Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 19:34:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl1_25188/04_2023/7sl1_25188_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl1_25188/04_2023/7sl1_25188.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl1_25188/04_2023/7sl1_25188.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl1_25188/04_2023/7sl1_25188.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl1_25188/04_2023/7sl1_25188_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl1_25188/04_2023/7sl1_25188_neut.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 12534 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 110 5.16 5 C 8774 2.51 5 N 2374 2.21 5 O 2572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 576": "OD1" <-> "OD2" Residue "A PHE 868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 576": "OD1" <-> "OD2" Residue "B TYR 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 857": "OE1" <-> "OE2" Residue "B PHE 868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 13830 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 813, 6566 Classifications: {'peptide': 813} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 769} Chain breaks: 5 Chain: "B" Number of atoms: 6566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 813, 6566 Classifications: {'peptide': 813} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 769} Chain breaks: 5 Chain: "C" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 185 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "D" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 185 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "E" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 164 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Chain: "F" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 164 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Time building chain proxies: 7.43, per 1000 atoms: 0.54 Number of scatterers: 13830 At special positions: 0 Unit cell: (155.21, 108.73, 141.93, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 110 16.00 O 2572 8.00 N 2374 7.00 C 8774 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 159 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 188 " distance=2.04 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 304 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 468 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 862 " distance=2.03 Simple disulfide: pdb=" SG CYS A 788 " - pdb=" SG CYS A 797 " distance=2.04 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 26 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 188 " distance=2.03 Simple disulfide: pdb=" SG CYS B 192 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 274 " distance=2.04 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 304 " - pdb=" SG CYS B 308 " distance=2.03 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 435 " - pdb=" SG CYS B 468 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 862 " distance=2.03 Simple disulfide: pdb=" SG CYS B 788 " - pdb=" SG CYS B 797 " distance=2.04 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS E 7 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS E 20 " distance=2.03 Simple disulfide: pdb=" SG CYS D 7 " - pdb=" SG CYS F 7 " distance=2.03 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS F 20 " distance=2.03 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 11 " distance=2.03 Simple disulfide: pdb=" SG CYS F 6 " - pdb=" SG CYS F 11 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.34 Conformation dependent library (CDL) restraints added in 1.9 seconds 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3228 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 32 sheets defined 13.9% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 16 through 24 removed outlier: 4.195A pdb=" N ARG A 19 " --> pdb=" O ASN A 16 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N HIS A 21 " --> pdb=" O THR A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 47 removed outlier: 3.520A pdb=" N ARG A 47 " --> pdb=" O GLU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 268 removed outlier: 4.182A pdb=" N ASN A 268 " --> pdb=" O PHE A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 330 removed outlier: 3.574A pdb=" N ALA A 327 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 359 Processing helix chain 'A' and resid 435 through 446 removed outlier: 3.833A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 640 through 644 Processing helix chain 'A' and resid 692 through 711 Processing helix chain 'A' and resid 865 through 872 Processing helix chain 'B' and resid 16 through 24 removed outlier: 4.183A pdb=" N ARG B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N HIS B 21 " --> pdb=" O THR B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 47 removed outlier: 3.523A pdb=" N ARG B 47 " --> pdb=" O GLU B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 268 removed outlier: 4.217A pdb=" N ASN B 268 " --> pdb=" O PHE B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 318 Processing helix chain 'B' and resid 323 through 330 removed outlier: 3.595A pdb=" N ALA B 327 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU B 329 " --> pdb=" O THR B 325 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 