689 (mtt-85) REVERT: E 95 ASP cc_start: 0.8823 (t0) cc_final: 0.8394 (m-30) REVERT: F 32 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8029 (mt-10) REVERT: G 90 ASP cc_start: 0.9149 (m-30) cc_final: 0.8847 (m-30) REVERT: G 149 MET cc_start: 0.9195 (tpp) cc_final: 0.8984 (tpp) REVERT: I 316 MET cc_start: 0.9345 (mtm) cc_final: 0.9077 (mpp) REVERT: J 75 GLN cc_start: 0.9512 (mt0) cc_final: 0.9158 (mp10) REVERT: J 95 ASP cc_start: 0.8851 (t0) cc_final: 0.8109 (m-30) REVERT: K 4 MET cc_start: 0.8685 (mpp) cc_final: 0.8463 (mmp) REVERT: K 75 ILE cc_start: 0.8491 (mt) cc_final: 0.8167 (mt) REVERT: K 78 LEU cc_start: 0.7989 (mp) cc_final: 0.7454 (mp) REVERT: K 86 TYR cc_start: 0.8289 (m-10) cc_final: 0.7953 (m-10) outliers start: 12 outliers final: 6 residues processed: 199 average time/residue: 0.3405 time to fit residues: 101.7188 Evaluate side-chains 104 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 2.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain G residue 169 ASN Chi-restraints excluded: chain I residue 136 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 179 optimal weight: 0.9980 chunk 161 optimal weight: 0.3980 chunk 89 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 86 optimal weight: 7.9990 chunk 166 optimal weight: 0.5980 chunk 64 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 193 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 HIS L 27 GLN D 322 ASN ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 231 ASN J 81 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17943 Z= 0.188 Angle : 0.689 9.185 24330 Z= 0.347 Chirality : 0.043 0.229 2706 Planarity : 0.006 0.143 3117 Dihedral : 8.649 61.303 3000 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.87 % Favored : 95.04 % Rotamer: Outliers : 2.91 % Allowed : 25.12 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 2.15 % 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: -1.23 (0.17), residues: 2157 helix: 1.08 (0.26), residues: 381 sheet: -0.16 (0.27), residues: 393 loop : -1.66 (0.15), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 153 HIS 0.007 0.001 HIS C 25 PHE 0.015 0.001 PHE A 258 TYR 0.015 0.001 TYR E 79 ARG 0.011 0.001 ARG E 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 129 time to evaluate : 1.950 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: symmetry clash REVERT: B 19 ASP cc_start: 0.8508 (p0) cc_final: 0.7896 (p0) REVERT: B 62 GLN cc_start: 0.9222 (tp40) cc_final: 0.8824 (mp10) REVERT: B 90 ASP cc_start: 0.9042 (m-30) cc_final: 0.8651 (m-30) REVERT: B 149 MET cc_start: 0.9248 (tpp) cc_final: 0.8657 (mmm) REVERT: A 24 ASP cc_start: 0.9234 (m-30) cc_final: 0.8961 (t0) REVERT: H 95 ASP cc_start: 0.8833 (t0) cc_final: 0.8270 (m-30) REVERT: L 32 GLU cc_start: 0.8977 (mt-10) cc_final: 0.8612 (mt-10) REVERT: C 19 ASP cc_start: 0.9094 (m-30) cc_final: 0.8642 (p0) REVERT: C 62 GLN cc_start: 0.9276 (tp40) cc_final: 0.8873 (mp10) REVERT: C 149 MET cc_start: 0.9227 (tpp) cc_final: 0.8894 (tpp) REVERT: E 13 ARG cc_start: 0.9400 (mtp85) cc_final: 0.8675 (mtt-85) REVERT: E 72 ASP cc_start: 0.7888 (t70) cc_final: 0.7398 (t0) REVERT: E 75 GLN cc_start: 0.9452 (mt0) cc_final: 0.9139 (mt0) REVERT: E 95 ASP cc_start: 0.8822 (t0) cc_final: 0.8347 (m-30) REVERT: F 82 ASP cc_start: 0.7929 (m-30) cc_final: 0.7662 (m-30) REVERT: G 59 MET cc_start: 0.8702 (tpp) cc_final: 0.8450 (mmp) REVERT: G 90 ASP cc_start: 0.9249 (m-30) cc_final: 0.8992 (m-30) REVERT: G 149 MET cc_start: 0.9217 (tpp) cc_final: 0.8967 (tpp) REVERT: I 292 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8839 (mm) REVERT: J 72 ASP cc_start: 0.8201 (t70) cc_final: 0.6856 (t70) REVERT: J 75 GLN cc_start: 0.9592 (mt0) cc_final: 0.9137 (mp10) REVERT: J 95 ASP cc_start: 0.8872 (t0) cc_final: 0.8183 (m-30) outliers start: 55 outliers final: 23 residues processed: 180 average time/residue: 0.2911 time to fit residues: 81.5714 Evaluate side-chains 126 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain C residue 146 ASN Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain I residue 18 HIS Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 292 LEU Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain K residue 106 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 107 optimal weight: 9.9990 chunk 60 optimal weight: 0.0870 chunk 160 optimal weight: 3.9990 chunk 131 optimal weight: 9.9990 chunk 53 optimal weight: 0.0010 chunk 193 optimal weight: 8.9990 chunk 209 optimal weight: 20.0000 chunk 172 optimal weight: 0.0570 chunk 192 optimal weight: 5.9990 chunk 66 optimal weight: 0.0980 chunk 155 optimal weight: 10.0000 overall best weight: 0.8484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17943 Z= 0.161 Angle : 0.636 11.142 24330 Z= 0.313 Chirality : 0.043 0.238 2706 Planarity : 0.005 0.142 3117 Dihedral : 7.127 55.631 2990 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.73 % Favored : 95.18 % Rotamer: Outliers : 3.29 % Allowed : 23.85 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.18), residues: 2157 helix: 1.30 (0.26), residues: 381 sheet: -0.11 (0.26), residues: 438 loop : -1.49 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 92 HIS 0.005 0.001 HIS C 25 PHE 0.014 0.001 PHE G 110 TYR 0.011 0.001 TYR F 49 ARG 0.006 0.000 ARG H 13 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 117 time to evaluate : 2.191 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: symmetry clash revert: symmetry clash REVERT: B 19 ASP cc_start: 0.8444 (p0) cc_final: 0.7974 (p0) REVERT: B 77 MET cc_start: 0.8800 (mpp) cc_final: 0.8290 (tpp) REVERT: B 149 MET cc_start: 0.9200 (tpp) cc_final: 0.8841 (mmm) REVERT: A 24 ASP cc_start: 0.9261 (m-30) cc_final: 0.9006 (t0) REVERT: H 95 ASP cc_start: 0.8876 (t0) cc_final: 0.8343 (m-30) REVERT: L 4 MET cc_start: 0.8167 (mmm) cc_final: 0.7702 (mmm) REVERT: L 32 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8556 (mt-10) REVERT: C 19 ASP cc_start: 0.9084 (m-30) cc_final: 0.8626 (p0) REVERT: C 149 MET cc_start: 0.9204 (tpp) cc_final: 0.8861 (tpp) REVERT: E 72 ASP cc_start: 0.7947 (t70) cc_final: 0.7492 (t70) REVERT: E 75 GLN cc_start: 0.9444 (mt0) cc_final: 0.9115 (mt0) REVERT: E 95 ASP cc_start: 0.8834 (t0) cc_final: 0.8335 (m-30) REVERT: F 82 ASP cc_start: 0.7965 (m-30) cc_final: 0.7675 (m-30) REVERT: G 77 MET cc_start: 0.8396 (mmt) cc_final: 0.7986 (mmt) REVERT: G 149 MET cc_start: 0.9236 (tpp) cc_final: 0.8975 (tpp) REVERT: J 72 ASP cc_start: 0.8166 (t70) cc_final: 0.7961 (p0) REVERT: J 75 GLN cc_start: 0.9597 (mt0) cc_final: 0.9048 (mp10) REVERT: J 95 ASP cc_start: 0.8913 (t0) cc_final: 0.8199 (m-30) outliers start: 62 outliers final: 27 residues processed: 175 average time/residue: 0.2865 time to fit residues: 79.3505 Evaluate side-chains 122 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain I residue 18 HIS Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain K residue 47 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 191 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 100 optimal weight: 0.4980 chunk 21 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 130 optimal weight: 0.0050 chunk 194 optimal weight: 2.9990 chunk 205 optimal weight: 30.0000 chunk 101 optimal weight: 6.9990 chunk 184 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 overall best weight: 1.0598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 17943 Z= 0.171 Angle : 0.614 11.366 24330 Z= 0.303 Chirality : 0.042 0.238 2706 Planarity : 0.005 0.143 3117 Dihedral : 6.663 55.826 2990 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.01 % Favored : 94.90 % Rotamer: Outliers : 2.76 % Allowed : 23.85 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.18), residues: 2157 helix: 1.37 (0.26), residues: 381 sheet: 0.08 (0.25), residues: 438 loop : -1.48 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 153 HIS 0.004 0.001 HIS C 25 PHE 0.017 0.001 PHE E 67 TYR 0.014 0.001 TYR D 98 ARG 0.008 0.000 ARG H 13 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 105 time to evaluate : 2.170 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 