Starting phenix.real_space_refine on Tue Nov 19 05:38:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ssz_40752/11_2024/8ssz_40752_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ssz_40752/11_2024/8ssz_40752.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ssz_40752/11_2024/8ssz_40752.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ssz_40752/11_2024/8ssz_40752.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ssz_40752/11_2024/8ssz_40752_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ssz_40752/11_2024/8ssz_40752_trim.cif" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 S 138 5.16 5 Na 1 4.78 5 C 16816 2.51 5 N 4249 2.21 5 O 4916 1.98 5 H 25319 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 51441 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 6401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 6401 Classifications: {'peptide': 393} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 373} Chain breaks: 1 Chain: "B" Number of atoms: 6197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 6197 Classifications: {'peptide': 384} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 362} Chain breaks: 1 Chain: "C" Number of atoms: 6197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 6197 Classifications: {'peptide': 384} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 362} Chain breaks: 1 Chain: "D" Number of atoms: 6401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 6401 Classifications: {'peptide': 393} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 373} Chain breaks: 1 Chain: "E" Number of atoms: 6197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 6197 Classifications: {'peptide': 384} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 362} Chain breaks: 1 Chain: "F" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3325 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 206} Chain: "G" Number of atoms: 3267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3267 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 202} Chain: "H" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3325 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 206} Chain: "I" Number of atoms: 3267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3267 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 202} Chain: "J" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3325 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 206} Chain: "K" Number of atoms: 3267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3267 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 202} Chain: "L" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "M" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "N" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 53 Unusual residues: {' CA': 1, 'ACH': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 53 Unusual residues: {' CA': 1, 'ACH': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {' NA': 1, 'OCT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 24.64, per 1000 atoms: 0.48 Number of scatterers: 51441 At special positions: 0 Unit cell: (201.773, 154.297, 183.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 2 19.99 S 138 16.00 Na 1 11.00 O 4916 8.00 N 4249 7.00 C 16816 6.00 H 25319 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.04 Simple disulfide: pdb=" SG CYS A 199 " - pdb=" SG CYS A 200 " distance=2.04 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 144 " distance=2.04 Simple disulfide: pdb=" SG CYS C 130 " - pdb=" SG CYS C 144 " distance=2.04 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " distance=2.04 Simple disulfide: pdb=" SG CYS D 199 " - pdb=" SG CYS D 200 " distance=2.04 Simple disulfide: pdb=" SG CYS E 130 " - pdb=" SG CYS E 144 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 93 " distance=2.03 Simple disulfide: pdb=" SG CYS F 139 " - pdb=" SG CYS F 199 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 97 " distance=2.04 Simple disulfide: pdb=" SG CYS G 147 " - pdb=" SG CYS G 202 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 93 " distance=2.04 Simple disulfide: pdb=" SG CYS H 139 " - pdb=" SG CYS H 199 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 97 " distance=2.03 Simple disulfide: pdb=" SG CYS I 147 " - pdb=" SG CYS I 202 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 93 " distance=2.03 Simple disulfide: pdb=" SG CYS J 139 " - pdb=" SG CYS J 199 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 97 " distance=2.03 Simple disulfide: pdb=" SG CYS K 147 " - pdb=" SG CYS K 202 " distance=2.03 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 ALPHA1-3 " BMA L 3 " - " MAN L 4 " " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " BETA1-4 " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " 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-ASN " NAG A 701 " - " ASN A 31 " " NAG A 702 " - " ASN A 81 " " NAG A 703 " - " ASN A 148 " " NAG D 701 " - " ASN D 31 " " NAG D 702 " - " ASN D 81 " " NAG D 703 " - " ASN D 148 " " NAG L 1 " - " ASN B 143 " " NAG M 1 " - " ASN C 143 " " NAG N 1 " - " ASN E 143 " Time building additional restraints: 13.21 Conformation dependent library (CDL) restraints added in 3.8 seconds 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6176 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 51 sheets defined 30.2% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.45 Creating SS restraints... Processing helix chain 'A' and resid 6 through 19 Processing helix chain 'A' and resid 75 through 79 Processing helix chain 'A' and resid 90 through 92 No H-bonds generated for 'chain 'A' and resid 90 through 92' Processing helix chain 'A' and resid 217 through 233 removed outlier: 4.575A pdb=" N ILE A 226 " --> pdb=" O ILE A 222 " (cutoff:3.500A) Proline residue: A 227 - end of helix Processing helix chain 'A' and resid 234 through 235 No H-bonds generated for 'chain 'A' and resid 234 through 235' Processing helix chain 'A' and resid 236 through 240 Processing helix chain 'A' and resid 247 through 268 Processing helix chain 'A' and resid 278 through 306 Processing helix chain 'A' and resid 315 through 330 removed outlier: 5.633A pdb=" N VAL A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) Proline residue: A 327 - end of helix Processing helix chain 'A' and resid 539 through 599 Proline residue: A 594 - end of helix Processing helix chain 'B' and resid 2 through 13 Processing helix chain 'B' and resid 70 through 75 removed outlier: 4.204A pdb=" N ASP B 75 " --> pdb=" O GLU B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 87 No H-bonds generated for 'chain 'B' and resid 85 through 87' Processing helix chain 'B' and resid 209 through 226 removed outlier: 4.644A pdb=" N ILE B 218 " --> pdb=" O ILE B 214 " (cutoff:3.500A) Proline residue: B 219 - end of helix removed outlier: 3.660A pdb=" N LEU B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 233 removed outlier: 4.362A pdb=" N VAL B 230 " --> pdb=" O ALA B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 262 Processing helix chain 'B' and resid 270 through 298 Processing helix chain 'B' and resid 307 through 315 Processing helix chain 'B' and resid 316 through 322 removed outlier: 3.764A pdb=" N ALA B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 449 removed outlier: 3.672A pdb=" N THR B 449 " --> pdb=" O CYS B 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 65 through 68 removed outlier: 3.976A pdb=" N THR C 68 " --> pdb=" O TYR C 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 65 through 68' Processing helix chain 'C' and resid 70 through 75 removed outlier: 3.676A pdb=" N ASP C 75 " --> pdb=" O GLU C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 87 No H-bonds generated for 'chain 'C' and resid 85 through 87' Processing helix chain 'C' and resid 209 through 225 removed outlier: 4.549A pdb=" N ILE C 218 " --> pdb=" O ILE C 214 " (cutoff:3.500A) Proline residue: C 219 - end of helix Processing helix chain 'C' and resid 226 through 233 removed outlier: 4.212A pdb=" N VAL C 230 " --> pdb=" O ALA C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 238 removed outlier: 3.681A pdb=" N GLY C 238 " --> pdb=" O SER C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 262 