359 Processing helix chain 'B' and resid 435 through 446 removed outlier: 3.813A pdb=" N ILE B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 640 through 644 Processing helix chain 'B' and resid 692 through 711 Processing helix chain 'B' and resid 865 through 872 Processing helix chain 'C' and resid 8 through 19 Processing helix chain 'D' and resid 8 through 19 Processing helix chain 'E' and resid 2 through 7 removed outlier: 3.549A pdb=" N CYS E 7 " --> pdb=" O GLU E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 18 Processing helix chain 'F' and resid 2 through 7 removed outlier: 3.563A pdb=" N CYS F 7 " --> pdb=" O GLU F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 18 Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 14 removed outlier: 7.007A pdb=" N CYS A 8 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N HIS A 32 " --> pdb=" O CYS A 8 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLY A 10 " --> pdb=" O HIS A 32 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N GLN A 34 " --> pdb=" O GLY A 10 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ASP A 12 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU A 36 " --> pdb=" O ASP A 12 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ARG A 14 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N MET A 38 " --> pdb=" O ARG A 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 7 through 14 removed outlier: 7.007A pdb=" N CYS A 8 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N HIS A 32 " --> pdb=" O CYS A 8 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLY A 10 " --> pdb=" O HIS A 32 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N GLN A 34 " --> pdb=" O GLY A 10 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ASP A 12 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU A 36 " --> pdb=" O ASP A 12 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ARG A 14 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N MET A 38 " --> pdb=" O ARG A 14 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N LEU A 62 " --> pdb=" O GLY A 31 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU A 33 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N PHE A 64 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE A 35 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N VAL A 66 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N LEU A 37 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU A 61 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N PHE A 96 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU A 63 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ARG A 118 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL A 94 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N GLU A 120 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N PHE A 96 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ASN A 122 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ASN A 148 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 172 removed outlier: 3.538A pdb=" N THR A 172 " --> pdb=" O VAL A 179 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 231 through 233 Processing sheet with id=AA5, first strand: chain 'A' and resid 245 through 248 Processing sheet with id=AA6, first strand: chain 'A' and resid 278 through 280 Processing sheet with id=AA7, first strand: chain 'A' and resid 292 through 294 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 321 removed outlier: 6.764A pdb=" N VAL A 335 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N GLN A 313 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ASN A 337 " --> pdb=" O GLN A 313 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU A 315 " --> pdb=" O ASN A 337 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N SER A 339 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N GLY A 317 " --> pdb=" O SER A 339 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE A 341 " --> pdb=" O GLY A 317 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LYS A 319 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 311 through 321 removed outlier: 6.764A pdb=" N VAL A 335 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N GLN A 313 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ASN A 337 " --> pdb=" O GLN A 313 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU A 315 " --> pdb=" O ASN A 337 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N SER A 339 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N GLY A 317 " --> pdb=" O SER A 339 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE A 341 " --> pdb=" O GLY A 317 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LYS A 319 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N LYS A 369 " --> pdb=" O GLY A 338 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU A 340 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ARG A 371 " --> pdb=" O LEU A 340 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ILE A 342 " --> pdb=" O ARG A 371 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N LYS A 425 " --> pdb=" O TYR A 398 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE A 400 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 471 through 473 removed outlier: 6.329A pdb=" N GLU A 471 " --> pdb=" O LYS A 584 