Starting phenix.real_space_refine on Tue Feb 20 00:27:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl1_25188/02_2024/7sl1_25188_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl1_25188/02_2024/7sl1_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_25188/02_2024/7sl1_25188.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl1_25188/02_2024/7sl1_25188.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl1_25188/02_2024/7sl1_25188_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl1_25188/02_2024/7sl1_25188_neut.pdb" } resolution = 3.4 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= 0.001 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-dev-5238/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: 7.22, per 1000 atoms: 0.52 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: 5.48 Conformation dependent library (CDL) restraints added in 2.7 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: 1.73 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: 4.91 Time building geometry restraints manager: 5.94 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: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.010 Extract box with map and model: 10.370 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 38.810 Find NCS groups from input model: 0.830 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: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.200 ------------------------------------------------------------------------------- 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 % Allowed : 0.19 % Favored : 99.81 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 834 HIS 0.003 0.001 HIS A 831 PHE 0.011 0.001 PHE A 178 TYR 0.030 0.001 TYR C 16 ARG 0.004 0.000 ARG B 479 *********************** 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 : 1.728 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8262 (mmt) cc_final: 0.8057 (mmp) REVERT: A 863 VAL cc_start: 0.8018 (t) cc_final: 0.7709 (t) REVERT: B 794 ASP cc_start: 0.7362 (t70) cc_final: 0.7081 (t70) REVERT: B 863 VAL cc_start: 0.8082 (t) cc_final: 0.7770 (t) REVERT: D 22 ARG cc_start: 0.6801 (ptt90) cc_final: 0.6585 (ptt90) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.2771 time to fit residues: 47.0406 Evaluate side-chains 84 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.648 ------------------------------------------------------------------------------- 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** ** A 867 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 455 ASN ** B 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 867 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 14164 Z= 0.372 Angle : 0.654 10.333 19186 Z= 0.338 Chirality : 0.047 0.161 2076 Planarity : 0.004 0.049 2480 Dihedral : 5.025 24.047 1870 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 0.84 % Allowed : 7.46 % Favored : 91.71 % 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: -1.15 (0.21), residues: 1682 helix: 0.34 (0.39), residues: 180 sheet: -0.69 (0.26), residues: 408 loop : -0.99 (0.20), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 529 HIS 0.009 0.001 HIS A 831 PHE 0.017 0.002 PHE A 178 TYR 0.025 0.002 TYR B 633 ARG 0.005 0.000 ARG B 389 *********************** 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 113 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 1.791 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 454 ARG cc_start: 0.7464 (tpt-90) cc_final: 0.7163 (ptt90) REVERT: B 454 ARG cc_start: 0.7447 (tpt-90) cc_final: 0.7149 (ptt90) REVERT: B 504 MET cc_start: 0.8354 (mtt) cc_final: 0.8023 (mtm) REVERT: B 794 ASP cc_start: 0.7510 (t70) cc_final: 0.7215 (t70) outliers start: 13 outliers final: 7 residues processed: 106 average time/residue: 0.2645 time to fit residues: 42.4619 Evaluate side-chains 95 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 867 HIS Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 867 HIS Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain F residue 17 GLU 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: 5.9990 chunk 128 optimal weight: 1.9990 chunk 105 optimal weight: 0.0570 chunk 42 optimal weight: 0.8980 chunk 154 optimal weight: 10.0000 chunk 167 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 153 optimal weight: 0.0470 chunk 52 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- 