Processing helix chain 'C' and resid 270 through 298 Processing helix chain 'C' and resid 307 through 315 Processing helix chain 'C' and resid 316 through 322 removed outlier: 3.789A pdb=" N ALA C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 449 Processing helix chain 'D' and resid 6 through 19 Processing helix chain 'D' and resid 75 through 80 removed outlier: 4.170A pdb=" N GLU D 80 " --> pdb=" O ALA D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing helix chain 'D' and resid 217 through 224 Processing helix chain 'D' and resid 224 through 233 Processing helix chain 'D' and resid 234 through 235 No H-bonds generated for 'chain 'D' and resid 234 through 235' Processing helix chain 'D' and resid 236 through 241 Processing helix chain 'D' and resid 242 through 246 removed outlier: 3.796A pdb=" N GLY D 246 " --> pdb=" O SER D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 270 removed outlier: 3.727A pdb=" N ILE D 269 " --> pdb=" O LEU D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 306 Processing helix chain 'D' and resid 315 through 330 removed outlier: 6.328A pdb=" N VAL D 326 " --> pdb=" O PHE D 322 " (cutoff:3.500A) Proline residue: D 327 - end of helix Processing helix chain 'D' and resid 539 through 599 Proline residue: D 594 - end of helix Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 65 through 68 removed outlier: 3.734A pdb=" N THR E 68 " --> pdb=" O TYR E 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 65 through 68' Processing helix chain 'E' and resid 70 through 75 removed outlier: 4.137A pdb=" N ASP E 75 " --> pdb=" O GLU E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 87 No H-bonds generated for 'chain 'E' and resid 85 through 87' Processing helix chain 'E' and resid 209 through 216 Processing helix chain 'E' and resid 216 through 225 Processing helix chain 'E' and resid 226 through 227 No H-bonds generated for 'chain 'E' and resid 226 through 227' Processing helix chain 'E' and resid 228 through 233 Processing helix chain 'E' and resid 239 through 262 Processing helix chain 'E' and resid 270 through 298 Processing helix chain 'E' and resid 307 through 323 removed outlier: 5.473A pdb=" N LEU E 318 " --> pdb=" O PHE E 314 " (cutoff:3.500A) Proline residue: E 319 - end of helix Processing helix chain 'E' and resid 397 through 448 Processing helix chain 'F' and resid 84 through 88 Processing helix chain 'F' and resid 126 through 133 Processing helix chain 'F' and resid 188 through 192 Processing helix chain 'G' and resid 29 through 33 removed outlier: 3.520A pdb=" N TYR G 33 " --> pdb=" O PHE G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 66 removed outlier: 3.649A pdb=" N ARG G 66 " --> pdb=" O GLU G 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 63 through 66' Processing helix chain 'G' and resid 88 through 92 Processing helix chain 'G' and resid 193 through 198 removed outlier: 4.028A pdb=" N SER G 197 " --> pdb=" O SER G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 210 Processing helix chain 'H' and resid 84 through 88 Processing helix chain 'H' and resid 126 through 133 Processing helix chain 'H' and resid 188 through 192 removed outlier: 3.768A pdb=" N GLU H 192 " --> pdb=" O LYS H 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 188 through 192' Processing helix chain 'I' and resid 29 through 33 removed outlier: 3.505A pdb=" N TYR I 33 " --> pdb=" O PHE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 66 Processing helix chain 'I' and resid 88 through 92 removed outlier: 3.517A pdb=" N SER I 92 " --> pdb=" O SER I 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 84 through 88 removed outlier: 3.949A pdb=" N LEU J 88 " --> pdb=" O ALA J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 133 Processing helix chain 'J' and resid 187 through 194 removed outlier: 3.873A pdb=" N HIS J 194 " --> pdb=" O GLU J 190 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 33 removed outlier: 3.522A pdb=" N TYR K 33 " --> pdb=" O PHE K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 66 removed outlier: 3.543A pdb=" N ARG K 66 " --> pdb=" O GLU K 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 63 through 66' Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 88 removed outlier: 3.918A pdb=" N ARG A 122 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLY A 121 " --> pdb=" O ASP A 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 88 removed outlier: 3.918A pdb=" N ARG A 122 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLY A 121 " --> pdb=" O ASP A 69 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N MET A 56 " --> pdb=" O ASP A 49 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASP A 49 " --> pdb=" O MET A 56 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N THR A 58 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N LEU A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASN A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N HIS A 68 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU A 37 " --> pdb=" O HIS A 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 99 removed outlier: 4.378A pdb=" N SER A 155 " --> pdb=" O PRO A 205 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ARG A 214 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ILE A 185 " --> pdb=" O ARG A 214 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 79 through 83 removed outlier: 3.911A pdb=" N SER B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 79 through 83 removed outlier: 3.911A pdb=" N SER B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE B 51 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N SER B 44 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR B 53 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N LEU B 42 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ASN B 55 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLU B 63 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N THR B 32 " --> pdb=" O GLU B 63 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 92 through 94 removed outlier: 5.068A pdb=" N SER B 150 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N VAL B 197 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE B 204 " --> pdb=" O VAL B 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 92 through 94 removed outlier: 5.068A pdb=" N SER B 150 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N VAL B 197 " --> pdb=" O SER B 150 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 79 through 83 removed outlier: 3.961A pdb=" N SER C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 79 through 83 removed outlier: 3.961A pdb=" N SER C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ILE C 51 " --> pdb=" O SER C 44 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N SER C 44 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N THR C 53 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N LEU C 42 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASN C 55 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLU C 63 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N THR C 32 " --> pdb=" O GLU C 63 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 92 through 94 removed outlier: 5.115A pdb=" N SER C 150 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL C 197 " --> pdb=" O SER C 150 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE C 204 " --> pdb=" O VAL C 181 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 92 through 94 removed outlier: 5.115A pdb=" N SER C 150 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL C 197 " --> pdb=" O SER C 150 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 84 through 88 removed outlier: 4.013A pdb=" N ARG D 122 " --> pdb=" O PHE D 118 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 84 through 88 removed outlier: 4.013A pdb=" N ARG D 122 " --> pdb=" O PHE D 118 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N MET D 56 " --> pdb=" O ASP D 49 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASP D 49 " --> pdb=" O MET D 56 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N THR D 58 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N LEU D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASN D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N HIS D 68 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU D 37 " --> pdb=" O HIS D 68 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 97 through 99 removed outlier: 4.423A pdb=" N SER D 155 " --> pdb=" O PRO D 205 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N GLU D 202 " --> pdb=" O TYR D 197 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N TYR D 197 " --> pdb=" O GLU D 202 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ARG D 214 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ILE D 185 " --> pdb=" O ARG D 214 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 79 through 83 removed outlier: 4.084A pdb=" N SER E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 79 through 83 removed outlier: 4.084A pdb=" N SER E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASN E 55 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N LEU E 42 " --> pdb=" O ASN E 55 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N TRP E 57 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ALA E 40 " --> pdb=" O TRP E 57 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N THR E 59 " --> pdb=" O SER E 38 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N SER E 38 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N GLU E 61 " --> pdb=" O MET E 36 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N MET E 36 " --> pdb=" O GLU E 61 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N GLU E 63 " --> pdb=" O GLN E 34 " (cutoff:3.500A) removed outlier: 9.568A pdb=" N GLN E 34 " --> pdb=" O GLU E 63 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 92 through 94 removed outlier: 5.300A pdb=" N SER E 150 " --> pdb=" O VAL E 197 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL E 197 " --> pdb=" O SER E 150 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE E 204 " --> pdb=" O VAL E 181 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 92 through 94 removed outlier: 5.300A pdb=" N SER E 150 " --> pdb=" O VAL E 197 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL E 197 " --> pdb=" O SER E 150 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AC2, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.575A pdb=" N GLU F 110 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU F 38 " --> pdb=" O TYR F 54 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TYR F 54 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TRP F 40 " --> pdb=" O LEU F 52 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.575A pdb=" N GLU F 110 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR F 102 " --> pdb=" O GLN F 95 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 119 through 123 removed outlier: 3.705A pdb=" N ASN F 142 " --> pdb=" O THR F 119 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TYR F 178 " --> pdb=" O ASN F 143 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER F 179 " --> pdb=" O THR F 169 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 158 through 159 removed outlier: 3.576A pdb=" N ASN F 150 " --> pdb=" O THR F 202 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS F 154 " --> pdb=" O THR F 198 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR F 198 " --> pdb=" O LYS F 154 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 4 through 7 removed outlier: 4.006A pdb=" N THR G 79 " --> pdb=" O ASP G 74 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 11 through 13 removed outlier: 3.534A pdb=" N MET G 13 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE G 35 " --> pdb=" O GLU G 51 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLU G 51 " --> pdb=" O ILE G 35 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N TRP G 37 " --> pdb=" O ILE G 49 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 127 through 130 removed outlier: 6.506A pdb=" N TYR G 182 " --> pdb=" O GLY G 151 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N SER G 185 " --> pdb=" O PRO G 174 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 142 through 145 removed outlier: 3.572A pdb=" N VAL G 143 " --> pdb=" O VAL G 190 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 158 through 160 removed outlier: 4.754A pdb=" N CYS G 202 " --> pdb=" O LYS G 215 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LYS G 215 " --> pdb=" O CYS G 202 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.569A pdb=" N GLU H 110 " --> pdb=" O LEU H 11 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY H 89 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU H 42 " --> pdb=" O LEU H 51 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LEU H 51 " --> pdb=" O LEU H 42 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 119 through 123 removed outlier: 3.573A pdb=" N VAL H 138 " --> pdb=" O PHE H 123 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL H 137 " --> pdb=" O LEU H 184 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N TYR H 178 " --> pdb=" O ASN H 143 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER H 179 " --> pdb=" O THR H 169 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 149 through 152 Processing sheet with id=AD6, first strand: chain 'H' and resid 154 through 155 Processing sheet with id=AD7, first strand: chain 'H' and resid 196 through 198 Processing sheet with id=AD8, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.535A pdb=" N VAL I 19 " --> pdb=" O LEU I 84 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR I 79 " --> pdb=" O ASP I 74 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 11 through 13 removed outlier: 6.424A pdb=" N ILE I 35 " --> pdb=" O GLU I 51 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLU I 51 " --> pdb=" O ILE I 35 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N TRP I 37 " --> pdb=" O ILE I 49 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 127 through 128 removed outlier: 6.508A pdb=" N TYR I 182 " --> pdb=" O GLY I 151 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL I 143 " --> pdb=" O VAL I 190 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 127 through 128 removed outlier: 6.508A pdb=" N TYR I 182 " --> pdb=" O GLY I 151 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER I 187 " --> pdb=" O HIS I 171 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 201 through 206 removed outlier: 4.395A pdb=" N CYS I 202 " --> pdb=" O LYS I 215 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LYS I 215 " --> pdb=" O CYS I 202 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AE5, first strand: chain 'J' and resid 10 through 12 removed outlier: 5.841A pdb=" N LEU J 11 " --> pdb=" O GLU J 110 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL J 90 " --> pdb=" O GLN J 43 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU J 38 " --> pdb=" O TYR J 54 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TYR J 54 " --> pdb=" O LEU J 38 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N TRP J 40 " --> pdb=" O LEU J 52 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 119 through 123 removed outlier: 3.793A pdb=" N VAL J 137 " --> pdb=" O LEU J 184 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N TYR J 178 " --> pdb=" O ASN J 143 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 119 through 123 removed outlier: 3.793A pdb=" N VAL J 137 " --> pdb=" O LEU J 184 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N TYR J 178 " --> pdb=" O ASN J 143 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N SER J 179 " --> pdb=" O THR J 169 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 149 through 152 removed outlier: 3.525A pdb=" N ASN J 150 " --> pdb=" O THR J 202 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR J 202 " --> pdb=" O ASN J 150 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS J 152 " --> pdb=" O GLU J 200 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 154 through 155 Processing sheet with id=AF1, first strand: chain 'J' and resid 196 through 198 Processing sheet with id=AF2, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.636A pdb=" N VAL K 19 " --> pdb=" O LEU K 84 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 11 through 13 removed outlier: 6.403A pdb=" N ILE K 35 " --> pdb=" O GLU K 51 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU K 51 " --> pdb=" O ILE K 35 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N TRP K 37 " --> pdb=" O ILE K 49 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 127 through 130 removed outlier: 3.527A pdb=" N LEU K 148 " --> pdb=" O TYR K 129 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL K 149 " --> pdb=" O LEU K 184 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N TYR K 182 " --> pdb=" O GLY K 151 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 142 through 144 removed outlier: 3.705A pdb=" N VAL K 143 " --> pdb=" O VAL K 190 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 202 through 206 removed outlier: 4.144A pdb=" N CYS K 202 " --> pdb=" O LYS K 215 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS K 215 " --> pdb=" O CYS K 202 " (cutoff:3.500A) 1287 hydrogen bonds defined for protein. 