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 475 through 480 removed outlier: 3.797A pdb=" N PHE A 477 " --> pdb=" O ARG A 488 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A 479 " --> pdb=" O LEU A 486 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 530 through 534 removed outlier: 3.567A pdb=" N GLY A 502 " --> pdb=" O LEU A 571 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 604 through 607 removed outlier: 3.805A pdb=" N ILE A 613 " --> pdb=" O ILE A 772 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 761 through 765 Processing sheet with id=AB6, first strand: chain 'A' and resid 830 through 832 Processing sheet with id=AB7, first strand: chain 'A' and resid 858 through 864 removed outlier: 3.790A pdb=" N LEU A 846 " --> pdb=" O THR A 891 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU A 848 " --> pdb=" O ARG A 889 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG A 889 " --> pdb=" O GLU A 848 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE A 905 " --> pdb=" O TYR A 884 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 7 through 14 removed outlier: 7.010A pdb=" N CYS B 8 " --> pdb=" O GLU B 30 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N HIS B 32 " --> pdb=" O CYS B 8 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLY B 10 " --> pdb=" O HIS B 32 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N GLN B 34 " --> pdb=" O GLY B 10 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ASP B 12 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LEU B 36 " --> pdb=" O ASP B 12 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ARG B 14 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N MET B 38 " --> pdb=" O ARG B 14 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 7 through 14 removed outlier: 7.010A pdb=" N CYS B 8 " --> pdb=" O GLU B 30 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N HIS B 32 " --> pdb=" O CYS B 8 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLY B 10 " --> pdb=" O HIS B 32 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N GLN B 34 " --> pdb=" O GLY B 10 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ASP B 12 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LEU B 36 " --> pdb=" O ASP B 12 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ARG B 14 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N MET B 38 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N LEU B 62 " --> pdb=" O GLY B 31 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU B 33 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N PHE B 64 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE B 35 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N VAL B 66 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N LEU B 37 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU B 61 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N PHE B 96 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU B 63 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ARG B 118 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL B 94 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N GLU B 120 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N PHE B 96 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ASN B 122 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ASN B 148 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 171 through 172 removed outlier: 3.537A pdb=" N THR B 172 " --> pdb=" O VAL B 179 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 231 through 233 Processing sheet with id=AC3, first strand: chain 'B' and resid 245 through 248 Processing sheet with id=AC4, first strand: chain 'B' and resid 278 through 280 Processing sheet with id=AC5, first strand: chain 'B' and resid 292 through 294 Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 313 removed outlier: 6.925A pdb=" N CYS B 312 " --> pdb=" O ASN B 337 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 319 through 321 removed outlier: 6.176A pdb=" N LYS B 319 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU B 340 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ARG B 371 " --> pdb=" O LEU B 340 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ILE B 342 " --> pdb=" O ARG B 371 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N LYS B 425 " --> pdb=" O TYR B 398 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE B 400 " --> pdb=" O LYS B 425 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 471 through 473 removed outlier: 6.329A pdb=" N GLU B 471 " --> pdb=" O LYS B 584 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 475 through 480 removed outlier: 6.612A pdb=" N ARG B 488 " --> pdb=" O SER B 476 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE B 478 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU B 486 " --> pdb=" O ILE B 478 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 530 through 534 removed outlier: 3.586A pdb=" N GLY B 502 " --> pdb=" O LEU B 571 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 604 through 607 removed outlier: 3.636A pdb=" N ILE B 613 " --> pdb=" O ILE B 772 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 761 through 765 Processing sheet with id=AD4, first strand: chain 'B' and resid 830 through 832 Processing sheet with id=AD5, first strand: chain 'B' and resid 858 through 864 removed outlier: 3.787A pdb=" N LEU B 846 " --> pdb=" O THR B 891 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU B 848 " --> pdb=" O ARG B 889 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG B 889 " --> pdb=" O GLU B 848 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG B 852 " --> pdb=" O SER B 885 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE B 905 " --> pdb=" O TYR B 884 " (cutoff:3.500A) 317 hydrogen bonds defined for protein. 