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: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14164 Z= 0.178 Angle : 0.574 11.102 19186 Z= 0.293 Chirality : 0.044 0.152 2076 Planarity : 0.003 0.047 2480 Dihedral : 4.757 21.744 1870 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 0.39 % Allowed : 10.99 % Favored : 88.62 % 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: 0.57 (0.40), residues: 180 sheet: -0.66 (0.26), residues: 408 loop : -0.97 (0.20), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 251 HIS 0.003 0.000 HIS B 831 PHE 0.019 0.001 PHE B 703 TYR 0.014 0.001 TYR B 507 ARG 0.003 0.000 ARG B 479 *********************** 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 101 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 95 time to evaluate : 1.554 Fit side-chains REVERT: A 110 MET cc_start: 0.8716 (mmt) cc_final: 0.8513 (mmt) REVERT: A 454 ARG cc_start: 0.7404 (tpt-90) cc_final: 0.7077 (ptt90) REVERT: A 901 GLU cc_start: 0.7940 (pp20) cc_final: 0.7680 (pp20) REVERT: B 401 TYR cc_start: 0.8929 (t80) cc_final: 0.8696 (t80) REVERT: B 454 ARG cc_start: 0.7390 (tpt-90) cc_final: 0.7062 (ptt90) REVERT: B 504 MET cc_start: 0.8402 (mtt) cc_final: 0.8196 (mtp) REVERT: B 794 ASP cc_start: 0.7458 (t70) cc_final: 0.7142 (t70) outliers start: 6 outliers final: 2 residues processed: 98 average time/residue: 0.2590 time to fit residues: 38.9161 Evaluate side-chains 83 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 81 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain D residue 13 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 164 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 GLN ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7903 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 14164 Z= 0.429 Angle : 0.672 10.692 19186 Z= 0.343 Chirality : 0.047 0.154 2076 Planarity : 0.004 0.050 2480 Dihedral : 5.260 24.928 1870 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 1.41 % Allowed : 13.56 % Favored : 85.03 % 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: -1.34 (0.21), residues: 1682 helix: 0.12 (0.37), residues: 192 sheet: -0.83 (0.26), residues: 408 loop : -1.12 (0.20), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 529 HIS 0.008 0.001 HIS B 831 PHE 0.019 0.002 PHE A 703 TYR 0.021 0.002 TYR A 633 ARG 0.004 0.000 ARG A 389 *********************** 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 104 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 82 time to evaluate : 1.558 Fit side-chains REVERT: A 110 MET cc_start: 0.8722 (mmt) cc_final: 0.8456 (mmt) REVERT: A 454 ARG cc_start: 0.7436 (tpt-90) cc_final: 0.7187 (ptt90) REVERT: B 454 ARG cc_start: 0.7459 (tpt-90) cc_final: 0.7199 (ptt90) REVERT: B 794 ASP cc_start: 0.7644 (t70) cc_final: 0.7303 (t70) outliers start: 22 outliers final: 15 residues processed: 97 average time/residue: 0.2279 time to fit residues: 35.3230 Evaluate side-chains 90 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 75 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 710 TYR Chi-restraints excluded: chain A residue 867 HIS Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 710 TYR Chi-restraints excluded: chain B residue 867 HIS Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain E residue 12 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 140 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 147 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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: 0.7853 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14164 Z= 0.201 Angle : 0.579 11.414 19186 Z= 0.294 Chirality : 0.045 0.147 2076 Planarity : 0.003 0.043 2480 Dihedral : 4.937 21.917 1870 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 1.16 % Allowed : 14.14 % Favored : 84.70 % 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: -1.20 (0.21), residues: 1682 helix: 0.36 (0.39), residues: 192 sheet: -0.71 (0.26), residues: 398 loop : -1.06 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 834 HIS 0.002 0.001 HIS A 440 PHE 0.019 0.001 PHE B 703 TYR 0.018 0.001 TYR A 507 ARG 0.003 0.000 ARG A 479 *********************** 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 100 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 82 time to evaluate : 1.808 Fit side-chains REVERT: A 110 MET cc_start: 0.8729 (mmt) cc_final: 0.8457 (mmt) REVERT: A 454 ARG cc_start: 0.7449 (tpt-90) cc_final: 0.7191 (ptt90) REVERT: B 454 ARG cc_start: 0.7424 (tpt-90) cc_final: 0.7166 (ptt90) REVERT: B 794 ASP cc_start: 0.7548 (t70) cc_final: 0.7199 (t70) outliers start: 18 outliers final: 12 residues processed: 94 average time/residue: 0.2230 time to fit residues: 34.4100 Evaluate side-chains 92 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 80 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 710 TYR Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 867 HIS Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 710 TYR Chi-restraints excluded: chain B residue 845 VAL Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain D residue 13 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 96 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 164 optimal weight: 0.8980 chunk 136 optimal weight: 0.0870 chunk 76 optimal weight: 10.0000 chunk 13 optimal weight: 0.0670 chunk 54 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 overall best weight: 0.5896 ------------------------------------------------------------------------------- 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: 0.7829 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14164 Z= 0.162 Angle : 0.560 11.358 19186 Z= 0.283 Chirality : 0.044 0.148 2076 Planarity : 0.003 0.043 2480 Dihedral : 4.731 20.938 1870 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 0.77 % Allowed : 15.17 % Favored : 84.06 % 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: -1.00 (0.21), residues: 1682 helix: 0.79 (0.41), residues: 180 sheet: -0.60 (0.26), residues: 408 loop : -0.95 (0.20), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 834 HIS 0.004 0.001 HIS B 831 PHE 0.019 0.001 PHE B 703 TYR 0.020 0.001 TYR C 16 ARG 0.003 0.000 ARG A 479 *********************** 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 94 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 82 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8723 (mmt) cc_final: 0.8439 (mmt) REVERT: A 454 ARG cc_start: 0.7459 (tpt-90) cc_final: 0.7177 (ptt90) REVERT: B 454 ARG cc_start: 0.7423 (tpt-90) cc_final: 0.7156 (ptt90) REVERT: B 794 ASP cc_start: 0.7494 (t70) cc_final: 0.7140 (t70) REVERT: B 814 ASP cc_start: 0.7586 (OUTLIER) cc_final: 0.7328 (p0) REVERT: B 893 LEU cc_start: 0.9483 (mt) cc_final: 0.9227 (mp) outliers start: 12 outliers final: 9 residues processed: 91 average time/residue: 0.2381 time to fit residues: 34.3907 Evaluate side-chains 88 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 78 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 710 TYR Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 710 TYR Chi-restraints excluded: chain B residue 814 ASP Chi-restraints excluded: chain B residue 845 VAL Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain D residue 13 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 120 optimal weight: 0.9980 chunk 138 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 163 optimal weight: 5.9990 chunk 102 optimal weight: 0.1980 chunk 99 optimal weight: 1.9990 chunk 75 optimal weight: 20.0000 chunk 101 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7822 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14164 Z= 0.166 Angle : 0.557 13.275 19186 Z= 0.280 Chirality : 0.044 0.161 2076 Planarity : 0.003 0.045 2480 Dihedral : 4.645 20.579 1870 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 1.35 % Allowed : 15.10 % Favored : 83.55 % 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: -0.98 (0.21), residues: 1682 helix: 0.90 (0.41), residues: 180 sheet: -0.57 (0.26), residues: 408 loop : -0.96 (0.20), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 834 HIS 0.002 0.000 HIS B 440 PHE 0.019 0.001 PHE A 703 TYR 0.028 0.001 TYR E 19 ARG 0.003 0.000 ARG A 479 *********************** 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 103 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 82 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.8362 (tpt) cc_final: 0.8064 (tpt) REVERT: A 110 MET cc_start: 0.8725 (mmt) cc_final: 0.8406 (mmt) REVERT: A 454 ARG cc_start: 0.7484 (tpt-90) cc_final: 0.7204 (ptt90) REVERT: A 587 ILE cc_start: 0.9369 (mt) cc_final: 0.9121 (tt) REVERT: A 814 ASP cc_start: 0.7667 (OUTLIER) cc_final: 0.7405 (p0) REVERT: B 56 MET cc_start: 0.8339 (tpt) cc_final: 0.8028 (tpt) REVERT: B 454 ARG cc_start: 0.7438 (tpt-90) cc_final: 0.7166 (ptt90) REVERT: B 