Starting phenix.real_space_refine on Thu Sep 18 05:04:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6hin_0225/09_2025/6hin_0225_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hin_0225/09_2025/6hin_0225.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6hin_0225/09_2025/6hin_0225_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hin_0225/09_2025/6hin_0225_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6hin_0225/09_2025/6hin_0225.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hin_0225/09_2025/6hin_0225.map" } resolution = 4.1 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 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 9420 2.51 5 N 2220 2.21 5 O 2540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14220 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2761 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 17, 'TRANS': 317} Chain breaks: 1 Chain: "B" Number of atoms: 2761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2761 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 17, 'TRANS': 317} Chain breaks: 1 Chain: "C" Number of atoms: 2761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2761 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 17, 'TRANS': 317} Chain breaks: 1 Chain: "D" Number of atoms: 2761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2761 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 17, 'TRANS': 317} Chain breaks: 1 Chain: "E" Number of atoms: 2761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2761 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 17, 'TRANS': 317} Chain breaks: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 1, 'SRO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 1, 'SRO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 1, 'SRO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 1, 'SRO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 1, 'SRO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.29, per 1000 atoms: 0.23 Number of scatterers: 14220 At special positions: 0 Unit cell: (96.627, 96.627, 124.68, 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 40 16.00 O 2540 8.00 N 2220 7.00 C 9420 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.02 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 149 " distance=2.02 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 149 " distance=2.02 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " distance=2.02 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 149 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 501 " - " ASN A 82 " " NAG B 501 " - " ASN B 82 " " NAG C 501 " - " ASN C 82 " " NAG D 501 " - " ASN D 82 " " NAG E 902 " - " ASN E 82 " " NAG F 1 " - " ASN A 164 " " NAG G 1 " - " ASN A 148 " " NAG H 1 " - " ASN B 164 " " NAG I 1 " - " ASN B 148 " " NAG J 1 " - " ASN C 164 " " NAG K 1 " - " ASN C 148 " " NAG L 1 " - " ASN D 164 " " NAG M 1 " - " ASN D 148 " " NAG N 1 " - " ASN E 164 " " NAG O 1 " - " ASN E 148 " Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 513.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3250 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 15 sheets defined 38.5% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 11 through 20 removed outlier: 3.736A pdb=" N LEU A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 16 " --> pdb=" O LEU A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 141 through 144 Processing helix chain 'A' and resid 170 through 176 removed outlier: 3.658A pdb=" N VAL A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 227 removed outlier: 3.868A pdb=" N VAL A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 234 removed outlier: 3.654A pdb=" N PHE A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 241 Processing helix chain 'A' and resid 250 through 271 removed outlier: 4.137A pdb=" N THR A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU A 258 " --> pdb=" O PHE A 254 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY A 261 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N PHE A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 266 " --> pdb=" O TYR A 262 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL A 269 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 308 removed outlier: 3.799A pdb=" N PHE A 287 " --> pdb=" O ILE A 283 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A 295 " --> pdb=" O MET A 291 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ILE A 296 " --> pdb=" O ALA A 292 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL A 305 " --> pdb=" O THR A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 434 removed outlier: 3.625A pdb=" N TYR A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 446 removed outlier: 3.510A pdb=" N ILE A 440 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 442 " --> pdb=" O PHE A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 457 Processing helix chain 'B' and resid 11 through 20 removed outlier: 3.737A pdb=" N LEU B 15 " --> pdb=" O ALA B 11 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 74 Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 141 through 144 Processing helix chain 'B' and resid 170 through 176 removed outlier: 3.659A pdb=" N VAL B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER B 176 " --> pdb=" O GLU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 227 removed outlier: 3.867A pdb=" N VAL B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 234 removed outlier: 3.654A pdb=" N PHE B 233 " --> pdb=" O LEU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 241 Processing helix chain 'B' and resid 250 through 271 removed outlier: 4.137A pdb=" N THR B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU B 258 " --> pdb=" O PHE B 254 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY B 261 " --> pdb=" O THR B 257 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE B 265 " --> pdb=" O GLY B 261 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B 266 " --> pdb=" O TYR B 262 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL B 269 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP B 271 " --> pdb=" O ILE B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 308 removed outlier: 3.798A pdb=" N PHE B 287 " --> pdb=" O ILE B 283 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET B 291 " --> pdb=" O PHE B 287 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL B 295 " --> pdb=" O MET B 291 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ILE B 296 " --> pdb=" O ALA B 292 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL B 305 " --> pdb=" O THR B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 434 removed outlier: 3.625A pdb=" N TYR B 431 " --> pdb=" O LEU B 427 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL B 432 " --> pdb=" O ARG B 428 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 446 removed outlier: 3.510A pdb=" N ILE B 440 " --> pdb=" O LEU B 436 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU B 442 " --> pdb=" O PHE B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 457 Processing helix chain 'C' and resid 11 through 20 removed outlier: 3.736A pdb=" N LEU C 15 " --> pdb=" O ALA C 11 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 141 through 144 Processing helix chain 'C' and resid 170 through 176 removed outlier: 3.658A pdb=" N VAL C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER C 176 " --> pdb=" O GLU C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 227 removed outlier: 3.868A pdb=" N VAL C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 234 removed outlier: 3.654A pdb=" N PHE C 233 " --> pdb=" O LEU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 241 Processing helix chain 'C' and resid 250 through 271 removed outlier: 4.136A pdb=" N THR C 257 " --> pdb=" O SER C 253 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU C 258 " --> pdb=" O PHE C 254 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY C 261 " --> pdb=" O THR C 257 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL C 264 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE C 265 " --> pdb=" O GLY C 261 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU C 266 " --> pdb=" O TYR C 262 