798 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: 5.10 Time building geometry restraints manager: 5.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4533 1.35 - 1.47: 3389 1.47 - 1.59: 6108 1.59 - 1.71: 0 1.71 - 1.83: 134 Bond restraints: 14164 Sorted by residual: bond pdb=" N ASP B 234 " pdb=" CA ASP B 234 " ideal model delta sigma weight residual 1.457 1.474 -0.016 1.29e-02 6.01e+03 1.62e+00 bond pdb=" CA GLN B 538 " pdb=" CB GLN B 538 " ideal model delta sigma weight residual 1.523 1.537 -0.014 1.21e-02 6.83e+03 1.28e+00 bond pdb=" N TYR A 144 " pdb=" CA TYR A 144 " ideal model delta sigma weight residual 1.465 1.451 0.014 1.31e-02 5.83e+03 1.13e+00 bond pdb=" CA ASP B 464 " pdb=" C ASP B 464 " ideal model delta sigma weight residual 1.520 1.515 0.005 4.80e-03 4.34e+04 9.56e-01 bond pdb=" CG GLU B 391 " pdb=" CD GLU B 391 " ideal model delta sigma weight residual 1.516 1.539 -0.023 2.50e-02 1.60e+03 8.78e-01 ... (remaining 14159 not shown) Histogram of bond angle deviations from ideal: 99.19 - 106.16: 383 106.16 - 113.12: 7457 113.12 - 120.08: 4903 120.08 - 127.05: 6251 127.05 - 134.01: 192 Bond angle restraints: 19186 Sorted by residual: angle pdb=" C THR A 167 " pdb=" N ASN A 168 " pdb=" CA ASN A 168 " ideal model delta sigma weight residual 121.54 129.44 -7.90 1.91e+00 2.74e-01 1.71e+01 angle pdb=" C THR B 167 " pdb=" N ASN B 168 " pdb=" CA ASN B 168 " ideal model delta sigma weight residual 121.54 129.43 -7.89 1.91e+00 2.74e-01 1.71e+01 angle pdb=" C ARG A 454 " pdb=" N ASN A 455 " pdb=" CA ASN A 455 " ideal model delta sigma weight residual 121.54 127.38 -5.84 1.91e+00 2.74e-01 9.35e+00 angle pdb=" C ARG B 454 " pdb=" N ASN B 455 " pdb=" CA ASN B 455 " ideal model delta sigma weight residual 121.54 127.33 -5.79 1.91e+00 2.74e-01 9.20e+00 angle pdb=" C PRO B 837 " pdb=" N LYS B 838 " pdb=" CA LYS B 838 " ideal model delta sigma weight residual 120.38 124.71 -4.33 1.46e+00 4.69e-01 8.82e+00 ... (remaining 19181 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 7633 17.12 - 34.25: 782 34.25 - 51.37: 156 51.37 - 68.49: 23 68.49 - 85.61: 8 Dihedral angle restraints: 8602 sinusoidal: 3600 harmonic: 5002 Sorted by residual: dihedral pdb=" CB CYS A 169 " pdb=" SG CYS A 169 " pdb=" SG CYS A 188 " pdb=" CB CYS A 188 " ideal model delta sinusoidal sigma weight residual -86.00 -159.08 73.08 1 1.00e+01 1.00e-02 6.81e+01 dihedral pdb=" CB CYS B 169 " pdb=" SG CYS B 169 " pdb=" SG CYS B 188 " pdb=" CB CYS B 188 " ideal model delta sinusoidal sigma weight residual -86.00 -158.95 72.95 1 1.00e+01 1.00e-02 6.79e+01 dihedral pdb=" CB CYS A 435 " pdb=" SG CYS A 435 " pdb=" SG CYS A 468 " pdb=" CB CYS A 468 " ideal model delta sinusoidal sigma weight residual 93.00 163.28 -70.28 1 1.00e+01 1.00e-02 6.36e+01 ... (remaining 8599 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1198 0.028 - 0.056: 506 0.056 - 0.083: 191 0.083 - 0.111: 128 0.111 - 0.139: 53 Chirality restraints: 2076 Sorted by residual: chirality pdb=" CA ILE A 388 " pdb=" N ILE A 388 " pdb=" C ILE A 388 " pdb=" CB ILE A 388 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" CA ILE A 341 " pdb=" N ILE A 341 " pdb=" C ILE A 341 " pdb=" CB ILE A 341 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA ILE B 341 " pdb=" N ILE B 341 " pdb=" C ILE B 341 " pdb=" CB ILE B 341 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 2073 not shown) Planarity restraints: 2480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 169 " -0.031 5.00e-02 4.00e+02 4.75e-02 3.61e+00 pdb=" N PRO A 170 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 170 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 170 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 169 " -0.031 5.00e-02 4.00e+02 4.73e-02 3.59e+00 pdb=" N PRO B 170 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 170 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 170 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 16 " -0.009 2.00e-02 2.50e+03 1.23e-02 3.00e+00 pdb=" CG TYR C 16 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR C 16 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR C 16 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR C 16 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR C 16 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR C 16 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 16 " 0.000 2.00e-02 2.50e+03 ... (remaining 2477 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 677 2.73 - 3.27: 13737 3.27 - 3.81: 22587 3.81 - 4.36: 28015 4.36 - 4.90: 46799 Nonbonded interactions: 111815 Sorted by model distance: nonbonded pdb=" OD1 ASN B 295 " pdb=" OG SER B 297 " model vdw 2.186 2.440 nonbonded pdb=" OE1 GLN A 406 " pdb=" NE2 GLN B 406 " model vdw 2.188 2.520 nonbonded pdb=" OD1 ASN A 295 " pdb=" OG SER A 297 " model vdw 2.192 