2 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7619 (tt) REVERT: B 77 MET cc_start: 0.8776 (mpp) cc_final: 0.8324 (mmt) REVERT: B 149 MET cc_start: 0.9200 (tpp) cc_final: 0.8863 (mmm) REVERT: A 24 ASP cc_start: 0.9283 (m-30) cc_final: 0.9041 (t0) REVERT: H 13 ARG cc_start: 0.8819 (mtt-85) cc_final: 0.8235 (mtt-85) REVERT: H 95 ASP cc_start: 0.8875 (t0) cc_final: 0.8285 (m-30) REVERT: L 32 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8495 (mt-10) REVERT: C 19 ASP cc_start: 0.9097 (m-30) cc_final: 0.8665 (p0) REVERT: C 147 GLU cc_start: 0.9378 (OUTLIER) cc_final: 0.9144 (tp30) REVERT: C 149 MET cc_start: 0.9213 (tpp) cc_final: 0.8860 (tpp) REVERT: D 292 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8923 (mm) REVERT: E 72 ASP cc_start: 0.7996 (t70) cc_final: 0.7538 (t70) REVERT: E 75 GLN cc_start: 0.9457 (mt0) cc_final: 0.9129 (mt0) REVERT: E 95 ASP cc_start: 0.8858 (t0) cc_final: 0.8336 (m-30) REVERT: F 82 ASP cc_start: 0.8044 (m-30) cc_final: 0.7726 (m-30) REVERT: G 77 MET cc_start: 0.8472 (mmt) cc_final: 0.8088 (mmt) REVERT: G 147 GLU cc_start: 0.9417 (OUTLIER) cc_final: 0.9044 (tp30) REVERT: G 149 MET cc_start: 0.9221 (tpp) cc_final: 0.8988 (mmm) REVERT: I 199 ASN cc_start: 0.8984 (OUTLIER) cc_final: 0.8757 (p0) REVERT: I 292 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8736 (mm) REVERT: J 72 ASP cc_start: 0.8211 (t70) cc_final: 0.8008 (p0) REVERT: J 75 GLN cc_start: 0.9603 (mt0) cc_final: 0.9063 (mp10) REVERT: J 95 ASP cc_start: 0.8908 (t0) cc_final: 0.8228 (m-30) outliers start: 52 outliers final: 36 residues processed: 155 average time/residue: 0.2803 time to fit residues: 68.4027 Evaluate side-chains 135 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 93 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 76 CYS Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 18 HIS Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 163 ASN Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 199 ASN Chi-restraints excluded: chain I residue 269 THR Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 292 LEU Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain K residue 106 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 171 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 2 optimal weight: 8.9990 chunk 153 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 175 optimal weight: 6.9990 chunk 142 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 105 optimal weight: 0.8980 chunk 184 optimal weight: 6.9990 chunk 51 optimal weight: 20.0000 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 17943 Z= 0.314 Angle : 0.659 9.531 24330 Z= 0.332 Chirality : 0.043 0.253 2706 Planarity : 0.006 0.143 3117 Dihedral : 6.666 57.431 2990 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.49 % Favored : 93.37 % Rotamer: Outliers : 4.19 % Allowed : 22.58 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.18), residues: 2157 helix: 1.64 (0.27), residues: 372 sheet: -0.14 (0.24), residues: 456 loop : -1.37 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 94 HIS 0.005 0.001 HIS C 25 PHE 0.017 0.002 PHE E 67 TYR 0.014 0.002 TYR I 168 ARG 0.008 0.001 ARG H 13 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 100 time to evaluate : 2.097 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 2 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7606 (tt) REVERT: B 77 MET cc_start: 0.8635 (mpp) cc_final: 0.8128 (mmt) REVERT: B 149 MET cc_start: 0.9142 (tpp) cc_final: 0.8863 (mmm) REVERT: A 24 ASP cc_start: 0.9337 (m-30) cc_final: 0.9091 (t0) REVERT: A 225 ASP cc_start: 0.8808 (t70) cc_final: 0.8539 (t0) REVERT: A 278 ASP cc_start: 0.9075 (t0) cc_final: 0.8837 (t0) REVERT: H 13 ARG cc_start: 0.8896 (mtt-85) cc_final: 0.8187 (mtt-85) REVERT: H 95 ASP cc_start: 0.8969 (t0) cc_final: 0.8362 (m-30) REVERT: C 147 GLU cc_start: 0.9418 (OUTLIER) cc_final: 0.9198 (tp30) REVERT: C 149 MET cc_start: 0.9194 (tpp) cc_final: 0.8812 (tpp) REVERT: D 292 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9012 (mm) REVERT: E 72 ASP cc_start: 0.8052 (t70) cc_final: 0.7591 (t70) REVERT: E 75 GLN cc_start: 0.9509 (mt0) cc_final: 0.9199 (mt0) REVERT: E 95 ASP cc_start: 0.8930 (t0) cc_final: 0.8276 (m-30) REVERT: F 82 ASP cc_start: 0.8202 (m-30) cc_final: 0.7872 (m-30) REVERT: F 105 GLU cc_start: 0.7814 (tp30) cc_final: 0.7557 (tm-30) REVERT: G 149 MET cc_start: 0.9211 (tpp) cc_final: 0.8890 (mmm) REVERT: I 199 ASN cc_start: 0.9013 (OUTLIER) cc_final: 0.8786 (p0) REVERT: J 75 GLN cc_start: 0.9598 (mt0) cc_final: 0.9057 (mp10) REVERT: J 95 ASP cc_start: 0.9007 (t0) cc_final: 0.8206 (m-30) outliers start: 79 outliers final: 58 residues processed: 168 average time/residue: 0.2777 time to fit residues: 75.1454 Evaluate side-chains 152 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 90 time to evaluate : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 30 CYS Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 76 CYS Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 169 ASN Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 18 HIS Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 163 ASN Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 199 ASN Chi-restraints excluded: chain I residue 208 HIS Chi-restraints excluded: chain I residue 214 THR Chi-restraints excluded: chain I residue 269 THR Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain K residue 106 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 69 optimal weight: 3.9990 chunk 185 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 206 optimal weight: 7.9990 chunk 171 optimal weight: 0.0060 chunk 95 optimal weight: 0.7980 chunk 17 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 overall best weight: 2.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 GLN B 146 ASN ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 17943 Z= 0.231 Angle : 0.620 10.069 24330 Z= 0.313 Chirality : 0.043 0.246 2706 Planarity : 0.005 0.139 3117 Dihedral : 6.603 55.899 2990 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.52 % Favored : 94.34 % Rotamer: Outliers : 3.55 % Allowed : 24.06 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.18), residues: 2157 helix: 1.79 (0.27), residues: 372 sheet: -0.03 (0.25), residues: 429 loop : -1.39 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 153 HIS 0.004 0.001 HIS G 142 PHE 0.013 0.001 PHE D 118 TYR 0.009 0.001 TYR G 162 ARG 0.005 0.000 ARG H 13 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 96 time to evaluate : 2.073 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 2 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7668 (tt) REVERT: B 77 MET cc_start: 0.8533 (mpp) cc_final: 0.8035 (mmt) REVERT: B 149 MET cc_start: 0.9179 (tpp) cc_final: 0.8888 (mmm) REVERT: A 225 ASP cc_start: 0.8779 (t70) cc_final: 0.8467 (t0) REVERT: H 13 ARG cc_start: 0.8914 (mtt-85) cc_final: 0.8193 (mtt-85) REVERT: H 95 ASP cc_start: 0.8975 (t0) cc_final: 0.8369 (m-30) REVERT: C 147 GLU cc_start: 0.9419 (OUTLIER) cc_final: 0.9204 (tp30) REVERT: C 149 MET cc_start: 0.9214 (tpp) cc_final: 0.8811 (tpp) REVERT: D 292 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9025 (mm) REVERT: E 95 ASP cc_start: 0.8923 (t0) cc_final: 0.8261 (m-30) REVERT: F 32 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8485 (mt-10) REVERT: F 82 ASP cc_start: 0.8181 (m-30) cc_final: 0.7856 (m-30) REVERT: F 105 GLU cc_start: 0.7702 (tp30) cc_final: 0.7407 (tm-30) REVERT: G 147 GLU cc_start: 0.9457 (OUTLIER) cc_final: 0.9138 (tp30) REVERT: G 149 MET cc_start: 0.9219 (tpp) cc_final: 0.8920 (tpp) REVERT: I 199 ASN cc_start: 0.8982 (OUTLIER) cc_final: 0.8757 (p0) REVERT: I 292 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8966 (mm) REVERT: J 95 ASP cc_start: 0.8996 (t0) cc_final: 0.8175 (m-30) outliers start: 67 outliers final: 53 residues processed: 157 average time/residue: 0.2669 time to fit residues: 67.7705 Evaluate side-chains 147 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 88 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 30 