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL C 269 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP C 271 " --> pdb=" O ILE C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 308 removed outlier: 3.798A pdb=" N PHE C 287 " --> pdb=" O ILE C 283 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET C 291 " --> pdb=" O PHE C 287 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL C 295 " --> pdb=" O MET C 291 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ILE C 296 " --> pdb=" O ALA C 292 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL C 305 " --> pdb=" O THR C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 434 removed outlier: 3.624A pdb=" N TYR C 431 " --> pdb=" O LEU C 427 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL C 432 " --> pdb=" O ARG C 428 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP C 434 " --> pdb=" O GLY C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 446 removed outlier: 3.510A pdb=" N ILE C 440 " --> pdb=" O LEU C 436 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR C 441 " --> pdb=" O LEU C 437 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU C 442 " --> pdb=" O PHE C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 457 Processing helix chain 'D' and resid 11 through 20 removed outlier: 3.736A pdb=" N LEU D 15 " --> pdb=" O ALA D 11 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 74 Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 141 through 144 Processing helix chain 'D' and resid 170 through 176 removed outlier: 3.658A pdb=" N VAL D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER D 176 " --> pdb=" O GLU D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 227 removed outlier: 3.868A pdb=" N VAL D 225 " --> pdb=" O LEU D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 234 removed outlier: 3.653A pdb=" N PHE D 233 " --> pdb=" O LEU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 241 Processing helix chain 'D' and resid 250 through 271 removed outlier: 4.137A pdb=" N THR D 257 " --> pdb=" O SER D 253 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU D 258 " --> pdb=" O PHE D 254 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY D 261 " --> pdb=" O THR D 257 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL D 264 " --> pdb=" O LEU D 260 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE D 265 " --> pdb=" O GLY D 261 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU D 266 " --> pdb=" O TYR D 262 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL D 269 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP D 271 " --> pdb=" O ILE D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 308 removed outlier: 3.798A pdb=" N PHE D 287 " --> pdb=" O ILE D 283 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET D 291 " --> pdb=" O PHE D 287 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL D 295 " --> pdb=" O MET D 291 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ILE D 296 " --> pdb=" O ALA D 292 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL D 305 " --> pdb=" O THR D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 434 removed outlier: 3.625A pdb=" N TYR D 431 " --> pdb=" O LEU D 427 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL D 432 " --> pdb=" O ARG D 428 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP D 434 " --> pdb=" O GLY D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 446 removed outlier: 3.510A pdb=" N ILE D 440 " --> pdb=" O LEU D 436 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR D 441 " --> pdb=" O LEU D 437 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU D 442 " --> pdb=" O PHE D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 457 Processing helix chain 'E' and resid 11 through 20 removed outlier: 3.737A pdb=" N LEU E 15 " --> pdb=" O ALA E 11 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER E 16 " --> pdb=" O LEU E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 74 Processing helix chain 'E' and resid 91 through 93 No H-bonds generated for 'chain 'E' and resid 91 through 93' Processing helix chain 'E' and resid 141 through 144 Processing helix chain 'E' and resid 170 through 176 removed outlier: 3.658A pdb=" N VAL E 174 " --> pdb=" O SER E 170 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER E 176 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 227 removed outlier: 3.867A pdb=" N VAL E 225 " --> pdb=" O LEU E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 234 removed outlier: 3.654A pdb=" N PHE E 233 " --> pdb=" O LEU E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 241 Processing helix chain 'E' and resid 250 through 271 removed outlier: 4.136A pdb=" N THR E 257 " --> pdb=" O SER E 253 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU E 258 " --> pdb=" O PHE E 254 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY E 261 " --> pdb=" O THR E 257 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL E 264 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE E 265 " --> pdb=" O GLY E 261 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU E 266 " --> pdb=" O TYR E 262 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL E 269 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP E 271 " --> pdb=" O ILE E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 308 removed outlier: 3.799A pdb=" N PHE E 287 " --> pdb=" O ILE E 283 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET E 291 " --> pdb=" O PHE E 287 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL E 295 " --> pdb=" O MET E 291 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ILE E 296 " --> pdb=" O ALA E 292 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER E 297 " --> pdb=" O LEU E 293 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL E 305 " --> pdb=" O THR E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 434 removed outlier: 3.624A pdb=" N TYR E 431 " --> pdb=" O LEU E 427 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL E 432 " --> pdb=" O ARG E 428 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP E 434 " --> pdb=" O GLY E 430 " (cutoff:3.500A) Processing helix chain 'E' and resid 434 through 446 removed outlier: 3.509A pdb=" N ILE E 440 " --> pdb=" O LEU E 436 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR E 441 " --> pdb=" O LEU E 437 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU E 442 " --> pdb=" O PHE E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 457 Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 133 removed outlier: 7.537A pdb=" N VAL A 57 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N VAL A 51 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N THR A 59 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N TRP A 63 " --> pdb=" O MET A 45 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N MET A 45 " --> pdb=" O TRP A 63 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ARG A 65 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N VAL A 43 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N TYR A 67 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ILE A 41 " --> pdb=" O TYR A 67 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N THR A 69 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL A 39 " --> pdb=" O THR A 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 89 removed outlier: 3.533A pdb=" N LEU A 86 " --> pdb=" O VAL A 117 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 100 removed outlier: 5.352A pdb=" N ALA A 208 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU A 209 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS A 197 " --> pdb=" O GLU A 209 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN A 195 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU A 191 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ARG A 217 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LEU A 189 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 122 through 133 removed outlier: 7.537A pdb=" N VAL B 57 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N VAL B 51 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N THR B 59 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N TRP B 63 " --> pdb=" O MET B 45 