3588 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: 21.59 Time building geometry restraints manager: 15.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 25288 1.04 - 1.24: 3314 1.24 - 1.44: 8378 1.44 - 1.64: 14923 1.64 - 1.84: 210 Bond restraints: 52113 Sorted by residual: bond pdb=" N VAL E 92 " pdb=" CA VAL E 92 " ideal model delta sigma weight residual 1.460 1.492 -0.032 1.10e-02 8.26e+03 8.52e+00 bond pdb=" N ASN E 96 " pdb=" CA ASN E 96 " ideal model delta sigma weight residual 1.462 1.493 -0.032 1.15e-02 7.56e+03 7.57e+00 bond pdb=" N VAL D 36 " pdb=" CA VAL D 36 " ideal model delta sigma weight residual 1.460 1.489 -0.030 1.10e-02 8.26e+03 7.36e+00 bond pdb=" N ARG B 149 " pdb=" H ARG B 149 " ideal model delta sigma weight residual 0.860 0.914 -0.054 2.00e-02 2.50e+03 7.18e+00 bond pdb=" N TYR E 153 " pdb=" CA TYR E 153 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.22e-02 6.72e+03 7.17e+00 ... (remaining 52108 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.93: 93948 4.93 - 9.87: 25 9.87 - 14.80: 1 14.80 - 19.74: 0 19.74 - 24.67: 9 Bond angle restraints: 93983 Sorted by residual: angle pdb=" CB LEU I 53 " pdb=" CG LEU I 53 " pdb=" HG LEU I 53 " ideal model delta sigma weight residual 109.00 84.33 24.67 3.00e+00 1.11e-01 6.76e+01 angle pdb=" CB LEU G 53 " pdb=" CG LEU G 53 " pdb=" HG LEU G 53 " ideal model delta sigma weight residual 109.00 84.53 24.47 3.00e+00 1.11e-01 6.65e+01 angle pdb=" CB LEU K 53 " pdb=" CG LEU K 53 " pdb=" HG LEU K 53 " ideal model delta sigma weight residual 109.00 84.60 24.40 3.00e+00 1.11e-01 6.61e+01 angle pdb=" CD1 LEU I 53 " pdb=" CG LEU I 53 " pdb=" HG LEU I 53 " ideal model delta sigma weight residual 108.00 84.12 23.88 3.00e+00 1.11e-01 6.34e+01 angle pdb=" CD2 LEU I 53 " pdb=" CG LEU I 53 " pdb=" HG LEU I 53 " ideal model delta sigma weight residual 108.00 84.19 23.81 3.00e+00 1.11e-01 6.30e+01 ... (remaining 93978 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.86: 23539 21.86 - 43.72: 1225 43.72 - 65.57: 223 65.57 - 87.43: 54 87.43 - 109.29: 19 Dihedral angle restraints: 25060 sinusoidal: 13570 harmonic: 11490 Sorted by residual: dihedral pdb=" CB CYS J 23 " pdb=" SG CYS J 23 " pdb=" SG CYS J 93 " pdb=" CB CYS J 93 " ideal model delta sinusoidal sigma weight residual 93.00 -178.77 -88.23 1 1.00e+01 1.00e-02 9.30e+01 dihedral pdb=" CB CYS F 23 " pdb=" SG CYS F 23 " pdb=" SG CYS F 93 " pdb=" CB CYS F 93 " ideal model delta sinusoidal sigma weight residual 93.00 163.20 -70.20 1 1.00e+01 1.00e-02 6.35e+01 dihedral pdb=" CB CYS E 130 " pdb=" SG CYS E 130 " pdb=" SG CYS E 144 " pdb=" CB CYS E 144 " ideal model delta sinusoidal sigma weight residual 93.00 36.04 56.96 1 1.00e+01 1.00e-02 4.37e+01 ... (remaining 25057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.338: 4220 0.338 - 0.676: 0 0.676 - 1.014: 0 1.014 - 1.352: 0 1.352 - 1.690: 3 Chirality restraints: 4223 Sorted by residual: chirality pdb=" CG LEU K 53 " pdb=" CB LEU K 53 " pdb=" CD1 LEU K 53 " pdb=" CD2 LEU K 53 " both_signs ideal model delta sigma weight residual False -2.59 -0.90 -1.69 2.00e-01 2.50e+01 7.14e+01 chirality pdb=" CG LEU G 53 " pdb=" CB LEU G 53 " pdb=" CD1 LEU G 53 " pdb=" CD2 LEU G 53 " both_signs ideal model delta sigma weight residual False -2.59 -0.92 -1.67 2.00e-01 2.50e+01 7.00e+01 chirality pdb=" CG LEU I 53 " pdb=" CB LEU I 53 " pdb=" CD1 LEU I 53 " pdb=" CD2 LEU I 53 " both_signs ideal model delta sigma weight residual False -2.59 -0.94 -1.65 2.00e-01 2.50e+01 6.79e+01 ... (remaining 4220 not shown) Planarity restraints: 7554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 95 " -0.028 2.00e-02 2.50e+03 1.87e-02 1.05e+01 pdb=" CG TYR C 95 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR C 95 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR C 95 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR C 95 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR C 95 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR C 95 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR C 95 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 TYR C 95 " 0.003 2.00e-02 2.50e+03 pdb=" HD2 TYR C 95 " 0.004 2.00e-02 2.50e+03 pdb=" HE1 TYR C 95 " -0.002 2.00e-02 2.50e+03 pdb=" HE2 TYR C 95 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP E 91 " 0.016 2.00e-02 2.50e+03 2.93e-02 8.58e+00 pdb=" N VAL E 92 " -0.051 2.00e-02 2.50e+03 pdb=" CA VAL E 92 " 0.013 2.00e-02 2.50e+03 pdb=" H VAL E 92 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 593 " 0.047 5.00e-02 4.00e+02 7.10e-02 8.06e+00 pdb=" N PRO A 594 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 594 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 594 " 0.039 5.00e-02 4.00e+02 ... (remaining 7551 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 611 2.07 - 2.70: 80817 2.70 - 3.33: 145938 3.33 - 3.97: 192901 3.97 - 4.60: 299719 Nonbonded interactions: 719986 Sorted by model distance: nonbonded pdb=" HE2 LYS F 154 " pdb=" HA2 GLY F 157 " model vdw 1.437 2.440 nonbonded pdb=" O PRO H 125 " pdb="HH21 ARG I 220 " model vdw 1.443 2.450 nonbonded pdb="HH12 ARG G 48 " pdb=" OE1 GLU G 51 " model vdw 1.505 2.450 nonbonded pdb=" HZ2 LYS F 152 " pdb=" HD2 LYS F 154 " model vdw 1.531 2.270 nonbonded pdb=" HZ3 TRP J 101 " pdb=" OE1 GLU K 51 " model vdw 1.544 2.450 ... (remaining 719981 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' } ncs_group { reference = chain 'B' selection = chain 'C' selection = (chain 'E' and resid 1 through 449) } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.980 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: 0.860 Extract box with map and model: 1.740 Check model and map are aligned: 0.360 Set scattering table: 0.480 Process input model: 103.330 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 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 0.040 26794 Z= 0.281 Angle : 0.596 9.961 36521 Z= 0.316 Chirality : 0.064 1.690 4223 Planarity : 0.004 0.071 4527 Dihedral : 14.246 109.291 9922 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.15), residues: 3214 helix: 2.70 (0.18), residues: 765 sheet: -0.26 (0.17), residues: 995 loop : -0.39 (0.17), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 151 HIS 0.009 0.001 HIS E 329 PHE 0.021 0.002 PHE B 203 TYR 0.056 0.002 TYR C 95 ARG 0.006 0.001 ARG C 81 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 388 time to evaluate : 4.140 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 HIS cc_start: 0.7968 (t-170) cc_final: 0.7653 (m-70) REVERT: C 439 TRP cc_start: 0.7299 (m-10) cc_final: 0.6886 (m100) REVERT: D 332 MET cc_start: 0.8150 (ptm) cc_final: 0.7928 (ptm) REVERT: E 239 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7716 (mt-10) REVERT: E 417 ASP cc_start: 0.7463 (t70) cc_final: 0.7201 (t0) REVERT: F 101 TRP cc_start: 0.7561 (m-90) cc_final: 0.7296 (m-10) REVERT: F 180 MET cc_start: 0.5496 (tmm) cc_final: 0.4511 (ptm) REVERT: G 60 ASN cc_start: 0.7693 (m-40) cc_final: 0.7158 (m110) REVERT: G 64 LYS cc_start: 0.7283 (ttpp) cc_final: 0.7075 (tttp) REVERT: G 107 MET cc_start: 0.7922 (mtt) cc_final: 0.7501 (mtt) REVERT: G 142 MET cc_start: 0.0274 (tpp) cc_final: 0.0015 (tpp) REVERT: G 171 HIS cc_start: 0.4537 (m-70) cc_final: 0.4141 (m-70) REVERT: G 206 HIS cc_start: 0.4482 (t-170) cc_final: 0.4189 (t-90) REVERT: H 24 ARG cc_start: 0.6714 (ttm110) cc_final: 0.6404 (ttm-80) REVERT: H 79 LYS cc_start: 0.7097 (mmmm) cc_final: 0.6803 (mttp) REVERT: I 11 GLU cc_start: 0.7053 (mm-30) cc_final: 0.6579 (mp0) REVERT: J 3 LEU cc_start: 0.7944 (mt) cc_final: 0.7476 (tp) REVERT: J 9 LEU cc_start: 0.7323 (mt) cc_final: 0.7116 (tp) REVERT: K 11 GLU cc_start: 0.6690 (mm-30) cc_final: 0.5972 (mm-30) REVERT: K 85 SER cc_start: 0.6998 (t) cc_final: 0.6524 (p) REVERT: K 90 GLU cc_start: 0.4932 (tp30) cc_final: 0.4650 (tp30) REVERT: K 142 MET cc_start: 0.2771 (tpp) cc_final: 0.2348 (mmt) REVERT: K 213 VAL cc_start: 0.3175 (p) cc_final: 0.2849 (t) outliers start: 0 outliers final: 0 residues processed: 388 average time/residue: 2.9316 time to fit residues: 1321.4971 Evaluate side-chains 303 residues out of total 2941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 3.