CYS Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 30 CYS Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 76 CYS Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 18 HIS Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 163 ASN Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 199 ASN Chi-restraints excluded: chain I residue 214 THR Chi-restraints excluded: chain I residue 269 THR Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 292 LEU Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain K residue 106 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 198 optimal weight: 6.9990 chunk 23 optimal weight: 0.3980 chunk 117 optimal weight: 2.9990 chunk 150 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 205 optimal weight: 10.0000 chunk 128 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 17943 Z= 0.234 Angle : 0.628 10.031 24330 Z= 0.315 Chirality : 0.043 0.247 2706 Planarity : 0.005 0.143 3117 Dihedral : 6.526 55.781 2990 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.80 % Favored : 94.07 % Rotamer: Outliers : 4.08 % Allowed : 24.17 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.18), residues: 2157 helix: 1.77 (0.27), residues: 372 sheet: -0.05 (0.25), residues: 429 loop : -1.38 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 153 HIS 0.005 0.001 HIS B 142 PHE 0.011 0.001 PHE D 118 TYR 0.010 0.001 TYR G 162 ARG 0.008 0.000 ARG C 170 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 94 time to evaluate : 2.296 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 2 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7618 (tt) REVERT: B 77 MET cc_start: 0.8524 (mpp) cc_final: 0.8032 (mmt) REVERT: B 149 MET cc_start: 0.9147 (tpp) cc_final: 0.8903 (mmm) REVERT: A 225 ASP cc_start: 0.8800 (t70) cc_final: 0.8491 (t0) REVERT: H 13 ARG cc_start: 0.8964 (mtt-85) cc_final: 0.8267 (mtt-85) REVERT: H 95 ASP cc_start: 0.9021 (t0) cc_final: 0.8388 (m-30) REVERT: C 14 TRP cc_start: 0.9221 (OUTLIER) cc_final: 0.8943 (m-90) REVERT: C 147 GLU cc_start: 0.9424 (OUTLIER) cc_final: 0.9211 (tp30) REVERT: C 149 MET cc_start: 0.9205 (tpp) cc_final: 0.8800 (tpp) REVERT: D 292 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9069 (mm) REVERT: E 95 ASP cc_start: 0.8936 (t0) cc_final: 0.8350 (m-30) REVERT: F 82 ASP cc_start: 0.8192 (m-30) cc_final: 0.7865 (m-30) REVERT: F 105 GLU cc_start: 0.7424 (tp30) cc_final: 0.7143 (tm-30) REVERT: G 147 GLU cc_start: 0.9452 (OUTLIER) cc_final: 0.9157 (tp30) REVERT: G 149 MET cc_start: 0.9224 (tpp) cc_final: 0.8928 (tpp) REVERT: I 199 ASN cc_start: 0.8988 (OUTLIER) cc_final: 0.8769 (p0) REVERT: I 292 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8951 (mm) REVERT: J 95 ASP cc_start: 0.8992 (t0) cc_final: 0.8162 (m-30) REVERT: J 100 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.8752 (mtm-85) REVERT: K 6 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7152 (pt0) REVERT: K 32 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8407 (mt-10) outliers start: 77 outliers final: 57 residues processed: 164 average time/residue: 0.2819 time to fit residues: 73.7252 Evaluate side-chains 156 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 90 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 30 CYS Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain C residue 14 TRP Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 30 CYS Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 76 CYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 169 ASN Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 18 HIS Chi-restraints excluded: chain I residue 52 CYS Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 163 ASN Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 199 ASN Chi-restraints excluded: chain I residue 214 THR Chi-restraints excluded: chain I residue 269 THR Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 292 LEU Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain J residue 100 ARG Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 106 