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N MET B 45 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ARG B 65 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL B 43 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N TYR B 67 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ILE B 41 " --> pdb=" O TYR B 67 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N THR B 69 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL B 39 " --> pdb=" O THR B 69 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 85 through 89 removed outlier: 3.532A pdb=" N LEU B 86 " --> pdb=" O VAL B 117 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 100 removed outlier: 5.352A pdb=" N ALA B 208 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU B 209 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS B 197 " --> pdb=" O GLU B 209 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN B 195 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU B 191 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ARG B 217 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LEU B 189 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 122 through 133 removed outlier: 7.536A pdb=" N VAL C 57 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N VAL C 51 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N THR C 59 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N TRP C 63 " --> pdb=" O MET C 45 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N MET C 45 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ARG C 65 " --> pdb=" O VAL C 43 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL C 43 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N TYR C 67 " --> pdb=" O ILE C 41 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ILE C 41 " --> pdb=" O TYR C 67 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N THR C 69 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL C 39 " --> pdb=" O THR C 69 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 85 through 89 removed outlier: 3.532A pdb=" N LEU C 86 " --> pdb=" O VAL C 117 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 98 through 100 removed outlier: 5.353A pdb=" N ALA C 208 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU C 209 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS C 197 " --> pdb=" O GLU C 209 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN C 195 " --> pdb=" O LYS C 211 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU C 191 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ARG C 217 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N LEU C 189 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 122 through 133 removed outlier: 7.536A pdb=" N VAL D 57 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N VAL D 51 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N THR D 59 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N TRP D 63 " --> pdb=" O MET D 45 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N MET D 45 " --> pdb=" O TRP D 63 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ARG D 65 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL D 43 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N TYR D 67 " --> pdb=" O ILE D 41 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ILE D 41 " --> pdb=" O TYR D 67 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N THR D 69 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL D 39 " --> pdb=" O THR D 69 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 85 through 89 removed outlier: 3.533A pdb=" N LEU D 86 " --> pdb=" O VAL D 117 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 98 through 100 removed outlier: 5.353A pdb=" N ALA D 208 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU D 209 " --> pdb=" O LYS D 197 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS D 197 " --> pdb=" O GLU D 209 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN D 195 " --> pdb=" O LYS D 211 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU D 191 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ARG D 217 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LEU D 189 " --> pdb=" O ARG D 217 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 122 through 133 removed outlier: 7.537A pdb=" N VAL E 57 " --> pdb=" O VAL E 51 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N VAL E 51 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N THR E 59 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N TRP E 63 " --> pdb=" O MET E 45 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N MET E 45 " --> pdb=" O TRP E 63 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ARG E 65 " --> pdb=" O VAL E 43 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL E 43 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N TYR E 67 " --> pdb=" O ILE E 41 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ILE E 41 " --> pdb=" O TYR E 67 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N THR E 69 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL E 39 " --> pdb=" O THR E 69 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 85 through 89 removed outlier: 3.533A pdb=" N LEU E 86 " --> pdb=" O VAL E 117 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 98 through 100 removed outlier: 5.352A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU E 209 " --> pdb=" O LYS E 197 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS E 197 " --> pdb=" O GLU E 209 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN E 195 " --> pdb=" O LYS E 211 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU E 191 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ARG E 217 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N LEU E 189 " --> pdb=" O ARG E 217 " (cutoff:3.500A) 455 hydrogen bonds defined for protein. 1320 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: 1.98 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4142 1.34 - 1.45: 3065 1.45 - 1.57: 7353 1.57 - 1.69: 0 1.69 - 1.80: 60 Bond restraints: 14620 Sorted by residual: bond pdb=" CG SRO D 502 " pdb=" CD2 SRO D 502 " ideal model delta sigma weight residual 1.438 1.355 0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" CG SRO B 502 " pdb=" CD2 SRO B 502 " ideal model delta sigma weight residual 1.438 1.355 0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" CG SRO C 502 " pdb=" CD2 SRO C 502 " ideal model delta sigma weight residual 1.438 1.355 0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" CG SRO A 502 " pdb=" CD2 SRO A 502 " ideal model delta sigma weight residual 1.438 1.355 0.083 2.00e-02 2.50e+03 1.70e+01 bond pdb=" CG SRO E 901 " pdb=" CD2 SRO E 901 " ideal model delta sigma weight residual 1.438 1.356 0.082 2.00e-02 2.50e+03 1.68e+01 ... (remaining 14615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 19244 2.62 - 5.24: 614 5.24 - 7.86: 87 7.86 - 10.49: 32 10.49 - 13.11: 18 Bond angle restraints: 19995 Sorted by residual: angle pdb=" CB SRO D 502 " pdb=" CG SRO D 502 " pdb=" CD1 SRO D 502 " ideal model delta sigma weight residual 128.15 115.04 13.11 3.00e+00 1.11e-01 1.91e+01 angle pdb=" CB SRO E 901 " pdb=" CG SRO E 901 " pdb=" CD1 SRO E 901 " ideal model delta sigma weight residual 128.15 115.08 13.07 3.00e+00 1.11e-01 1.90e+01 angle pdb=" CB SRO B 502 " pdb=" CG SRO B 502 " pdb=" CD1 SRO B 502 " ideal model delta sigma weight residual 128.15 115.11 13.04 3.00e+00 1.11e-01 1.89e+01 angle pdb=" CB SRO C 502 " pdb=" CG SRO C 502 " pdb=" CD1 SRO C 502 " ideal model delta sigma weight residual 128.15 115.11 13.04 3.00e+00 1.11e-01 1.89e+01 angle pdb=" CB SRO A 502 " pdb=" CG SRO A 502 " pdb=" CD1 SRO A 502 " ideal model delta sigma weight residual 128.15 115.11 13.04 3.00e+00 1.11e-01 1.89e+01 ... (remaining 19990 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.35: 8056 15.35 - 30.70: 624 30.70 - 46.05: 140 46.05 - 61.40: 25 61.40 - 76.75: 15 Dihedral angle restraints: 8860 sinusoidal: 3860 harmonic: 5000 Sorted by residual: dihedral pdb=" CA GLN E 66 " pdb=" C GLN E 66 " pdb=" N TYR E 67 " pdb=" CA TYR E 67 " ideal model delta harmonic sigma weight residual 180.00 151.58 28.42 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA GLN C 66 " pdb=" C GLN C 66 " pdb=" N TYR C 67 " pdb=" CA TYR C 