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 20.0000 chunk 241 optimal weight: 7.9990 chunk 133 optimal weight: 0.0000 chunk 82 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 249 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 chunk 151 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 288 optimal weight: 10.0000 overall best weight: 1.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 35 ASN F 43 GLN H 43 GLN I 4 GLN I 6 GLN I 203 ASN J 35 ASN J 58 ASN K 60 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26794 Z= 0.219 Angle : 0.561 10.406 36521 Z= 0.294 Chirality : 0.062 1.669 4223 Planarity : 0.005 0.056 4527 Dihedral : 7.399 76.816 3883 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.95 % Allowed : 6.39 % Favored : 92.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.55 (0.15), residues: 3214 helix: 2.70 (0.18), residues: 794 sheet: -0.24 (0.16), residues: 1001 loop : -0.48 (0.17), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 596 HIS 0.005 0.001 HIS F 194 PHE 0.015 0.001 PHE H 123 TYR 0.028 0.001 TYR C 95 ARG 0.005 0.000 ARG G 48 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 310 time to evaluate : 3.978 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: B 46 HIS cc_start: 0.7981 (t-170) cc_final: 0.7662 (m-70) REVERT: B 131 LYS cc_start: 0.8102 (mtpt) cc_final: 0.7650 (mmtm) REVERT: C 81 ARG cc_start: 0.8512 (mtt90) cc_final: 0.8274 (mtt90) REVERT: C 439 TRP cc_start: 0.7307 (m-10) cc_final: 0.6901 (m100) REVERT: D 332 MET cc_start: 0.8132 (ptm) cc_final: 0.7823 (ptm) REVERT: E 239 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7614 (mt-10) REVERT: E 249 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8192 (tp) REVERT: F 47 GLN cc_start: 0.6241 (mt0) cc_final: 0.5871 (mt0) REVERT: F 66 ARG cc_start: 0.5568 (ptt-90) cc_final: 0.5027 (ptp-170) REVERT: G 60 ASN cc_start: 0.7533 (m-40) cc_final: 0.6988 (t0) REVERT: G 107 MET cc_start: 0.7929 (mtt) cc_final: 0.7486 (mtt) REVERT: G 142 MET cc_start: 0.0277 (tpp) cc_final: -0.0120 (tpp) REVERT: G 171 HIS cc_start: 0.4550 (m-70) cc_final: 0.4184 (m-70) REVERT: G 206 HIS cc_start: 0.4361 (t-170) cc_final: 0.4083 (t-90) REVERT: H 1 ASP cc_start: 0.6457 (m-30) cc_final: 0.6233 (m-30) REVERT: H 24 ARG cc_start: 0.6684 (ttm110) cc_final: 0.6462 (ttp-170) REVERT: H 79 LYS cc_start: 0.7073 (mmmm) cc_final: 0.6767 (mttp) REVERT: H 84 GLU cc_start: 0.6351 (OUTLIER) cc_final: 0.5859 (mp0) REVERT: I 90 GLU cc_start: 0.6304 (OUTLIER) cc_final: 0.5962 (mt-10) REVERT: I 171 HIS cc_start: 0.4767 (m90) cc_final: 0.4482 (m-70) REVERT: J 3 LEU cc_start: 0.7977 (mt) cc_final: 0.7520 (tp) REVERT: K 78 LYS cc_start: 0.8439 (mtmt) cc_final: 0.8064 (mtmt) REVERT: K 85 SER cc_start: 0.7021 (t) cc_final: 0.6523 (p) REVERT: K 90 GLU cc_start: 0.4858 (tp30) cc_final: 0.4574 (tp30) REVERT: K 142 MET cc_start: 0.3179 (tpp) cc_final: 0.2314 (mmt) outliers start: 28 outliers final: 10 residues processed: 327 average time/residue: 2.8035 time to fit residues: 1077.1531 Evaluate side-chains 282 residues out of total 2941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 269 time to evaluate : 4.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain I residue 90 GLU Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain J residue 93 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 240 optimal weight: 7.9990 chunk 196 optimal weight: 3.9990 chunk 79 optimal weight: 0.2980 chunk 289 optimal weight: 9.9990 chunk 312 optimal weight: 7.9990 chunk 257 optimal weight: 0.1980 chunk 286 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 232 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 326 GLN D 169 HIS E 215 ASN I 6 GLN J 58 ASN K 60 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26794 Z= 0.205 Angle : 0.534 10.245 36521 Z= 0.275 Chirality : 0.062 1.688 4223 Planarity : 0.004 0.053 4527 Dihedral : 6.311 59.486 3883 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.02 % Allowed : 7.58 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.58 (0.15), residues: 3214 helix: 2.77 (0.18), residues: 794 sheet: -0.15 (0.16), residues: 1001 loop : -0.56 (0.17), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 101 HIS 0.005 0.001 HIS F 194 PHE 0.014 0.001 PHE I 153 TYR 0.019 0.001 TYR C 95 ARG 0.004 0.000 ARG D 171 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 278 time to evaluate : 3.701 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: A 286 PHE cc_start: 0.7996 (m-80) cc_final: 0.7605 (m-10) REVERT: B 46 HIS cc_start: 0.7938 (t-170) cc_final: 0.7652 (m-70) REVERT: B 216 LEU cc_start: 0.8756 (tp) cc_final: 0.8467 (tt) REVERT: C 16 ARG cc_start: 0.7233 (OUTLIER) cc_final: 0.6935 (ppt170) REVERT: C 439 TRP cc_start: 0.7331 (m-10) cc_final: 0.6917 (m100) REVERT: D 187 ASP cc_start: 0.8103 (t0) cc_final: 0.7857 (t0) REVERT: D 332 MET cc_start: 0.8124 (ptm) cc_final: 0.7720 (ptm) REVERT: E 249 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8255 (tp) REVERT: F 47 GLN cc_start: 0.6267 (mt0) cc_final: 0.5998 (mt0) REVERT: F 66 ARG cc_start: 0.5613 (ptt-90) cc_final: 0.5071 (ptp-170) REVERT: F 88 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6664 (mm) REVERT: G 60 ASN cc_start: 0.7534 (m-40) cc_final: 0.7041 (t0) REVERT: G 107 MET cc_start: 0.7954 (mtt) cc_final: 0.7502 (mtt) REVERT: G 142 MET cc_start: 0.0325 (tpp) cc_final: -0.0143 (tpp) REVERT: G 206 HIS cc_start: 0.4296 (t-170) cc_final: 0.4034 (t-90) REVERT: H 1 ASP cc_start: 0.6442 (m-30) cc_final: 0.6217 (m-30) REVERT: H 24 ARG cc_start: 0.6690 (ttm110) cc_final: 0.6404 (ttm-80) REVERT: H 50 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7823 (mptt) REVERT: H 84 GLU cc_start: 0.6496 (OUTLIER) cc_final: 0.6067 (mp0) REVERT: H 108 LYS cc_start: 0.7337 (OUTLIER) cc_final: 0.6345 (tptt) REVERT: I 171 HIS cc_start: 0.4770 (m90) cc_final: 0.4413 (m-70) REVERT: J 3 LEU cc_start: 0.8014 (mt) cc_final: 0.7579 (tp) REVERT: J 11 LEU cc_start: 0.7442 (tp) cc_final: 0.7114 (tt) REVERT: K 85 SER cc_start: 0.6969 (t) cc_final: 0.6494 (p) REVERT: K 90 GLU cc_start: 0.4992 (tp30) cc_final: 0.4692 (tp30) REVERT: K 142 MET cc_start: 0.3043 (tpp) cc_final: 0.2291 (mmt) outliers start: 30 outliers final: 11 residues processed: 298 average time/residue: 2.7929 time to fit residues: 991.3974 Evaluate side-chains 275 residues out of total 2941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 258 time to evaluate : 4.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain J residue 93 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 0.7980 chunk 217 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 290 optimal weight: 10.0000 chunk 307 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 275 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 326 GLN G 40 GLN I 6 GLN J 35 ASN J 58 ASN K 60 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26794 Z= 0.208 Angle : 0.528 10.361 36521 Z= 0.273 Chirality : 0.062 1.682 4223 Planarity : 0.004 0.052 4527 Dihedral : 5.546 45.155 3883 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.12 % Allowed : 8.94 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.58 (0.15), residues: 3214 helix: 2.77 (0.18), residues: 794 sheet: -0.12 (0.16), residues: 1001 loop : -0.59 (0.17), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 161 HIS 0.009 0.001 HIS G 171 PHE 0.013 0.001 PHE I 153 TYR 0.013 0.001 TYR C 95 ARG 0.004 0.000 ARG D 215 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 263 time to evaluate : 3.