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 127 optimal weight: 0.5980 chunk 81 optimal weight: 6.9990 chunk 122 optimal weight: 20.0000 chunk 61 optimal weight: 9.9990 chunk 40 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 130 optimal weight: 10.0000 chunk 139 optimal weight: 8.9990 chunk 101 optimal weight: 9.9990 chunk 19 optimal weight: 0.1980 chunk 161 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 GLN G 169 ASN ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17943 Z= 0.149 Angle : 0.602 11.175 24330 Z= 0.300 Chirality : 0.042 0.241 2706 Planarity : 0.005 0.141 3117 Dihedral : 6.212 55.731 2988 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.24 % Favored : 94.62 % Rotamer: Outliers : 3.55 % Allowed : 24.38 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.18), residues: 2157 helix: 1.78 (0.27), residues: 372 sheet: 0.40 (0.26), residues: 399 loop : -1.36 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 100E HIS 0.003 0.000 HIS C 142 PHE 0.011 0.001 PHE D 118 TYR 0.015 0.001 TYR K 86 ARG 0.005 0.000 ARG C 170 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 97 time to evaluate : 2.119 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 2 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7674 (tt) REVERT: B 77 MET cc_start: 0.8435 (mpp) cc_final: 0.7958 (mmt) REVERT: B 149 MET cc_start: 0.9166 (tpp) cc_final: 0.8854 (mmm) REVERT: A 225 ASP cc_start: 0.8759 (t70) cc_final: 0.8450 (t0) REVERT: H 13 ARG cc_start: 0.8986 (mtt-85) cc_final: 0.8357 (mtt-85) REVERT: H 95 ASP cc_start: 0.8987 (t0) cc_final: 0.8391 (m-30) REVERT: L 4 MET cc_start: 0.8061 (mmm) cc_final: 0.7685 (mmm) REVERT: C 147 GLU cc_start: 0.9414 (OUTLIER) cc_final: 0.9203 (tp30) REVERT: C 149 MET cc_start: 0.9198 (tpp) cc_final: 0.8751 (tpp) REVERT: D 278 ASP cc_start: 0.9099 (t0) cc_final: 0.8745 (t0) REVERT: D 292 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9022 (mm) REVERT: E 95 ASP cc_start: 0.8927 (t0) cc_final: 0.8386 (m-30) REVERT: F 82 ASP cc_start: 0.8169 (m-30) cc_final: 0.7816 (m-30) REVERT: G 147 GLU cc_start: 0.9447 (OUTLIER) cc_final: 0.9149 (tp30) REVERT: I 199 ASN cc_start: 0.8990 (OUTLIER) cc_final: 0.8771 (p0) REVERT: I 292 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8931 (mm) REVERT: J 95 ASP cc_start: 0.8977 (t0) cc_final: 0.8134 (m-30) REVERT: J 100 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8681 (mtm-85) REVERT: K 6 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.6961 (pt0) outliers start: 67 outliers final: 52 residues processed: 158 average time/residue: 0.2705 time to fit residues: 68.4985 Evaluate side-chains 149 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 89 time to evaluate : 2.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 30 CYS Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 76 CYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 169 ASN Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 18 HIS Chi-restraints excluded: chain I residue 52 CYS Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 163 ASN Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 199 ASN Chi-restraints excluded: chain I residue 214 THR Chi-restraints excluded: chain I residue 269 THR Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 292 LEU Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain J residue 100 ARG Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 106 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 186 optimal weight: 6.9990 chunk 196 optimal weight: 6.9990 chunk 179 optimal weight: 0.0670 chunk 191 optimal weight: 0.7980 chunk 115 optimal weight: 8.9990 chunk 83 optimal weight: 10.0000 chunk 150 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 chunk 172 optimal weight: 2.9990 chunk 180 optimal weight: 7.9990 chunk 190 optimal weight: 0.9980 overall best weight: 2.3722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 169 ASN ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17943 Z= 0.223 Angle : 0.631 10.777 24330 Z= 0.314 