67 " ideal model delta harmonic sigma weight residual 180.00 151.60 28.40 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA GLN D 66 " pdb=" C GLN D 66 " pdb=" N TYR D 67 " pdb=" CA TYR D 67 " ideal model delta harmonic sigma weight residual 180.00 151.62 28.38 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 8857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1787 0.072 - 0.144: 533 0.144 - 0.215: 65 0.215 - 0.287: 10 0.287 - 0.359: 5 Chirality restraints: 2400 Sorted by residual: chirality pdb=" CG LEU C 131 " pdb=" CB LEU C 131 " pdb=" CD1 LEU C 131 " pdb=" CD2 LEU C 131 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" CG LEU D 131 " pdb=" CB LEU D 131 " pdb=" CD1 LEU D 131 " pdb=" CD2 LEU D 131 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CG LEU A 131 " pdb=" CB LEU A 131 " pdb=" CD1 LEU A 131 " pdb=" CD2 LEU A 131 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.17e+00 ... (remaining 2397 not shown) Planarity restraints: 2405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 168 " 0.017 2.00e-02 2.50e+03 1.72e-02 7.39e+00 pdb=" CG TRP C 168 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP C 168 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP C 168 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 168 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 168 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 168 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 168 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 168 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP C 168 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 168 " 0.017 2.00e-02 2.50e+03 1.70e-02 7.26e+00 pdb=" CG TRP B 168 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP B 168 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP B 168 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 168 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 168 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 168 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 168 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 168 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 168 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 168 " -0.017 2.00e-02 2.50e+03 1.70e-02 7.26e+00 pdb=" CG TRP D 168 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP D 168 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP D 168 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 168 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 168 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 168 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 168 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 168 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP D 168 " -0.002 2.00e-02 2.50e+03 ... (remaining 2402 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.90: 5417 2.90 - 3.40: 14039 3.40 - 3.90: 23344 3.90 - 4.40: 25782 4.40 - 4.90: 42633 Nonbonded interactions: 111215 Sorted by model distance: nonbonded pdb=" N ASP C 52 " pdb=" OD1 ASP C 52 " model vdw 2.394 3.120 nonbonded pdb=" N ASP B 52 " pdb=" OD1 ASP B 52 " model vdw 2.394 3.120 nonbonded pdb=" N ASP E 52 " pdb=" OD1 ASP E 52 " model vdw 2.395 3.120 nonbonded pdb=" N ASP A 52 " pdb=" OD1 ASP A 52 " model vdw 2.395 3.120 nonbonded pdb=" N ASP D 52 " pdb=" OD1 ASP D 52 " model vdw 2.395 3.120 ... (remaining 111210 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = (chain 'A' and resid 10 through 459) selection = (chain 'B' and resid 10 through 459) selection = (chain 'C' and resid 10 through 459) selection = (chain 'D' and resid 10 through 459) selection = (chain 'E' and resid 10 through 459) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.320 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.040 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 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 : 0.010 0.084 14650 Z= 0.429 Angle : 1.223 13.108 20080 Z= 0.609 Chirality : 0.067 0.359 2400 Planarity : 0.007 0.058 2390 Dihedral : 12.347 76.751 5595 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.32 % Allowed : 11.18 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.98 (0.16), residues: 1655 helix: -4.58 (0.09), residues: 515 sheet: -2.32 (0.24), residues: 380 loop : -2.75 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 251 TYR 0.025 0.004 TYR B 116 PHE 0.023 0.003 PHE A 287 TRP 0.045 0.004 TRP C 168 HIS 0.008 0.002 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00962 (14620) covalent geometry : angle 1.21109 (19995) SS BOND : bond 0.01080 ( 5) SS BOND : angle 1.55314 ( 10) hydrogen bonds : bond 0.33225 ( 455) hydrogen bonds : angle 11.37438 ( 1320) link_BETA1-4 : bond 0.00860 ( 10) link_BETA1-4 : angle 2.31315 ( 30) link_NAG-ASN : bond 0.00652 ( 15) link_NAG-ASN : angle 3.39824 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 274 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 TRP cc_start: 0.9357 (t60) cc_final: 0.8920 (t60) REVERT: A 197 LYS cc_start: 0.8828 (tptt) cc_final: 0.8609 (tmtt) REVERT: A 209 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7976 (tm-30) REVERT: A 435 ARG cc_start: 0.8746 (tpp-160) cc_final: 0.8008 (tpt170) REVERT: A 448 TYR cc_start: 0.7759 (t80) cc_final: 0.7554 (t80) REVERT: B 94 TRP cc_start: 0.9345 (t60) cc_final: 0.8904 (t60) REVERT: B 136 SER cc_start: 0.8760 (t) cc_final: 0.8381 (t) REVERT: B 209 GLU cc_start: 0.8266 (tm-30) cc_final: 0.8021 (tm-30) REVERT: B 290 CYS cc_start: 0.8523 (t) cc_final: 0.8006 (t) REVERT: B 435 ARG cc_start: 0.8571 (tpp-160) cc_final: 0.8113 (tpt170) REVERT: B 436 LEU cc_start: 0.8294 (tt) cc_final: 0.7898 (pp) REVERT: C 94 TRP cc_start: 0.9363 (t60) cc_final: 0.8866 (t60) REVERT: C 197 LYS cc_start: 0.8819 (tptt) cc_final: 0.8500 (tptt) REVERT: C 209 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7894 (tm-30) REVERT: C 290 CYS cc_start: 0.8447 (t) cc_final: 0.7886 (t) REVERT: C 435 ARG cc_start: 0.8582 (tpp-160) cc_final: 0.8256 (tpt170) REVERT: D 94 TRP cc_start: 0.9369 (t60) cc_final: 0.8855 (t60) REVERT: D 197 LYS cc_start: 0.8825 (tptt) cc_final: 0.8432 (tptt) REVERT: D 209 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7955 (tm-30) REVERT: D 435 ARG cc_start: 0.8474 (tpp-160) cc_final: 0.8079 (tpt170) REVERT: D 436 LEU cc_start: 0.8132 (tt) cc_final: 0.7834 (pp) REVERT: D 448 TYR cc_start: 0.7714 (t80) cc_final: 0.7459 (t80) REVERT: E 94 TRP cc_start: 0.9384 (t60) cc_final: 0.8460 (t60) REVERT: E 197 LYS cc_start: 0.8925 (tptt) cc_final: 0.8651 (tptt) REVERT: E 435 ARG cc_start: 0.8743 (tpp-160) cc_final: 0.8372 (tpt170) REVERT: E 436 LEU cc_start: 0.8321 (tt) cc_final: 0.7894 (pp) outliers start: 5 outliers final: 0 residues processed: 274 average time/residue: 0.1168 time to fit residues: 46.7949 Evaluate side-chains 158 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 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 101 ASN ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN B 119 HIS C 101 ASN C 119 HIS ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN D 119 HIS E 119 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.125730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.102486 restraints weight = 28986.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.102774 restraints weight = 21693.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.103465 restraints weight = 15658.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.104426 restraints weight = 14323.