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.9267 (mtp) cc_final: 0.9054 (mtp) REVERT: B 46 HIS cc_start: 0.8028 (t-170) cc_final: 0.7826 (m-70) REVERT: B 131 LYS cc_start: 0.8112 (mtpt) cc_final: 0.7659 (mmtm) REVERT: B 216 LEU cc_start: 0.8762 (tp) cc_final: 0.8479 (tt) REVERT: C 16 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.6973 (ppt170) REVERT: C 439 TRP cc_start: 0.7331 (m-10) cc_final: 0.6901 (m100) REVERT: D 104 ASP cc_start: 0.6986 (t0) cc_final: 0.6612 (t0) REVERT: D 187 ASP cc_start: 0.8070 (t0) cc_final: 0.7854 (t0) REVERT: D 332 MET cc_start: 0.8123 (ptm) cc_final: 0.7706 (ptm) REVERT: D 573 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7586 (m-30) REVERT: E 249 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8237 (tp) REVERT: F 66 ARG cc_start: 0.5612 (ptt-90) cc_final: 0.5056 (ptp-170) REVERT: F 88 LEU cc_start: 0.7225 (OUTLIER) cc_final: 0.6361 (tm) REVERT: G 60 ASN cc_start: 0.7531 (m-40) cc_final: 0.7080 (t0) REVERT: G 107 MET cc_start: 0.8001 (mtt) cc_final: 0.7587 (mtt) REVERT: G 142 MET cc_start: 0.0346 (tpp) cc_final: 0.0002 (tpp) REVERT: G 206 HIS cc_start: 0.4284 (t-170) cc_final: 0.4012 (t-90) REVERT: H 1 ASP cc_start: 0.6443 (m-30) cc_final: 0.6189 (m-30) REVERT: H 24 ARG cc_start: 0.6696 (ttm110) cc_final: 0.6409 (ttm-80) REVERT: H 50 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7701 (mptt) REVERT: H 84 GLU cc_start: 0.6535 (OUTLIER) cc_final: 0.6104 (mm-30) REVERT: J 3 LEU cc_start: 0.8083 (mt) cc_final: 0.7640 (tp) REVERT: J 11 LEU cc_start: 0.7394 (tp) cc_final: 0.7044 (tt) REVERT: J 24 ARG cc_start: 0.7083 (mtm-85) cc_final: 0.6721 (mtm110) REVERT: K 85 SER cc_start: 0.7238 (t) cc_final: 0.6710 (p) REVERT: K 90 GLU cc_start: 0.4952 (tp30) cc_final: 0.4639 (tp30) REVERT: K 142 MET cc_start: 0.2820 (tpp) cc_final: 0.2166 (mmt) outliers start: 33 outliers final: 21 residues processed: 284 average time/residue: 2.6312 time to fit residues: 886.4622 Evaluate side-chains 281 residues out of total 2941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 254 time to evaluate : 3.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 573 ASP Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 93 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 228 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 chunk 262 optimal weight: 0.9990 chunk 212 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 156 optimal weight: 0.7980 chunk 275 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN C 326 GLN E 50 GLN E 215 ASN I 6 GLN K 60 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 26794 Z= 0.246 Angle : 0.542 10.436 36521 Z= 0.281 Chirality : 0.062 1.672 4223 Planarity : 0.004 0.054 4527 Dihedral : 5.274 43.766 3883 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.73 % Allowed : 9.32 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.53 (0.15), residues: 3214 helix: 2.70 (0.18), residues: 794 sheet: -0.10 (0.16), residues: 1001 loop : -0.64 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 565 HIS 0.005 0.001 HIS G 171 PHE 0.014 0.001 PHE A 262 TYR 0.014 0.001 TYR F 37 ARG 0.004 0.000 ARG D 215 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 266 time to evaluate : 4.130 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: A 151 MET cc_start: 0.9276 (mtp) cc_final: 0.9038 (mtp) REVERT: B 216 LEU cc_start: 0.8784 (tp) cc_final: 0.8505 (tt) REVERT: B 318 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8369 (mt) REVERT: C 16 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.7008 (ppt170) REVERT: C 268 ASP cc_start: 0.7669 (t0) cc_final: 0.7397 (m-30) REVERT: D 104 ASP cc_start: 0.7080 (t0) cc_final: 0.6765 (t0) REVERT: D 187 ASP cc_start: 0.8080 (t0) cc_final: 0.7824 (t0) REVERT: D 332 MET cc_start: 0.8124 (ptm) cc_final: 0.7690 (ptm) REVERT: E 249 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8305 (tp) REVERT: F 66 ARG cc_start: 0.5633 (ptt-90) cc_final: 0.5380 (pmm-80) REVERT: F 88 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.6375 (tm) REVERT: G 60 ASN cc_start: 0.7573 (m-40) cc_final: 0.7135 (t0) REVERT: G 142 MET cc_start: 0.0344 (tpp) cc_final: -0.0135 (tpp) REVERT: G 206 HIS cc_start: 0.4295 (t-170) cc_final: 0.4030 (t-90) REVERT: H 1 ASP cc_start: 0.6304 (m-30) cc_final: 0.6056 (m-30) REVERT: H 24 ARG cc_start: 0.6708 (ttm110) cc_final: 0.6420 (ttm-80) REVERT: H 39 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7302 (mt-10) REVERT: H 50 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7701 (mptt) REVERT: H 84 GLU cc_start: 0.6558 (OUTLIER) cc_final: 0.6130 (mm-30) REVERT: I 47 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7842 (mt-10) REVERT: I 90 GLU cc_start: 0.6261 (OUTLIER) cc_final: 0.5879 (mt-10) REVERT: J 3 LEU cc_start: 0.8178 (mt) cc_final: 0.7666 (tp) REVERT: J 9 LEU cc_start: 0.7115 (tp) cc_final: 0.6593 (mm) REVERT: J 11 LEU cc_start: 0.7410 (tp) cc_final: 0.7032 (tt) REVERT: J 24 ARG cc_start: 0.7091 (mtm-85) cc_final: 0.6761 (mtm110) REVERT: K 85 SER cc_start: 0.7018 (t) cc_final: 0.6556 (p) REVERT: K 90 GLU cc_start: 0.5017 (tp30) cc_final: 0.4696 (tp30) REVERT: K 142 MET cc_start: 0.2803 (tpp) cc_final: 0.2165 (mmt) REVERT: K 155 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6626 (mt-10) outliers start: 51 outliers final: 29 residues processed: 292 average time/residue: 2.7292 time to fit residues: 946.7084 Evaluate side-chains 292 residues out of total 2941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 254 time to evaluate : 4.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 573 ASP Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 90 GLU Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 93 CYS Chi-restraints excluded: chain K residue 107 MET Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 213 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 2.9990 chunk 276 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 307 optimal weight: 2.9990 chunk 255 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 161 optimal weight: 0.4980 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 326 GLN H 43 GLN I 6 GLN K 60 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 26794 Z= 0.264 Angle : 0.558 10.422 36521 Z= 0.290 Chirality : 0.062 1.661 4223 Planarity : 0.005 0.054 4527 Dihedral : 5.149 47.320 3883 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.84 % Allowed : 9.62 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.44 (0.15), residues: 3214 helix: 2.61 (0.18), residues: 794 sheet: -0.12 (0.16), residues: 1003 loop : -0.71 (0.16), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 168 HIS 0.005 0.001 HIS K 44 PHE 0.018 0.002 PHE I 153 TYR 0.020 0.002 TYR G 105 ARG 0.005 0.001 ARG D 215 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 263 time to evaluate : 3.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.9287 (mtp) cc_final: 0.9036 (mtp) REVERT: B 131 LYS cc_start: 0.8043 (mtpt) cc_final: 0.7591 (mmtm) REVERT: B 216 LEU cc_start: 0.8787 (tp) cc_final: 0.8527 (tt) REVERT: B 318 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8350 (mt) REVERT: C 16 ARG cc_start: 0.7257 (OUTLIER) cc_final: 0.7007 (ppt170) REVERT: C 268 ASP cc_start: 0.7618 (t0) cc_final: 0.7369 (m-30) REVERT: D 104 ASP cc_start: 0.7114 (t0) cc_final: 0.6897 (t0) REVERT: D 187 ASP cc_start: 0.8111 (t0) cc_final: 0.7851 (t0) REVERT: D 332 MET cc_start: 0.8120 (ptm) cc_final: 0.7803 (ptm) REVERT: E 249 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8304 (tp) REVERT: F 66 ARG cc_start: 0.5761 (ptt-90) cc_final: 0.5452 (pmm-80) REVERT: F 88 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6352 (tm) REVERT: G 107 MET cc_start: 0.8188 (mtt) cc_final: 0.7904 (mtt) REVERT: G 142 MET cc_start: 0.0557 (tpp) cc_final: 0.0105 (tpp) REVERT: G 206 HIS cc_start: 0.4326 (t-170) cc_final: 0.4009 (t-90) REVERT: H 24 ARG cc_start: 0.6764 (ttm110) cc_final: 0.6475 (ttm-80) REVERT: H 39 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7293 (mt-10) REVERT: H 44 LYS cc_start: 0.7688 (mtpt) cc_final: 0.7436 (mttm) REVERT: H 50 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7688 (mptt) REVERT: H 72 SER cc_start: 0.6587 (m) cc_final: 0.6384 (p) REVERT: H 84 GLU cc_start: 0.6458 (OUTLIER) cc_final: 0.6041 (mm-30) REVERT: I 47 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7867 (mt-10) REVERT: I 90 GLU cc_start: 0.6124 (OUTLIER) cc_final: 0.5773 (mt-10) REVERT: I 171 HIS cc_start: 0.4048 (m-70) cc_final: 0.3780 (m-70) REVERT: J 3 LEU cc_start: 0.8187 (mt) cc_final: 0.7355 (tt) REVERT: J 9 LEU cc_start: 0.7094 (tp) cc_final: 0.6588 (mm) REVERT: J 24 ARG cc_start: 0.7004 (mtm-85) cc_final: 0.6715 (mtm110) REVERT: K 85 SER cc_start: 0.7253 (t) cc_final: 0.6740 (p) REVERT: K 90 GLU cc_start: 0.5126 (tp30) cc_final: 0.4853 (tp30) REVERT: K 142 MET cc_start: 0.2897 (tpp) cc_final: 0.2307 (mmt) REVERT: K 155 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6622 (mt-10) outliers start: 54 outliers final: 26 residues processed: 294 average time/residue: 2.6255 time to fit residues: 914.8628 Evaluate side-chains 289 residues out of total 2941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 254 time to evaluate : 4.