Chirality : 0.042 0.248 2706 Planarity : 0.005 0.142 3117 Dihedral : 6.166 55.808 2988 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.03 % Favored : 93.83 % Rotamer: Outliers : 3.55 % Allowed : 24.06 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.18), residues: 2157 helix: 1.85 (0.27), residues: 372 sheet: -0.04 (0.25), residues: 456 loop : -1.26 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP C 14 HIS 0.004 0.001 HIS C 25 PHE 0.010 0.001 PHE A 213 TYR 0.018 0.001 TYR L 86 ARG 0.005 0.000 ARG G 170 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 92 time to evaluate : 2.185 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 2 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7651 (tt) REVERT: B 77 MET cc_start: 0.8493 (mpp) cc_final: 0.7996 (mmt) REVERT: B 149 MET cc_start: 0.9162 (tpp) cc_final: 0.8874 (mmm) REVERT: A 225 ASP cc_start: 0.8792 (t70) cc_final: 0.8590 (t0) REVERT: H 13 ARG cc_start: 0.9005 (mtt-85) cc_final: 0.8346 (mtt-85) REVERT: H 95 ASP cc_start: 0.8999 (t0) cc_final: 0.8549 (t70) REVERT: L 4 MET cc_start: 0.8096 (mmm) cc_final: 0.7701 (mmm) REVERT: C 149 MET cc_start: 0.9211 (tpp) cc_final: 0.8746 (tpp) REVERT: D 292 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9017 (mm) REVERT: E 95 ASP cc_start: 0.8935 (t0) cc_final: 0.8362 (m-30) REVERT: F 82 ASP cc_start: 0.8170 (m-30) cc_final: 0.7793 (m-30) REVERT: G 147 GLU cc_start: 0.9442 (OUTLIER) cc_final: 0.9167 (tp30) REVERT: I 199 ASN cc_start: 0.8997 (OUTLIER) cc_final: 0.8774 (p0) REVERT: I 292 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8879 (mm) REVERT: J 95 ASP cc_start: 0.8999 (t0) cc_final: 0.8153 (m-30) REVERT: J 100 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.8743 (mtm-85) REVERT: K 6 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7176 (pt0) REVERT: K 32 GLU cc_start: 0.8958 (mt-10) cc_final: 0.8416 (mt-10) outliers start: 67 outliers final: 55 residues processed: 152 average time/residue: 0.2708 time to fit residues: 65.9163 Evaluate side-chains 151 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 89 time to evaluate : 2.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 30 CYS Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 30 CYS Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 76 CYS Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 169 ASN Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 18 HIS Chi-restraints excluded: chain I residue 52 CYS Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 163 ASN Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 199 ASN Chi-restraints excluded: chain I residue 214 THR Chi-restraints excluded: chain I residue 269 THR Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 292 LEU Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain J residue 100 ARG Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 125 optimal weight: 6.9990 chunk 202 optimal weight: 8.9990 chunk 123 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 140 optimal weight: 0.8980 chunk 212 optimal weight: 0.8980 chunk 195 optimal weight: 3.9990 chunk 168 optimal weight: 0.3980 chunk 17 optimal weight: 8.9990 chunk 130 optimal weight: 0.9990 chunk 103 optimal weight: 0.0040 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 169 ASN I 183 HIS K 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17943 Z= 0.151 Angle : 0.612 11.369 24330 Z= 0.303 Chirality : 0.042 0.240 2706 Planarity : 0.005 0.140 3117 Dihedral : 5.963 55.718 2988 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.24 % Favored : 94.62 % Rotamer: Outliers : 3.23 % Allowed : 24.27 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.18), residues: 2157 helix: 1.85 (0.27), residues: 372 sheet: 0.36 (0.26), residues: 411 loop : -1.27 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 14 HIS 0.004 0.001 HIS C 25 PHE 0.010 0.001 PHE D 118 TYR 0.017 0.001 TYR L 86 ARG 0.005 0.000 ARG H 13 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4314 Ramachandran restraints generated. 