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.104695 restraints weight = 11961.803| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14650 Z= 0.171 Angle : 0.776 8.548 20080 Z= 0.398 Chirality : 0.048 0.164 2400 Planarity : 0.005 0.038 2390 Dihedral : 8.644 53.082 2370 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.08 (0.18), residues: 1655 helix: -3.35 (0.14), residues: 595 sheet: -2.03 (0.24), residues: 375 loop : -2.26 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 28 TYR 0.022 0.002 TYR B 67 PHE 0.041 0.002 PHE B 287 TRP 0.018 0.002 TRP A 168 HIS 0.003 0.001 HIS D 158 Details of bonding type rmsd covalent geometry : bond 0.00377 (14620) covalent geometry : angle 0.77074 (19995) SS BOND : bond 0.00326 ( 5) SS BOND : angle 0.42566 ( 10) hydrogen bonds : bond 0.05112 ( 455) hydrogen bonds : angle 7.82079 ( 1320) link_BETA1-4 : bond 0.00400 ( 10) link_BETA1-4 : angle 1.29614 ( 30) link_NAG-ASN : bond 0.00113 ( 15) link_NAG-ASN : angle 1.98111 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: A 73 LEU cc_start: 0.9253 (mt) cc_final: 0.8892 (mp) REVERT: A 94 TRP cc_start: 0.9396 (t60) cc_final: 0.8934 (t60) REVERT: A 130 GLN cc_start: 0.8264 (mt0) cc_final: 0.7716 (mp10) REVERT: A 184 GLN cc_start: 0.7595 (pm20) cc_final: 0.7367 (pm20) REVERT: A 197 LYS cc_start: 0.8459 (tptt) cc_final: 0.8256 (tmtt) REVERT: A 209 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7747 (tm-30) REVERT: A 235 MET cc_start: 0.8488 (ttm) cc_final: 0.8149 (tpp) REVERT: A 291 MET cc_start: 0.8755 (mmp) cc_final: 0.7623 (mmm) REVERT: A 435 ARG cc_start: 0.8548 (tpp-160) cc_final: 0.8128 (tpt170) REVERT: A 436 LEU cc_start: 0.8520 (tt) cc_final: 0.8095 (pp) REVERT: A 448 TYR cc_start: 0.7726 (t80) cc_final: 0.7357 (t80) REVERT: B 209 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7735 (tm-30) REVERT: B 235 MET cc_start: 0.8387 (ttm) cc_final: 0.7777 (tpp) REVERT: B 291 MET cc_start: 0.8649 (mmp) cc_final: 0.7943 (mmm) REVERT: B 435 ARG cc_start: 0.8422 (tpp-160) cc_final: 0.8005 (tpt170) REVERT: B 436 LEU cc_start: 0.8113 (tt) cc_final: 0.7767 (pp) REVERT: B 448 TYR cc_start: 0.7343 (t80) cc_final: 0.7082 (t80) REVERT: C 197 LYS cc_start: 0.8431 (tptt) cc_final: 0.8201 (tptt) REVERT: C 209 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7731 (tm-30) REVERT: C 235 MET cc_start: 0.8574 (ttp) cc_final: 0.8097 (tpp) REVERT: C 255 LYS cc_start: 0.7839 (tttp) cc_final: 0.7492 (tttp) REVERT: C 291 MET cc_start: 0.8744 (mmp) cc_final: 0.7522 (mmm) REVERT: D 197 LYS cc_start: 0.8569 (tptt) cc_final: 0.8266 (tptt) REVERT: D 209 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7571 (tt0) REVERT: D 291 MET cc_start: 0.8859 (mmp) cc_final: 0.7660 (mmm) REVERT: D 436 LEU cc_start: 0.8121 (tt) cc_final: 0.7901 (pp) REVERT: D 448 TYR cc_start: 0.7686 (t80) cc_final: 0.7323 (t80) REVERT: E 209 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7506 (tt0) REVERT: E 210 MET cc_start: 0.8675 (tmm) cc_final: 0.8207 (tmm) REVERT: E 235 MET cc_start: 0.8414 (ttm) cc_final: 0.7958 (tpp) REVERT: E 291 MET cc_start: 0.8702 (mmp) cc_final: 0.7390 (mmm) REVERT: E 436 LEU cc_start: 0.8309 (tt) cc_final: 0.7972 (pp) REVERT: E 448 TYR cc_start: 0.7548 (t80) cc_final: 0.7255 (t80) outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.1130 time to fit residues: 41.7359 Evaluate side-chains 175 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 129 optimal weight: 0.0370 chunk 103 optimal weight: 0.1980 chunk 51 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 48 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 125 optimal weight: 10.0000 chunk 96 optimal weight: 7.9990 chunk 107 optimal weight: 0.0770 chunk 100 optimal weight: 0.8980 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.128307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.105389 restraints weight = 28819.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.106726 restraints weight = 18649.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.107512 restraints weight = 13218.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.108102 restraints weight = 12045.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.108151 restraints weight = 10441.110| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14650 Z= 0.128 Angle : 0.710 8.060 20080 Z= 0.356 Chirality : 0.047 0.170 2400 Planarity : 0.004 0.028 2390 Dihedral : 7.126 37.516 2370 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.54 (0.19), residues: 1655 helix: -2.68 (0.17), residues: 595 sheet: -1.91 (0.25), residues: 375 loop : -2.06 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 120 TYR 0.021 0.002 TYR B 67 PHE 0.032 0.002 PHE B 287 TRP 0.027 0.001 TRP A 187 HIS 0.008 0.001 HIS D 119 Details of bonding type rmsd covalent geometry : bond 0.00288 (14620) covalent geometry : angle 0.70371 (19995) SS BOND : bond 0.00140 ( 5) SS BOND : angle 0.46148 ( 10) hydrogen bonds : bond 0.04187 ( 455) hydrogen bonds : angle 6.95926 ( 1320) link_BETA1-4 : bond 0.00440 ( 10) link_BETA1-4 : angle 1.17801 ( 30) link_NAG-ASN : bond 0.00165 ( 15) link_NAG-ASN : angle 1.90879 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LEU cc_start: 0.9227 (mt) cc_final: 0.8856 (mp) REVERT: A 94 TRP cc_start: 0.9383 (t60) cc_final: 0.8898 (t60) REVERT: A 209 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7570 (tm-30) REVERT: A 291 MET cc_start: 0.8868 (mmp) cc_final: 0.8559 (mmm) REVERT: A 435 ARG cc_start: 0.8544 (tpp-160) cc_final: 0.8134 (tpt170) REVERT: A 436 LEU cc_start: 0.8490 (tt) cc_final: 0.8039 (pp) REVERT: A 448 TYR cc_start: 0.7782 (t80) cc_final: 0.7405 (t80) REVERT: B 130 GLN cc_start: 0.8209 (mt0) cc_final: 0.7768 (mp10) REVERT: B 209 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7363 (tt0) REVERT: B 210 MET cc_start: 0.8765 (tmm) cc_final: 0.8244 (tmm) REVERT: B 235 MET cc_start: 0.7890 (ttm) cc_final: 0.7568 (tpp) REVERT: B 435 ARG cc_start: 0.8404 (tpp-160) cc_final: 0.8006 (tpt170) REVERT: B 436 LEU cc_start: 0.7983 (tt) cc_final: 0.7696 (pp) REVERT: B 448 TYR cc_start: 0.7574 (t80) cc_final: 0.7360 (t80) REVERT: C 197 LYS cc_start: 0.8131 (tptt) cc_final: 0.7822 (tptt) REVERT: C 209 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7473 (tm-30) REVERT: C 266 LEU cc_start: 0.8477 (pp) cc_final: 0.8073 (tp) REVERT: D 209 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7461 (tt0) REVERT: D 235 MET cc_start: 0.8626 (tpp) cc_final: 0.8422 (tpp) REVERT: D 291 MET cc_start: 0.8882 (mmp) cc_final: 0.8656 (mmm) REVERT: D 436 LEU cc_start: 0.8156 (tt) cc_final: 0.7923 (pp) REVERT: D 448 TYR cc_start: 0.7816 (t80) cc_final: 0.7503 (t80) REVERT: E 209 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7543 (tm-30) REVERT: E 210 MET cc_start: 0.8586 (tmm) cc_final: 0.8292 (tmm) REVERT: E 436 LEU cc_start: 0.8261 (tt) cc_final: 0.7950 (pp) REVERT: E 452 LEU cc_start: 0.8750 (mt) cc_final: 0.8067 (tt) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.1120 time to fit residues: 42.7264 Evaluate side-chains 163 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 58 optimal weight: 0.3980 chunk 127 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 79 optimal weight: 0.1980 chunk 129 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 chunk 153 optimal weight: 1.9990 chunk 68 optimal weight: 0.0670 chunk 45 optimal weight: 0.6980 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 HIS ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.128180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.105564 restraints weight = 29088.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.106014 restraints weight = 20474.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.106940 restraints weight = 15787.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.107427 restraints weight = 14165.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.107600 restraints weight = 12043.151| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14650 Z= 0.125 Angle : 0.703 8.612 20080 Z= 0.347 Chirality : 0.046 0.160 2400 Planarity : 0.004 0.028 2390 Dihedral : 6.390 32.071 2370 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.24 (0.19), residues: 1655 helix: -2.18 (0.18), residues: 585 sheet: -2.13 (0.23), residues: 415 loop : -1.85 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 65 TYR 0.026 0.002 TYR C 67 PHE 0.040 0.002 PHE B 287 TRP 0.017 0.001 TRP A 187 HIS 0.002 0.001 HIS E 158 Details of bonding type rmsd covalent geometry : bond 0.00284 (14620) covalent geometry : angle 0.69751 (19995) SS BOND : bond 0.00365 ( 5) SS BOND : angle 0.25101 ( 10) hydrogen bonds : bond 0.03732 ( 455) hydrogen bonds : angle 6.59450 ( 1320) link_BETA1-4 : bond 0.00446 ( 10) link_BETA1-4 : angle 1.19181 ( 30) link_NAG-ASN : bond 0.00112 ( 15) link_NAG-ASN : angle 1.76511 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LEU cc_start: 0.9195 (mt) cc_final: 0.8826 (mt) REVERT: A 197 LYS cc_start: 0.7975 (tmtt) cc_final: 0.7540 (tmtt) REVERT: A 209 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7452 (tm-30) REVERT: A 210 MET