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 573 ASP Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 90 GLU Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain J residue 93 CYS Chi-restraints excluded: chain K residue 107 MET Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 213 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 224 optimal weight: 8.9990 chunk 174 optimal weight: 1.9990 chunk 259 optimal weight: 3.9990 chunk 171 optimal weight: 0.9980 chunk 306 optimal weight: 2.9990 chunk 191 optimal weight: 0.9990 chunk 186 optimal weight: 3.9990 chunk 141 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 326 GLN E 215 ASN F 35 ASN H 43 GLN H 58 ASN I 6 GLN J 27 GLN J 58 ASN J 171 GLN K 60 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26794 Z= 0.207 Angle : 0.531 10.482 36521 Z= 0.274 Chirality : 0.062 1.697 4223 Planarity : 0.004 0.052 4527 Dihedral : 4.935 46.481 3883 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.36 % Allowed : 10.81 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.50 (0.15), residues: 3214 helix: 2.73 (0.18), residues: 794 sheet: -0.10 (0.16), residues: 1003 loop : -0.70 (0.16), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 101 HIS 0.005 0.001 HIS C 297 PHE 0.018 0.001 PHE I 153 TYR 0.018 0.001 TYR G 105 ARG 0.004 0.000 ARG D 215 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 271 time to evaluate : 3.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.9286 (mtp) cc_final: 0.9036 (mtp) REVERT: B 131 LYS cc_start: 0.8188 (mtpt) cc_final: 0.7682 (mmtm) REVERT: B 216 LEU cc_start: 0.8767 (tp) cc_final: 0.8508 (tt) REVERT: B 318 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8386 (mt) REVERT: C 268 ASP cc_start: 0.7669 (t0) cc_final: 0.7429 (m-30) REVERT: D 187 ASP cc_start: 0.8063 (t0) cc_final: 0.7802 (t0) REVERT: D 332 MET cc_start: 0.8142 (ptm) cc_final: 0.7683 (ptm) REVERT: E 249 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8220 (tp) REVERT: F 66 ARG cc_start: 0.5813 (ptt-90) cc_final: 0.5502 (pmm-80) REVERT: F 88 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.6367 (tm) REVERT: G 107 MET cc_start: 0.8191 (mtt) cc_final: 0.7840 (mtt) REVERT: G 142 MET cc_start: 0.0631 (tpp) cc_final: 0.0217 (tpp) REVERT: G 206 HIS cc_start: 0.4331 (t-170) cc_final: 0.4066 (t-90) REVERT: H 24 ARG cc_start: 0.6750 (ttm110) cc_final: 0.6466 (ttm-80) REVERT: H 44 LYS cc_start: 0.7626 (mtpt) cc_final: 0.7372 (mttm) REVERT: H 50 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7676 (mptt) REVERT: H 84 GLU cc_start: 0.6463 (OUTLIER) cc_final: 0.6079 (mm-30) REVERT: I 47 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7869 (mt-10) REVERT: I 90 GLU cc_start: 0.6037 (OUTLIER) cc_final: 0.5693 (mt-10) REVERT: I 171 HIS cc_start: 0.4118 (m-70) cc_final: 0.3820 (m-70) REVERT: J 3 LEU cc_start: 0.8195 (mt) cc_final: 0.7355 (tt) REVERT: J 9 LEU cc_start: 0.7075 (tp) cc_final: 0.6584 (mm) REVERT: K 85 SER cc_start: 0.6984 (t) cc_final: 0.6557 (p) REVERT: K 90 GLU cc_start: 0.5059 (tp30) cc_final: 0.4781 (tp30) REVERT: K 142 MET cc_start: 0.2800 (tpp) cc_final: 0.2303 (mmt) REVERT: K 155 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6602 (mt-10) outliers start: 40 outliers final: 21 residues processed: 293 average time/residue: 2.7207 time to fit residues: 948.2776 Evaluate side-chains 289 residues out of total 2941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 261 time to evaluate : 4.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 90 GLU Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain J residue 93 CYS Chi-restraints excluded: chain K residue 107 MET Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 213 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 92 optimal weight: 0.1980 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 208 optimal weight: 10.0000 chunk 151 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 240 optimal weight: 8.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 35 ASN G 6 GLN H 58 ASN I 6 GLN J 171 GLN K 60 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26794 Z= 0.216 Angle : 0.531 10.464 36521 Z= 0.274 Chirality : 0.062 1.677 4223 Planarity : 0.004 0.053 4527 Dihedral : 4.915 47.906 3883 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.43 % Allowed : 11.15 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.51 (0.15), residues: 3214 helix: 2.73 (0.18), residues: 794 sheet: -0.07 (0.16), residues: 1003 loop : -0.72 (0.16), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 101 HIS 0.005 0.001 HIS F 194 PHE 0.019 0.001 PHE I 153 TYR 0.017 0.001 TYR G 105 ARG 0.006 0.000 ARG J 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 265 time to evaluate : 3.887 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: A 151 MET cc_start: 0.9284 (mtp) cc_final: 0.9035 (mtp) REVERT: B 131 LYS cc_start: 0.8184 (mtpt) cc_final: 0.7680 (mmtm) REVERT: B 216 LEU cc_start: 0.8772 (tp) cc_final: 0.8507 (tt) REVERT: B 318 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8424 (mt) REVERT: C 268 ASP cc_start: 0.7677 (t0) cc_final: 0.7440 (m-30) REVERT: D 187 ASP cc_start: 0.8095 (t0) cc_final: 0.7834 (t0) REVERT: D 332 MET cc_start: 0.8101 (ptm) cc_final: 0.7646 (ptm) REVERT: D 578 TRP cc_start: 0.7628 (m-10) cc_final: 0.7072 (m100) REVERT: E 249 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8296 (tp) REVERT: F 66 ARG cc_start: 0.5832 (ptt-90) cc_final: 0.5244 (ptp-170) REVERT: F 88 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6386 (tm) REVERT: G 142 MET cc_start: 0.0619 (tpp) cc_final: 0.0220 (tpp) REVERT: G 206 HIS cc_start: 0.4222 (t-170) cc_final: 0.3948 (t-90) REVERT: H 1 ASP cc_start: 0.6615 (m-30) cc_final: 0.6396 (m-30) REVERT: H 24 ARG cc_start: 0.6765 (ttm110) cc_final: 0.6483 (ttm-80) REVERT: H 44 LYS cc_start: 0.7622 (mtpt) cc_final: 0.7362 (mttm) REVERT: H 47 GLN cc_start: 0.7103 (OUTLIER) cc_final: 0.6649 (mt0) REVERT: H 50 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7681 (mptt) REVERT: H 84 GLU cc_start: 0.6466 (mp0) cc_final: 0.6096 (mm-30) REVERT: I 47 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7844 (mt-10) REVERT: I 90 GLU cc_start: 0.6032 (OUTLIER) cc_final: 0.5686 (mt-10) REVERT: I 105 TYR cc_start: 0.7870 (OUTLIER) cc_final: 0.7326 (p90) REVERT: I 171 HIS cc_start: 0.4111 (m-70) cc_final: 0.3846 (m-70) REVERT: J 3 LEU cc_start: 0.8198 (mt) cc_final: 0.7357 (tt) REVERT: J 9 LEU cc_start: 0.7084 (tp) cc_final: 0.6618 (mm) REVERT: K 85 SER cc_start: 0.7261 (t) cc_final: 0.6760 (p) REVERT: K 90 GLU cc_start: 0.5005 (tp30) cc_final: 0.4726 (tp30) REVERT: K 142 MET cc_start: 0.2954 (tpp) cc_final: 0.2314 (mmt) REVERT: K 155 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6582 (mt-10) outliers start: 42 outliers final: 24 residues processed: 289 average time/residue: 2.6811 time to fit residues: 915.1342 Evaluate side-chains 290 residues out of total 2941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 258 time to evaluate : 4.