2157 Oldfield, 0 Emsley, 2157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 95 time to evaluate : 2.140 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 2 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7706 (tt) REVERT: B 77 MET cc_start: 0.8395 (mpp) cc_final: 0.7918 (mmt) REVERT: B 149 MET cc_start: 0.9183 (tpp) cc_final: 0.8862 (mmm) REVERT: A 225 ASP cc_start: 0.8796 (t70) cc_final: 0.8466 (t0) REVERT: H 13 ARG cc_start: 0.8999 (mtt-85) cc_final: 0.8338 (mtt-85) REVERT: H 82 MET cc_start: 0.7661 (ppp) cc_final: 0.7000 (ppp) REVERT: H 95 ASP cc_start: 0.8973 (t0) cc_final: 0.8353 (m-30) REVERT: L 4 MET cc_start: 0.8102 (mmm) cc_final: 0.7729 (mmm) REVERT: L 82 ASP cc_start: 0.7947 (m-30) cc_final: 0.7639 (m-30) REVERT: C 149 MET cc_start: 0.9210 (tpp) cc_final: 0.8833 (tpp) REVERT: D 225 ASP cc_start: 0.8796 (t0) cc_final: 0.8498 (t0) REVERT: D 283 THR cc_start: 0.9521 (OUTLIER) cc_final: 0.9223 (p) REVERT: D 292 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.8993 (mm) REVERT: E 95 ASP cc_start: 0.8912 (t0) cc_final: 0.8354 (m-30) REVERT: F 82 ASP cc_start: 0.8171 (m-30) cc_final: 0.7808 (m-30) REVERT: G 147 GLU cc_start: 0.9442 (OUTLIER) cc_final: 0.9162 (tp30) REVERT: I 199 ASN cc_start: 0.8983 (OUTLIER) cc_final: 0.8767 (p0) REVERT: I 292 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8862 (mm) REVERT: J 95 ASP cc_start: 0.8983 (t0) cc_final: 0.8600 (t70) REVERT: K 6 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7023 (pt0) outliers start: 61 outliers final: 52 residues processed: 150 average time/residue: 0.2762 time to fit residues: 66.0124 Evaluate side-chains 150 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 91 time to evaluate : 2.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 169 ASN Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 30 CYS Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain C residue 14 TRP Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 30 CYS Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 76 CYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 169 ASN Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 52 CYS Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 163 ASN Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 183 HIS Chi-restraints excluded: chain I residue 199 ASN Chi-restraints excluded: chain I residue 214 THR Chi-restraints excluded: chain I residue 269 THR Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 292 LEU Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 134 optimal weight: 8.9990 chunk 180 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 chunk 155 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 169 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 chunk 173 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 GLN C 146 ASN ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 169 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.042548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.031483 restraints weight = 113815.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.032656 restraints weight = 62327.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.033451 restraints weight = 43234.107| |-----------------------------------------------------------------------------| r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17943 Z= 0.226 Angle : 0.626 10.892 24330 Z= 0.312 Chirality : 0.042 0.243 2706 Planarity : 0.005 0.142 3117 Dihedral : 5.971 55.700 2988 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.84 % Favored : 94.02 % Rotamer: Outliers : 3.60 % Allowed : 23.74 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.18), residues: 2157 helix: 1.92 (0.26), residues: 372 sheet: -0.04 (0.25), residues: 441 loop : -1.24 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 14 HIS 0.009 0.001 HIS I 184 PHE 0.010 0.001 PHE E 67 TYR 0.021 0.001 TYR L 86 ARG 0.004 0.000 ARG H 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2911.40 seconds wall clock time: 55 minutes 1.01 seconds (3301.01 seconds total)