cc_start: 0.8545 (tmm) cc_final: 0.8168 (tmm) REVERT: A 291 MET cc_start: 0.8827 (mmp) cc_final: 0.8511 (mmm) REVERT: A 435 ARG cc_start: 0.8470 (tpp-160) cc_final: 0.8225 (tmt170) REVERT: A 436 LEU cc_start: 0.8324 (tt) cc_final: 0.8004 (pp) REVERT: B 209 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7344 (tt0) REVERT: B 210 MET cc_start: 0.8770 (tmm) cc_final: 0.8236 (tmm) REVERT: B 255 LYS cc_start: 0.8259 (mtpt) cc_final: 0.8029 (mtpt) REVERT: B 435 ARG cc_start: 0.8415 (tpp-160) cc_final: 0.8076 (tpt170) REVERT: C 152 THR cc_start: 0.8705 (p) cc_final: 0.8213 (p) REVERT: C 195 GLN cc_start: 0.8700 (tm-30) cc_final: 0.8191 (tm-30) REVERT: C 209 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7344 (tt0) REVERT: C 266 LEU cc_start: 0.8468 (pp) cc_final: 0.8026 (tp) REVERT: D 130 GLN cc_start: 0.8163 (mp10) cc_final: 0.7647 (mp10) REVERT: D 152 THR cc_start: 0.8718 (p) cc_final: 0.8307 (p) REVERT: D 209 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7563 (tt0) REVERT: D 235 MET cc_start: 0.8575 (tpp) cc_final: 0.8349 (tpp) REVERT: D 291 MET cc_start: 0.8847 (mmp) cc_final: 0.8639 (mmm) REVERT: E 130 GLN cc_start: 0.8252 (mp10) cc_final: 0.7955 (mp10) REVERT: E 209 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7408 (tt0) REVERT: E 210 MET cc_start: 0.8577 (tmm) cc_final: 0.8119 (tmm) REVERT: E 235 MET cc_start: 0.8383 (tpp) cc_final: 0.8063 (tpp) REVERT: E 266 LEU cc_start: 0.8606 (pp) cc_final: 0.8144 (tp) REVERT: E 436 LEU cc_start: 0.8383 (tt) cc_final: 0.8094 (pp) REVERT: E 452 LEU cc_start: 0.8704 (mt) cc_final: 0.8023 (tt) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1138 time to fit residues: 39.7761 Evaluate side-chains 170 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 99 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 43 optimal weight: 0.6980 chunk 145 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 ASN ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.125800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.103176 restraints weight = 29206.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.103724 restraints weight = 22210.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.104687 restraints weight = 16971.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.105560 restraints weight = 13541.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.105646 restraints weight = 11786.613| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14650 Z= 0.159 Angle : 0.712 9.234 20080 Z= 0.354 Chirality : 0.046 0.157 2400 Planarity : 0.004 0.031 2390 Dihedral : 6.182 31.871 2370 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.03 (0.20), residues: 1655 helix: -1.91 (0.19), residues: 590 sheet: -2.21 (0.24), residues: 380 loop : -1.75 (0.25), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 65 TYR 0.028 0.002 TYR D 286 PHE 0.036 0.002 PHE B 287 TRP 0.018 0.002 TRP A 168 HIS 0.003 0.001 HIS A 158 Details of bonding type rmsd covalent geometry : bond 0.00367 (14620) covalent geometry : angle 0.70766 (19995) SS BOND : bond 0.00118 ( 5) SS BOND : angle 0.27861 ( 10) hydrogen bonds : bond 0.03706 ( 455) hydrogen bonds : angle 6.42861 ( 1320) link_BETA1-4 : bond 0.00442 ( 10) link_BETA1-4 : angle 1.19059 ( 30) link_NAG-ASN : bond 0.00140 ( 15) link_NAG-ASN : angle 1.73889 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 LYS cc_start: 0.8141 (tmtt) cc_final: 0.7738 (tmtt) REVERT: A 209 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7597 (tm-30) REVERT: A 210 MET cc_start: 0.8661 (tmm) cc_final: 0.8226 (tmm) REVERT: A 235 MET cc_start: 0.8219 (tpp) cc_final: 0.7997 (tpp) REVERT: A 266 LEU cc_start: 0.8548 (pp) cc_final: 0.8256 (tp) REVERT: A 291 MET cc_start: 0.8792 (mmp) cc_final: 0.8458 (mmm) REVERT: A 436 LEU cc_start: 0.8369 (tt) cc_final: 0.8049 (pp) REVERT: B 197 LYS cc_start: 0.8092 (tptt) cc_final: 0.7883 (tmtt) REVERT: B 209 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7452 (tt0) REVERT: B 210 MET cc_start: 0.8803 (tmm) cc_final: 0.8504 (tmm) REVERT: C 209 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7511 (tt0) REVERT: C 266 LEU cc_start: 0.8516 (pp) cc_final: 0.8041 (tp) REVERT: D 209 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7578 (tt0) REVERT: D 291 MET cc_start: 0.8762 (mmp) cc_final: 0.8551 (mmm) REVERT: E 130 GLN cc_start: 0.8349 (mp10) cc_final: 0.8018 (mp10) REVERT: E 197 LYS cc_start: 0.8099 (tmtt) cc_final: 0.7761 (tptt) REVERT: E 209 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7684 (tt0) REVERT: E 210 MET cc_start: 0.8652 (tmm) cc_final: 0.8359 (tmm) REVERT: E 266 LEU cc_start: 0.8551 (pp) cc_final: 0.8099 (tp) REVERT: E 436 LEU cc_start: 0.8284 (tt) cc_final: 0.8015 (pp) REVERT: E 448 TYR cc_start: 0.7843 (t80) cc_final: 0.7474 (t80) REVERT: E 452 LEU cc_start: 0.8719 (mt) cc_final: 0.7955 (tt) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.1143 time to fit residues: 40.3944 Evaluate side-chains 168 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 49 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 160 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 122 optimal weight: 0.2980 chunk 86 optimal weight: 4.9990 chunk 156 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 161 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 HIS C 158 HIS ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 GLN E 158 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.125425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.101268 restraints weight = 28983.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.103441 restraints weight = 18451.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.104729 restraints weight = 13466.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.105736 restraints weight = 10959.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.106179 restraints weight = 9496.203| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14650 Z= 0.136 Angle : 0.704 9.700 20080 Z= 0.346 Chirality : 0.046 0.162 2400 Planarity : 0.004 0.031 2390 Dihedral : 6.014 31.661 2370 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.90 (0.20), residues: 1655 helix: -1.82 (0.20), residues: 590 sheet: -2.01 (0.24), residues: 390 loop : -1.72 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 120 TYR 0.023 0.002 TYR A 286 PHE 0.035 0.002 PHE E 287 TRP 0.012 0.001 TRP A 168 HIS 0.009 0.001 HIS E 119 Details of bonding type rmsd covalent geometry : bond 0.00316 (14620) covalent geometry : angle 0.69916 (19995) SS BOND : bond 0.00108 ( 5) SS BOND : angle 0.18788 ( 10) hydrogen bonds : bond 0.03428 ( 455) hydrogen bonds : angle 6.26646 ( 1320) link_BETA1-4 : bond 0.00457 ( 10) link_BETA1-4 : angle 1.16099 ( 30) link_NAG-ASN : bond 0.00081 ( 15) link_NAG-ASN : angle 1.77097 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 PHE cc_start: 0.8867 (p90) cc_final: 0.8563 (p90) REVERT: A 197 LYS cc_start: 0.7960 (tmtt) cc_final: 0.7545 (tmtt) REVERT: A 209 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7567 (tm-30) REVERT: A 210 MET cc_start: 0.8607 (tmm) cc_final: 0.8235 (tmm) REVERT: A 235 MET cc_start: 0.8286 (tpp) cc_final: 0.8010 (tpp) REVERT: A 266 LEU cc_start: 0.8515 (pp) cc_final: 0.8201 (tp) REVERT: A 291 MET cc_start: 0.8922 (mmp) cc_final: 0.8640 (mmm) REVERT: A 298 LEU cc_start: 0.8700 (tp) cc_final: 0.8436 (tp) REVERT: A 436 LEU cc_start: 0.8270 (tt) cc_final: 0.8025 (pp) REVERT: B 197 LYS cc_start: 0.8035 (tptt) cc_final: 0.7820 (tmtt) REVERT: B 209 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7327 (tt0) REVERT: B 210 MET cc_start: 0.8795 (tmm) cc_final: 0.8551 (tmm) REVERT: C 209 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7423 (tt0) REVERT: C 210 MET cc_start: 0.8546 (tmm) cc_final: 0.8180 (tmm) REVERT: C 266 LEU cc_start: 0.8455 (pp) cc_final: 0.7985 (tp) REVERT: C 436 LEU cc_start: 0.8031 (tt) cc_final: 0.7812 (pp) REVERT: D 130 GLN cc_start: 0.8244 (mp10) cc_final: 0.7570 (mp10) REVERT: D 209 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7508 (tt0) REVERT: D 210 MET cc_start: 0.8663 (tmm) cc_final: 0.8311 (tmm) REVERT: D 266 LEU cc_start: 0.8574 (pp) cc_final: 0.8200 (tp) REVERT: E 136 SER cc_start: 0.8894 (t) cc_final: 0.8688 (m) REVERT: E 197 LYS cc_start: 0.8080 (tmtt) cc_final: 0.7708 (tptt) REVERT: E 209 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7382 (tt0) REVERT: E 210 MET cc_start: 0.8623 (tmm) cc_final: 0.8251 (tmm) REVERT: E 266 LEU cc_start: 0.8509 (pp) cc_final: 0.8109 (tp) REVERT: E 436 LEU cc_start: 0.8235 (tt) cc_final: 0.7978 (pp) REVERT: E 448 TYR cc_start: 0.7562 (t80) cc_final: 0.7323 (t80) REVERT: E 452 LEU cc_start: 0.8705 (mt) cc_final: 0.7958 (tt) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.1063 time to fit residues: 38.0536 Evaluate side-chains 171 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 22 optimal weight: 10.0000 chunk 4 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 150 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 GLN ** 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 = 0.3612 r_free = 0.3612 target = 0.123642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.099283 restraints weight = 29295.