2.440 nonbonded pdb=" OG SER A 399 " pdb=" O GLN A 423 " model vdw 2.195 2.440 nonbonded pdb=" OG SER B 399 " pdb=" O GLN B 423 " model vdw 2.200 2.440 ... (remaining 111810 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.010 Extract box with map and model: 10.730 Check model and map are aligned: 0.200 Set scattering table: 0.110 Process input model: 37.090 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 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 : 0.002 0.045 14164 Z= 0.158 Angle : 0.597 10.038 19186 Z= 0.316 Chirality : 0.044 0.139 2076 Planarity : 0.003 0.048 2480 Dihedral : 13.617 85.613 5248 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.79 % Favored : 91.97 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.21), residues: 1682 helix: 0.30 (0.41), residues: 180 sheet: -0.83 (0.27), residues: 384 loop : -0.80 (0.20), residues: 1118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.669 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.2720 time to fit residues: 46.1923 Evaluate side-chains 83 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.654 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 8.9990 chunk 128 optimal weight: 0.8980 chunk 71 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 133 optimal weight: 4.9990 chunk 51 optimal weight: 0.0970 chunk 81 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 154 optimal weight: 7.9990 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 ASN ** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 455 ASN ** B 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.095 14164 Z= 0.379 Angle : 0.670 10.871 19186 Z= 0.344 Chirality : 0.047 0.162 2076 Planarity : 0.004 0.051 2480 Dihedral : 5.099 23.913 1870 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.21), residues: 1682 helix: 0.38 (0.39), residues: 176 sheet: -0.74 (0.26), residues: 410 loop : -1.01 (0.20), residues: 1096 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 101 time to evaluate : 1.719 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 103 average time/residue: 0.2758 time to fit residues: 43.2751 Evaluate side-chains 90 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 85 time to evaluate : 1.716 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1584 time to fit residues: 3.6123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 128 optimal weight: 0.0370 chunk 105 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 154 optimal weight: 10.0000 chunk 167 optimal weight: 0.8980 chunk 137 optimal weight: 0.9990 chunk 153 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 overall best weight: 0.7658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 14164 Z= 0.175 Angle : 0.576 11.039 19186 Z= 0.294 Chirality : 0.044 0.151 2076 Planarity : 0.003 0.049 2480 Dihedral : 4.768 21.793 1870 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.21), residues: 1682 helix: 0.44 (0.40), residues: 180 sheet: -0.68 (0.26), residues: 408 loop : -0.96 (0.20), residues: 1094 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 1.639 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 97 average time/residue: 0.2571 time to fit residues: 38.3616 Evaluate side-chains 85 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 1.610 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1608 time to fit residues: 3.5523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 7.9990 chunk 116 optimal weight: 5.9990 chunk 80 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 164 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN ** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 GLN ** B 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 ASN F 21 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.099 14164 Z= 0.438 Angle : 0.664 10.576 19186 Z= 0.340 Chirality : 0.047 0.155 2076 Planarity : 0.004 0.050 2480 Dihedral : 5.228 24.589 1870 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.21), residues: 1682 helix: 0.06 (0.38), residues: 192 sheet: -0.83 (0.26), residues: 408 loop : -1.13 (0.20), residues: 1082 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 80 time to evaluate : 1.592 Fit side-chains outliers start: 20 outliers final: 12 residues processed: 95 average time/residue: 0.2341 time to fit residues: 35.9054 Evaluate side-chains 86 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 74 time to evaluate : 1.719 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1287 time to fit residues: 5.2753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 67 optimal weight: 9.9990 chunk 140 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 83 optimal weight: 0.0970 chunk 147 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 14164 Z= 0.175 Angle : 0.578 13.138 19186 Z= 0.291 Chirality : 0.044 0.149 2076 Planarity : 0.003 0.043 2480 Dihedral : 4.847 21.736 1870 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.21), residues: 1682 helix: 0.35 (0.39), residues: 192 sheet: -0.68 (0.26), residues: 398 loop : -1.04 (0.20), residues: 1092 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 82 time to evaluate : 1.684 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 87 average time/residue: 0.2425 time to fit residues: 33.7539 Evaluate side-chains 77 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.658 