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 90 GLU Chi-restraints excluded: chain I residue 105 TYR Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain J residue 93 CYS Chi-restraints excluded: chain K residue 105 TYR Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 213 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 4.9990 chunk 293 optimal weight: 7.9990 chunk 267 optimal weight: 3.9990 chunk 285 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 224 optimal weight: 9.9990 chunk 87 optimal weight: 0.8980 chunk 258 optimal weight: 3.9990 chunk 270 optimal weight: 0.7980 chunk 284 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 35 ASN G 6 GLN H 35 ASN H 58 ASN I 6 GLN J 171 GLN K 60 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 26794 Z= 0.245 Angle : 0.549 10.419 36521 Z= 0.284 Chirality : 0.062 1.677 4223 Planarity : 0.005 0.054 4527 Dihedral : 5.035 50.747 3883 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.46 % Allowed : 11.46 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.47 (0.15), residues: 3214 helix: 2.66 (0.18), residues: 794 sheet: -0.07 (0.16), residues: 1001 loop : -0.74 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 101 HIS 0.005 0.001 HIS C 297 PHE 0.019 0.002 PHE I 153 TYR 0.020 0.001 TYR G 105 ARG 0.005 0.000 ARG D 215 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 260 time to evaluate : 4.035 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: A 151 MET cc_start: 0.9285 (mtp) cc_final: 0.9033 (mtp) REVERT: B 131 LYS cc_start: 0.8230 (mtpt) cc_final: 0.7722 (mmtm) REVERT: B 216 LEU cc_start: 0.8778 (tp) cc_final: 0.8520 (tt) REVERT: B 318 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8396 (mt) REVERT: C 268 ASP cc_start: 0.7688 (t0) cc_final: 0.7448 (m-30) REVERT: D 187 ASP cc_start: 0.8117 (t0) cc_final: 0.7854 (t0) REVERT: D 332 MET cc_start: 0.8089 (ptm) cc_final: 0.7632 (ptm) REVERT: D 578 TRP cc_start: 0.7644 (m-10) cc_final: 0.7091 (m100) REVERT: E 249 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8303 (tp) REVERT: F 66 ARG cc_start: 0.5805 (ptt-90) cc_final: 0.5429 (pmm-80) REVERT: F 88 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6381 (tm) REVERT: G 142 MET cc_start: 0.0708 (tpp) cc_final: 0.0363 (tpp) REVERT: H 24 ARG cc_start: 0.6755 (ttm110) cc_final: 0.6543 (ttp-170) REVERT: H 47 GLN cc_start: 0.7094 (OUTLIER) cc_final: 0.6663 (mt0) REVERT: H 50 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7680 (mptt) REVERT: H 84 GLU cc_start: 0.6490 (OUTLIER) cc_final: 0.6092 (mm-30) REVERT: I 47 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7842 (mt-10) REVERT: I 90 GLU cc_start: 0.6025 (OUTLIER) cc_final: 0.5685 (mt-10) REVERT: I 105 TYR cc_start: 0.7928 (OUTLIER) cc_final: 0.7373 (p90) REVERT: I 171 HIS cc_start: 0.4163 (m-70) cc_final: 0.3869 (m-70) REVERT: J 3 LEU cc_start: 0.8201 (mt) cc_final: 0.7314 (tt) REVERT: J 9 LEU cc_start: 0.7073 (tp) cc_final: 0.6614 (mm) REVERT: J 195 ASN cc_start: 0.4942 (m-40) cc_final: 0.4352 (p0) REVERT: K 85 SER cc_start: 0.6995 (t) cc_final: 0.6570 (p) REVERT: K 90 GLU cc_start: 0.4992 (tp30) cc_final: 0.4707 (tp30) REVERT: K 142 MET cc_start: 0.2930 (tpp) cc_final: 0.2375 (mmt) REVERT: K 155 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6558 (mt-10) outliers start: 43 outliers final: 26 residues processed: 286 average time/residue: 2.7536 time to fit residues: 938.3521 Evaluate side-chains 291 residues out of total 2941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 256 time to evaluate : 3.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 90 GLU Chi-restraints excluded: chain I residue 105 TYR Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain J residue 93 CYS Chi-restraints excluded: chain K residue 105 TYR Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 213 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 10.0000 chunk 302 optimal weight: 1.9990 chunk 184 optimal weight: 0.9990 chunk 143 optimal weight: 0.7980 chunk 209 optimal weight: 9.9990 chunk 316 optimal weight: 3.9990 chunk 291 optimal weight: 7.9990 chunk 252 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 194 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 35 ASN G 6 GLN H 58 ASN I 6 GLN J 171 GLN K 60 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26794 Z= 0.182 Angle : 0.518 10.505 36521 Z= 0.267 Chirality : 0.062 1.687 4223 Planarity : 0.004 0.052 4527 Dihedral : 4.859 48.754 3883 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.22 % Allowed : 11.90 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.57 (0.15), residues: 3214 helix: 2.81 (0.18), residues: 794 sheet: -0.00 (0.16), residues: 998 loop : -0.73 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 101 HIS 0.005 0.001 HIS G 206 PHE 0.018 0.001 PHE I 153 TYR 0.013 0.001 TYR G 105 ARG 0.002 0.000 ARG A 171 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 258 time to evaluate : 3.810 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: A 151 MET cc_start: 0.9294 (mtp) cc_final: 0.9045 (mtp) REVERT: B 91 ASP cc_start: 0.7843 (m-30) cc_final: 0.7596 (m-30) REVERT: B 131 LYS cc_start: 0.8194 (mtpt) cc_final: 0.7694 (mmtm) REVERT: B 216 LEU cc_start: 0.8751 (tp) cc_final: 0.8490 (tt) REVERT: B 318 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8432 (mt) REVERT: C 268 ASP cc_start: 0.7792 (t0) cc_final: 0.7564 (m-30) REVERT: D 187 ASP cc_start: 0.8046 (t0) cc_final: 0.7783 (t0) REVERT: D 332 MET cc_start: 0.8095 (ptm) cc_final: 0.7635 (ptm) REVERT: D 578 TRP cc_start: 0.7614 (m-10) cc_final: 0.7066 (m100) REVERT: E 249 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8203 (tp) REVERT: F 66 ARG cc_start: 0.5560 (ptt-90) cc_final: 0.5236 (pmm-80) REVERT: F 88 LEU cc_start: 0.7129 (OUTLIER) cc_final: 0.6326 (tm) REVERT: G 142 MET cc_start: 0.0739 (tpp) cc_final: 0.0391 (tpp) REVERT: H 24 ARG cc_start: 0.6741 (ttm110) cc_final: 0.6536 (ttp-170) REVERT: H 50 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7674 (mptt) REVERT: H 84 GLU cc_start: 0.6604 (OUTLIER) cc_final: 0.6229 (mm-30) REVERT: I 47 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7850 (mt-10) REVERT: I 105 TYR cc_start: 0.7832 (OUTLIER) cc_final: 0.7359 (p90) REVERT: I 171 HIS cc_start: 0.4155 (m-70) cc_final: 0.3883 (m-70) REVERT: J 3 LEU cc_start: 0.8198 (mt) cc_final: 0.7319 (tt) REVERT: J 9 LEU cc_start: 0.7045 (tp) cc_final: 0.6575 (mm) REVERT: J 195 ASN cc_start: 0.5198 (m-40) cc_final: 0.4436 (p0) REVERT: K 85 SER cc_start: 0.7181 (t) cc_final: 0.6707 (p) REVERT: K 90 GLU cc_start: 0.4979 (tp30) cc_final: 0.4699 (tp30) REVERT: K 142 MET cc_start: 0.2906 (tpp) cc_final: 0.2352 (mmt) REVERT: K 155 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6533 (mt-10) outliers start: 36 outliers final: 24 residues processed: 281 average time/residue: 2.8254 time to fit residues: 956.0419 Evaluate side-chains 286 residues out of total 2941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 255 time to evaluate : 4.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 181 SER Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 105 TYR Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain J residue 93 CYS Chi-restraints excluded: chain K residue 105 TYR Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 213 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 9.9990 chunk 268 optimal weight: 30.0000 chunk 77 optimal weight: 1.9990 chunk 232 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 252 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 259 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 35 ASN G 6 GLN H 58 ASN I 6 GLN J 171 GLN K 60 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.156379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.097846 restraints weight = 88921.748| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.98 r_work: 0.2944 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 26794 Z= 0.234 Angle : 0.543 10.427 36521 Z= 0.281 Chirality : 0.062 1.676 4223 Planarity : 0.004 0.053 4527 Dihedral : 4.946 50.184 3883 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.33 % Allowed : 11.93 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.52 (0.15), residues: 3214 helix: 2.72 (0.18), residues: 794 sheet: -0.00 (0.16), residues: 998 loop : -0.75 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 101 HIS 0.009 0.001 HIS G 206 PHE 0.018 0.001 PHE I 153 TYR 0.016 0.001 TYR G 105 ARG 0.004 0.000 ARG D 215 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17086.20 seconds wall clock time: 309 minutes 23.70 seconds (18563.70 seconds total)