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.101165 restraints weight = 19717.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.102463 restraints weight = 15021.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.103270 restraints weight = 12389.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.103784 restraints weight = 10919.113| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14650 Z= 0.204 Angle : 0.757 10.779 20080 Z= 0.378 Chirality : 0.047 0.179 2400 Planarity : 0.004 0.035 2390 Dihedral : 6.159 31.655 2370 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.90 (0.20), residues: 1655 helix: -1.67 (0.20), residues: 595 sheet: -2.30 (0.23), residues: 380 loop : -1.68 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 120 TYR 0.025 0.002 TYR D 286 PHE 0.032 0.002 PHE E 287 TRP 0.016 0.002 TRP A 168 HIS 0.008 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00472 (14620) covalent geometry : angle 0.75237 (19995) SS BOND : bond 0.00398 ( 5) SS BOND : angle 0.53412 ( 10) hydrogen bonds : bond 0.03744 ( 455) hydrogen bonds : angle 6.36983 ( 1320) link_BETA1-4 : bond 0.00477 ( 10) link_BETA1-4 : angle 1.18659 ( 30) link_NAG-ASN : bond 0.00233 ( 15) link_NAG-ASN : angle 1.79970 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 PHE cc_start: 0.8880 (p90) cc_final: 0.8627 (p90) REVERT: A 197 LYS cc_start: 0.8335 (tmtt) cc_final: 0.7922 (tmtt) REVERT: A 210 MET cc_start: 0.8766 (tmm) cc_final: 0.8477 (tmm) REVERT: A 255 LYS cc_start: 0.8215 (mtmm) cc_final: 0.7862 (ptmt) REVERT: A 266 LEU cc_start: 0.8562 (pp) cc_final: 0.8258 (tp) REVERT: A 458 ILE cc_start: 0.7592 (mm) cc_final: 0.7357 (mm) REVERT: B 209 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7544 (tt0) REVERT: B 266 LEU cc_start: 0.8662 (pp) cc_final: 0.8206 (tp) REVERT: C 195 GLN cc_start: 0.8724 (tm-30) cc_final: 0.8460 (tm-30) REVERT: C 209 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7713 (tt0) REVERT: C 210 MET cc_start: 0.8716 (tmm) cc_final: 0.8354 (tmm) REVERT: C 266 LEU cc_start: 0.8519 (pp) cc_final: 0.8079 (tp) REVERT: C 436 LEU cc_start: 0.8084 (tt) cc_final: 0.7836 (pp) REVERT: D 210 MET cc_start: 0.8755 (tmm) cc_final: 0.8363 (tmm) REVERT: D 266 LEU cc_start: 0.8706 (pp) cc_final: 0.8281 (tp) REVERT: E 197 LYS cc_start: 0.8294 (tmtt) cc_final: 0.8026 (tptt) REVERT: E 209 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7640 (tt0) REVERT: E 266 LEU cc_start: 0.8620 (pp) cc_final: 0.8169 (tp) REVERT: E 291 MET cc_start: 0.8335 (mmm) cc_final: 0.7635 (mmm) REVERT: E 436 LEU cc_start: 0.8158 (tt) cc_final: 0.7933 (pp) REVERT: E 448 TYR cc_start: 0.7710 (t80) cc_final: 0.7097 (t80) REVERT: E 458 ILE cc_start: 0.7736 (mm) cc_final: 0.7528 (mm) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1045 time to fit residues: 36.9949 Evaluate side-chains 167 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 44 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 98 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 GLN D 101 ASN D 158 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.125261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.100802 restraints weight = 28932.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.103032 restraints weight = 18136.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.104512 restraints weight = 13173.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.105297 restraints weight = 10624.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.105712 restraints weight = 9311.494| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14650 Z= 0.133 Angle : 0.715 8.954 20080 Z= 0.353 Chirality : 0.046 0.161 2400 Planarity : 0.004 0.034 2390 Dihedral : 5.982 31.216 2370 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.67 (0.21), residues: 1655 helix: -1.50 (0.21), residues: 595 sheet: -2.02 (0.24), residues: 390 loop : -1.62 (0.26), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 120 TYR 0.021 0.002 TYR B 286 PHE 0.036 0.002 PHE E 287 TRP 0.015 0.001 TRP B 156 HIS 0.001 0.000 HIS D 119 Details of bonding type rmsd covalent geometry : bond 0.00314 (14620) covalent geometry : angle 0.71010 (19995) SS BOND : bond 0.00346 ( 5) SS BOND : angle 0.22833 ( 10) hydrogen bonds : bond 0.03284 ( 455) hydrogen bonds : angle 6.13190 ( 1320) link_BETA1-4 : bond 0.00475 ( 10) link_BETA1-4 : angle 1.11009 ( 30) link_NAG-ASN : bond 0.00070 ( 15) link_NAG-ASN : angle 1.84475 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLN cc_start: 0.7892 (mm110) cc_final: 0.7668 (mm110) REVERT: A 103 PHE cc_start: 0.9028 (p90) cc_final: 0.8747 (p90) REVERT: A 197 LYS cc_start: 0.8017 (tmtt) cc_final: 0.7298 (tmtt) REVERT: A 209 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7291 (tm-30) REVERT: A 210 MET cc_start: 0.8667 (tmm) cc_final: 0.8023 (tmm) REVERT: A 266 LEU cc_start: 0.8556 (pp) cc_final: 0.8213 (tp) REVERT: A 436 LEU cc_start: 0.8246 (tt) cc_final: 0.7981 (pp) REVERT: B 209 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7453 (tt0) REVERT: B 210 MET cc_start: 0.8710 (tmm) cc_final: 0.8113 (tmm) REVERT: B 266 LEU cc_start: 0.8598 (pp) cc_final: 0.8143 (tp) REVERT: B 291 MET cc_start: 0.8014 (mmm) cc_final: 0.7445 (mmm) REVERT: C 195 GLN cc_start: 0.8611 (tm-30) cc_final: 0.8269 (tm-30) REVERT: C 209 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7627 (tt0) REVERT: C 210 MET cc_start: 0.8635 (tmm) cc_final: 0.8315 (tmm) REVERT: C 266 LEU cc_start: 0.8553 (pp) cc_final: 0.8085 (tp) REVERT: C 291 MET cc_start: 0.8295 (mmt) cc_final: 0.7644 (mmm) REVERT: C 436 LEU cc_start: 0.8021 (tt) cc_final: 0.7813 (pp) REVERT: D 130 GLN cc_start: 0.8297 (mp10) cc_final: 0.7618 (mp10) REVERT: D 197 LYS cc_start: 0.8083 (tmtt) cc_final: 0.7752 (tptt) REVERT: D 266 LEU cc_start: 0.8633 (pp) cc_final: 0.8259 (tp) REVERT: E 197 LYS cc_start: 0.8149 (tmtt) cc_final: 0.7854 (tptt) REVERT: E 209 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7551 (tt0) REVERT: E 210 MET cc_start: 0.8803 (tmm) cc_final: 0.8225 (tmm) REVERT: E 266 LEU cc_start: 0.8626 (pp) cc_final: 0.8166 (tp) REVERT: E 291 MET cc_start: 0.8401 (mmm) cc_final: 0.7675 (mmm) REVERT: E 436 LEU cc_start: 0.8084 (tt) cc_final: 0.7863 (pp) REVERT: E 448 TYR cc_start: 0.7762 (t80) cc_final: 0.7104 (t80) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.1103 time to fit residues: 40.9884 Evaluate side-chains 174 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 158 optimal weight: 0.0770 chunk 148 optimal weight: 0.0980 chunk 126 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN C 147 GLN ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 GLN E 101 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.126610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.102379 restraints weight = 28909.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.104632 restraints weight = 17950.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.106134 restraints weight = 12975.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.106918 restraints weight = 10360.