794 ASP cc_start: 0.7512 (t70) cc_final: 0.7149 (t70) REVERT: B 814 ASP cc_start: 0.7596 (OUTLIER) cc_final: 0.7332 (p0) REVERT: B 893 LEU cc_start: 0.9476 (mt) cc_final: 0.9239 (mp) outliers start: 21 outliers final: 16 residues processed: 99 average time/residue: 0.1713 time to fit residues: 28.0554 Evaluate side-chains 96 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 78 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 710 TYR Chi-restraints excluded: chain A residue 814 ASP Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 710 TYR Chi-restraints excluded: chain B residue 814 ASP Chi-restraints excluded: chain B residue 845 VAL Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain F residue 6 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 111 optimal weight: 0.0270 chunk 81 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 128 optimal weight: 0.6980 chunk 149 optimal weight: 8.9990 overall best weight: 1.1444 ------------------------------------------------------------------------------- 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: 0.7833 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14164 Z= 0.196 Angle : 0.566 14.675 19186 Z= 0.284 Chirality : 0.044 0.156 2076 Planarity : 0.003 0.044 2480 Dihedral : 4.692 20.495 1870 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 1.35 % Allowed : 15.87 % Favored : 82.78 % 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: -0.97 (0.21), residues: 1682 helix: 0.93 (0.41), residues: 180 sheet: -0.59 (0.26), residues: 408 loop : -0.95 (0.20), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 834 HIS 0.002 0.001 HIS B 440 PHE 0.019 0.001 PHE B 703 TYR 0.025 0.001 TYR F 19 ARG 0.002 0.000 ARG A 479 *********************** 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 101 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 80 time to evaluate : 1.769 Fit side-chains REVERT: A 110 MET cc_start: 0.8725 (mmt) cc_final: 0.8412 (mmt) REVERT: A 454 ARG cc_start: 0.7478 (tpt-90) cc_final: 0.7218 (ptt90) REVERT: A 814 ASP cc_start: 0.7664 (OUTLIER) cc_final: 0.7421 (p0) REVERT: B 454 ARG cc_start: 0.7458 (tpt-90) cc_final: 0.7196 (ptt90) REVERT: B 794 ASP cc_start: 0.7518 (t70) cc_final: 0.7162 (t70) REVERT: B 814 ASP cc_start: 0.7616 (OUTLIER) cc_final: 0.7377 (p0) outliers start: 21 outliers final: 17 residues processed: 98 average time/residue: 0.2113 time to fit residues: 33.9502 Evaluate side-chains 95 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 76 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 710 TYR Chi-restraints excluded: chain A residue 814 ASP Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 710 TYR Chi-restraints excluded: chain B residue 814 ASP Chi-restraints excluded: chain B residue 845 VAL Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain F residue 6 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 20.0000 chunk 143 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 119 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 137 optimal weight: 0.9980 chunk 144 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 chunk 161 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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: 0.7841 moved from start: 0.1948 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= 0.211 Angle : 0.582 14.844 19186 Z= 0.293 Chirality : 0.045 0.197 2076 Planarity : 0.004 0.063 2480 Dihedral : 4.761 20.435 1870 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 1.48 % Allowed : 16.13 % Favored : 82.39 % 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: -0.98 (0.21), residues: 1682 helix: 0.94 (0.40), residues: 182 sheet: -0.54 (0.26), residues: 398 loop : -0.99 (0.20), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 834 HIS 0.002 0.001 HIS B 440 PHE 0.019 0.001 PHE B 703 TYR 0.044 0.001 TYR E 19 ARG 0.003 0.000 ARG A 479 *********************** 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 105 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 82 time to evaluate : 1.769 Fit side-chains REVERT: A 110 MET cc_start: 0.8732 (mmt) cc_final: 0.8426 (mmt) REVERT: A 454 ARG cc_start: 0.7520 (tpt-90) cc_final: 0.7248 (ptt90) REVERT: A 814 ASP cc_start: 0.7687 (OUTLIER) cc_final: 0.7438 (p0) REVERT: B 98 MET cc_start: 0.9142 (mmm) cc_final: 0.8879 (tpp) REVERT: B 454 ARG cc_start: 0.7487 (tpt-90) cc_final: 0.7189 (ptt90) REVERT: B 794 ASP cc_start: 0.7552 (t70) cc_final: 0.7193 (t70) REVERT: B 814 ASP cc_start: 0.7642 (OUTLIER) cc_final: 0.7395 (p0) REVERT: B 893 LEU cc_start: 0.9468 (mt) cc_final: 0.9238 (mp) outliers start: 23 outliers final: 17 residues processed: 102 average time/residue: 0.2239 time to fit residues: 36.7220 Evaluate side-chains 96 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 77 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 710 TYR Chi-restraints excluded: chain A residue 814 ASP Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 710 TYR Chi-restraints excluded: chain B residue 814 ASP Chi-restraints excluded: chain B residue 845 VAL Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain F residue 6 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 169 optimal weight: 0.8980 chunk 155 optimal weight: 8.9990 chunk 134 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 82 optimal weight: 7.9990 chunk 107 optimal weight: 0.0070 chunk 143 optimal weight: 0.8980 overall best weight: 0.9400 ------------------------------------------------------------------------------- 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: 0.7830 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14164 Z= 0.186 Angle : 0.585 14.047 19186 Z= 0.294 Chirality : 0.045 0.240 2076 Planarity : 0.003 0.061 2480 Dihedral : 4.772 21.146 1870 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 1.16 % Allowed : 16.71 % Favored : 82.13 % 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: -0.97 (0.21), residues: 1682 helix: 0.93 (0.40), residues: 180 sheet: -0.52 (0.26), residues: 398 loop : -0.98 (0.20), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 834 HIS 0.002 0.000 HIS A 100 PHE 0.019 0.001 PHE B 703 TYR 0.043 0.001 TYR E 19 ARG 0.002 0.000 ARG A 479 ********************** 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 95 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 77 time to evaluate : 1.777 Fit side-chains REVERT: A 110 MET cc_start: 0.8737 (mmt) cc_final: 0.8432 (mmt) REVERT: A 454 ARG cc_start: 0.7538 (tpt-90) cc_final: 0.7195 (ptt90) REVERT: A 587 ILE cc_start: 0.9380 (mt) cc_final: 0.9153 (tt) REVERT: A 814 ASP cc_start: 0.7634 (OUTLIER) cc_final: 0.7384 (p0) REVERT: B 98 MET cc_start: 0.9156 (mmm) cc_final: 0.8898 (tpp) REVERT: B 454 ARG cc_start: 0.7522 (tpt-90) cc_final: 0.7175 (ptt90) REVERT: B 794 ASP cc_start: 0.7517 (t70) cc_final: 0.7154 (t70) REVERT: B 814 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7391 (p0) REVERT: B 893 LEU cc_start: 0.9466 (mt) cc_final: 0.9245 (mp) REVERT: F 17 GLU cc_start: 0.7913 (tt0) cc_final: 0.7704 (tt0) outliers start: 18 outliers final: 16 residues processed: 93 average time/residue: 0.2150 time to fit residues: 32.9203 Evaluate side-chains 92 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 74 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 710 TYR Chi-restraints excluded: chain A residue 814 ASP Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 710 TYR Chi-restraints excluded: chain B residue 814 ASP Chi-restraints excluded: chain B residue 845 VAL Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain F residue 6 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 138 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 7 optimal weight: 0.2980 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.089170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.065808 restraints weight = 42320.975| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 3.53 r_work: 0.3117 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3122 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3122 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14164 Z= 0.227 Angle : 0.586 13.578 19186 Z= 0.296 Chirality : 0.045 0.199 2076 Planarity : 0.004 0.061 2480 Dihedral : 4.851 21.453 1870 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 1.29 % Allowed : 16.58 % Favored : 82.13 % 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: -1.00 (0.21), residues: 1682 helix: 0.97 (0.41), residues: 180 sheet: -0.57 (0.26), residues: 400 loop : -1.00 (0.20), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 553 HIS 0.002 0.001 HIS B 831 PHE 0.019 0.001 PHE B 703 TYR 0.034 0.001 TYR E 19 ARG 0.002 0.000 ARG A 479 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2672.49 seconds wall clock time: 53 minutes 2.83 seconds (3182.83 seconds total)