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 164 optimal weight: 0.9980 chunk 136 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 ASN ** B 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 14164 Z= 0.261 Angle : 0.595 13.337 19186 Z= 0.300 Chirality : 0.045 0.148 2076 Planarity : 0.003 0.043 2480 Dihedral : 4.936 21.520 1870 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.21), residues: 1682 helix: 0.61 (0.40), residues: 180 sheet: -0.69 (0.26), residues: 408 loop : -1.00 (0.20), residues: 1094 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 77 time to evaluate : 1.840 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 84 average time/residue: 0.2450 time to fit residues: 33.4889 Evaluate side-chains 79 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 73 time to evaluate : 1.800 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1446 time to fit residues: 3.9902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 163 optimal weight: 0.5980 chunk 102 optimal weight: 10.0000 chunk 99 optimal weight: 0.9990 chunk 75 optimal weight: 20.0000 chunk 101 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 14164 Z= 0.215 Angle : 0.581 11.857 19186 Z= 0.294 Chirality : 0.045 0.180 2076 Planarity : 0.003 0.046 2480 Dihedral : 4.899 21.176 1870 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.21), residues: 1682 helix: 0.70 (0.40), residues: 180 sheet: -0.62 (0.26), residues: 398 loop : -1.01 (0.20), residues: 1104 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 1.775 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 83 average time/residue: 0.2515 time to fit residues: 33.7087 Evaluate side-chains 76 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 1.795 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1329 time to fit residues: 2.7215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 128 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 14164 Z= 0.237 Angle : 0.586 12.174 19186 Z= 0.296 Chirality : 0.045 0.175 2076 Planarity : 0.003 0.045 2480 Dihedral : 4.949 20.984 1870 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.21), residues: 1682 helix: 0.79 (0.40), residues: 178 sheet: -0.69 (0.26), residues: 408 loop : -1.02 (0.20), residues: 1096 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 81 time to evaluate : 1.675 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 88 average time/residue: 0.2300 time to fit residues: 33.3161 Evaluate side-chains 78 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 1.610 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1659 time to fit residues: 3.0525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 10.0000 chunk 143 optimal weight: 0.9990 chunk 152 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 119 optimal weight: 0.3980 chunk 46 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 144 optimal weight: 8.9990 chunk 100 optimal weight: 9.9990 chunk 161 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 14164 Z= 0.275 Angle : 0.610 11.404 19186 Z= 0.309 Chirality : 0.046 0.188 2076 Planarity : 0.004 0.063 2480 Dihedral : 5.084 25.494 1870 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.21), residues: 1682 helix: 0.85 (0.40), residues: 178 sheet: -0.75 (0.26), residues: 412 loop : -1.04 (0.20), residues: 1092 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 1.639 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 81 average time/residue: 0.2350 time to fit residues: 31.2442 Evaluate side-chains 77 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.611 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 6.9990 chunk 76 optimal weight: 8.9990 chunk 112 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 82 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 143 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 14164 Z= 0.268 Angle : 0.612 13.109 19186 Z= 0.309 Chirality : 0.046 0.197 2076 Planarity : 0.004 0.063 2480 Dihedral : 5.092 23.893 1870 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.21), residues: 1682 helix: 0.87 (0.41), residues: 178 sheet: -0.72 (0.26), residues: 404 loop : -1.06 (0.20), residues: 1100 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.661 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.2530 time to fit residues: 33.4590 Evaluate side-chains 79 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.579 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 37 optimal weight: 0.6980 chunk 135 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 ASN ** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.088599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.064885 restraints weight = 41797.540| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 3.57 r_work: 0.3081 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 14164 Z= 0.204 Angle : 0.589 12.268 19186 Z= 0.298 Chirality : 0.045 0.174 2076 Planarity : 0.004 0.061 2480 Dihedral : 4.989 22.780 1870 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.21), residues: 1682 helix: 0.96 (0.41), residues: 178 sheet: -0.63 (0.26), residues: 400 loop : -1.04 (0.20), residues: 1104 =============================================================================== Job complete usr+sys time: 2548.94 seconds wall clock time: 47 minutes 20.34 seconds (2840.34 seconds total)