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.107588 restraints weight = 9016.806| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14650 Z= 0.119 Angle : 0.710 11.137 20080 Z= 0.346 Chirality : 0.046 0.162 2400 Planarity : 0.004 0.031 2390 Dihedral : 5.786 32.024 2370 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.60 (0.21), residues: 1655 helix: -1.32 (0.21), residues: 590 sheet: -2.11 (0.23), residues: 415 loop : -1.56 (0.26), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 251 TYR 0.023 0.002 TYR D 286 PHE 0.036 0.002 PHE B 287 TRP 0.014 0.001 TRP A 426 HIS 0.002 0.000 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00281 (14620) covalent geometry : angle 0.70580 (19995) SS BOND : bond 0.00215 ( 5) SS BOND : angle 0.17856 ( 10) hydrogen bonds : bond 0.03140 ( 455) hydrogen bonds : angle 6.03874 ( 1320) link_BETA1-4 : bond 0.00471 ( 10) link_BETA1-4 : angle 1.07374 ( 30) link_NAG-ASN : bond 0.00092 ( 15) link_NAG-ASN : angle 1.75604 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 PHE cc_start: 0.8942 (p90) cc_final: 0.8637 (p90) REVERT: A 120 ARG cc_start: 0.8725 (mmp-170) cc_final: 0.7914 (mmp-170) REVERT: A 197 LYS cc_start: 0.7916 (tmtt) cc_final: 0.7247 (tmtt) REVERT: A 209 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7224 (tm-30) REVERT: A 210 MET cc_start: 0.8564 (tmm) cc_final: 0.8004 (tmm) REVERT: A 266 LEU cc_start: 0.8558 (pp) cc_final: 0.8191 (tp) REVERT: A 290 CYS cc_start: 0.7511 (p) cc_final: 0.7055 (p) REVERT: A 291 MET cc_start: 0.8042 (mmm) cc_final: 0.7511 (mmm) REVERT: B 209 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7283 (tt0) REVERT: B 210 MET cc_start: 0.8642 (tmm) cc_final: 0.8175 (tmm) REVERT: B 266 LEU cc_start: 0.8599 (pp) cc_final: 0.8130 (tp) REVERT: B 291 MET cc_start: 0.8136 (mmm) cc_final: 0.7540 (mmm) REVERT: C 195 GLN cc_start: 0.8633 (tm-30) cc_final: 0.8302 (tm-30) REVERT: C 209 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7500 (tt0) REVERT: C 210 MET cc_start: 0.8571 (tmm) cc_final: 0.8302 (tmm) REVERT: C 266 LEU cc_start: 0.8450 (pp) cc_final: 0.7982 (tp) REVERT: C 291 MET cc_start: 0.8179 (mmt) cc_final: 0.7537 (mmm) REVERT: C 436 LEU cc_start: 0.8015 (tt) cc_final: 0.7769 (pp) REVERT: D 130 GLN cc_start: 0.8269 (mp10) cc_final: 0.7616 (mp10) REVERT: D 197 LYS cc_start: 0.8027 (tmtt) cc_final: 0.7722 (tptt) REVERT: D 266 LEU cc_start: 0.8611 (pp) cc_final: 0.8214 (tp) REVERT: E 130 GLN cc_start: 0.8298 (mp10) cc_final: 0.7492 (mp10) REVERT: E 136 SER cc_start: 0.8876 (t) cc_final: 0.8649 (m) REVERT: E 197 LYS cc_start: 0.7987 (tmtt) cc_final: 0.7692 (tptt) REVERT: E 209 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7425 (tt0) REVERT: E 210 MET cc_start: 0.8735 (tmm) cc_final: 0.8265 (tmm) REVERT: E 266 LEU cc_start: 0.8653 (pp) cc_final: 0.8196 (tp) REVERT: E 436 LEU cc_start: 0.8087 (tt) cc_final: 0.7862 (pp) REVERT: E 448 TYR cc_start: 0.7713 (t80) cc_final: 0.7192 (t80) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.1143 time to fit residues: 41.5379 Evaluate side-chains 178 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 91 optimal weight: 0.5980 chunk 160 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 156 optimal weight: 0.8980 chunk 154 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 23 optimal weight: 0.0770 chunk 51 optimal weight: 8.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 GLN ** 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 = 0.3658 r_free = 0.3658 target = 0.127256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.103057 restraints weight = 29078.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.105299 restraints weight = 18200.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.106608 restraints weight = 13201.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.107504 restraints weight = 10699.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.108145 restraints weight = 9461.416| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14650 Z= 0.119 Angle : 0.707 10.205 20080 Z= 0.345 Chirality : 0.046 0.169 2400 Planarity : 0.004 0.032 2390 Dihedral : 5.663 31.831 2370 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.55 (0.21), residues: 1655 helix: -1.27 (0.21), residues: 590 sheet: -2.13 (0.22), residues: 425 loop : -1.50 (0.27), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 217 TYR 0.022 0.002 TYR B 286 PHE 0.032 0.002 PHE E 287 TRP 0.020 0.001 TRP A 426 HIS 0.002 0.000 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00279 (14620) covalent geometry : angle 0.70169 (19995) SS BOND : bond 0.00164 ( 5) SS BOND : angle 0.15077 ( 10) hydrogen bonds : bond 0.03090 ( 455) hydrogen bonds : angle 5.95702 ( 1320) link_BETA1-4 : bond 0.00465 ( 10) link_BETA1-4 : angle 1.12741 ( 30) link_NAG-ASN : bond 0.00134 ( 15) link_NAG-ASN : angle 1.77720 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 PHE cc_start: 0.8945 (p90) cc_final: 0.8605 (p90) REVERT: A 120 ARG cc_start: 0.8696 (mmp-170) cc_final: 0.8064 (mmp-170) REVERT: A 197 LYS cc_start: 0.7911 (tmtt) cc_final: 0.7536 (tmtt) REVERT: A 210 MET cc_start: 0.8513 (tmm) cc_final: 0.8056 (tmm) REVERT: A 266 LEU cc_start: 0.8581 (pp) cc_final: 0.8222 (tp) REVERT: B 197 LYS cc_start: 0.7936 (tmtt) cc_final: 0.7660 (tptt) REVERT: B 209 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7473 (tt0) REVERT: B 210 MET cc_start: 0.8643 (tmm) cc_final: 0.8189 (tmm) REVERT: B 266 LEU cc_start: 0.8582 (pp) cc_final: 0.8138 (tp) REVERT: B 291 MET cc_start: 0.8200 (mmm) cc_final: 0.7558 (mmm) REVERT: C 195 GLN cc_start: 0.8598 (tm-30) cc_final: 0.8274 (tm-30) REVERT: C 209 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7521 (tt0) REVERT: C 210 MET cc_start: 0.8519 (tmm) cc_final: 0.8284 (tmm) REVERT: C 266 LEU cc_start: 0.8476 (pp) cc_final: 0.8037 (tp) REVERT: C 291 MET cc_start: 0.8220 (mmt) cc_final: 0.7593 (mmm) REVERT: C 436 LEU cc_start: 0.8008 (tt) cc_final: 0.7763 (pp) REVERT: D 130 GLN cc_start: 0.8269 (mp10) cc_final: 0.7589 (mp10) REVERT: D 197 LYS cc_start: 0.8022 (tmtt) cc_final: 0.7700 (tptt) REVERT: D 255 LYS cc_start: 0.8199 (ptpp) cc_final: 0.7879 (ptmt) REVERT: D 266 LEU cc_start: 0.8558 (pp) cc_final: 0.8163 (tp) REVERT: E 130 GLN cc_start: 0.8132 (mp10) cc_final: 0.7364 (mp10) REVERT: E 195 GLN cc_start: 0.8722 (tm-30) cc_final: 0.8253 (tm-30) REVERT: E 197 LYS cc_start: 0.7984 (tmtt) cc_final: 0.7750 (tptt) REVERT: E 209 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7510 (tt0) REVERT: E 210 MET cc_start: 0.8632 (tmm) cc_final: 0.8250 (tmm) REVERT: E 266 LEU cc_start: 0.8650 (pp) cc_final: 0.8184 (tp) REVERT: E 436 LEU cc_start: 0.8121 (tt) cc_final: 0.7869 (pp) REVERT: E 448 TYR cc_start: 0.7830 (t80) cc_final: 0.7185 (t80) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.1081 time to fit residues: 39.3651 Evaluate side-chains 171 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 59 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 chunk 68 optimal weight: 0.3980 chunk 119 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 21 optimal weight: 0.1980 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 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.125748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.101536 restraints weight = 29082.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.103701 restraints weight = 18597.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.105084 restraints weight = 13659.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.105875 restraints weight = 11101.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.106561 restraints weight = 9690.061| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14650 Z= 0.150 Angle : 0.723 10.377 20080 Z= 0.356 Chirality : 0.046 0.164 2400 Planarity : 0.004 0.032 2390 Dihedral : 5.723 31.943 2370 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.50 (0.21), residues: 1655 helix: -1.24 (0.21), residues: 595 sheet: -2.14 (0.23), residues: 380 loop : -1.53 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 120 TYR 0.027 0.002 TYR B 286 PHE 0.035 0.002 PHE B 287 TRP 0.017 0.002 TRP A 426 HIS 0.003 0.001 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.00354 (14620) covalent geometry : angle 0.71796 (19995) SS BOND : bond 0.00073 ( 5) SS BOND : angle 0.23885 ( 10) hydrogen bonds : bond 0.03242 ( 455) hydrogen bonds : angle 5.96450 ( 1320) link_BETA1-4 : bond 0.00390 ( 10) link_BETA1-4 : angle 1.11814 ( 30) link_NAG-ASN : bond 0.00043 ( 15) link_NAG-ASN : angle 1.74732 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2019.71 seconds wall clock time: 35 minutes 59.49 seconds (2159.49 seconds total)