Starting phenix.real_space_refine on Fri Sep 27 09:33:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ene_28271/09_2024/8ene_28271.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ene_28271/09_2024/8ene_28271.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ene_28271/09_2024/8ene_28271.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ene_28271/09_2024/8ene_28271.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ene_28271/09_2024/8ene_28271.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ene_28271/09_2024/8ene_28271.cif" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.043 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 76 5.16 5 C 9805 2.51 5 N 2599 2.21 5 O 2916 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 15404 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3808 Classifications: {'peptide': 493} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 469} Chain: "B" Number of atoms: 3808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3808 Classifications: {'peptide': 493} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 469} Chain: "C" Number of atoms: 3804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3804 Classifications: {'peptide': 493} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 469} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 3808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3808 Classifications: {'peptide': 493} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 469} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.29, per 1000 atoms: 0.60 Number of scatterers: 15404 At special positions: 0 Unit cell: (109.08, 106.92, 100.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 76 16.00 P 8 15.00 O 2916 8.00 N 2599 7.00 C 9805 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 3.71 Conformation dependent library (CDL) restraints added in 1.9 seconds 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3568 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 22 sheets defined 45.2% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 56 through 71 Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 81 through 99 Processing helix chain 'A' and resid 99 through 112 Processing helix chain 'A' and resid 114 through 121 Processing helix chain 'A' and resid 121 through 137 Processing helix chain 'A' and resid 171 through 186 Proline residue: A 182 - end of helix Processing helix chain 'A' and resid 199 through 213 removed outlier: 3.512A pdb=" N LEU A 203 " --> pdb=" O PRO A 199 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A 213 " --> pdb=" O ILE A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 236 Processing helix chain 'A' and resid 247 through 261 Processing helix chain 'A' and resid 283 through 297 Processing helix chain 'A' and resid 298 through 301 Processing helix chain 'A' and resid 315 through 330 Processing helix chain 'A' and resid 347 through 365 Processing helix chain 'A' and resid 394 through 398 Processing helix chain 'A' and resid 413 through 423 Processing helix chain 'A' and resid 436 through 447 Processing helix chain 'A' and resid 479 through 485 removed outlier: 3.697A pdb=" N GLU A 485 " --> pdb=" O TYR A 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 71 Processing helix chain 'B' and resid 75 through 80 Processing helix chain 'B' and resid 81 through 99 Processing helix chain 'B' and resid 99 through 112 Processing helix chain 'B' and resid 114 through 121 Processing helix chain 'B' and resid 121 through 137 Processing helix chain 'B' and resid 171 through 186 Proline residue: B 182 - end of helix Processing helix chain 'B' and resid 199 through 213 removed outlier: 3.545A pdb=" N GLY B 213 " --> pdb=" O ILE B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 236 Processing helix chain 'B' and resid 247 through 261 Processing helix chain 'B' and resid 283 through 297 Processing helix chain 'B' and resid 298 through 301 Processing helix chain 'B' and resid 315 through 330 Processing helix chain 'B' and resid 347 through 365 Processing helix chain 'B' and resid 394 through 398 Processing helix chain 'B' and resid 413 through 423 Processing helix chain 'B' and resid 436 through 447 Processing helix chain 'B' and resid 479 through 485 removed outlier: 3.713A pdb=" N GLU B 485 " --> pdb=" O TYR B 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 71 Processing helix chain 'C' and resid 75 through 80 Processing helix chain 'C' and resid 81 through 99 Processing helix chain 'C' and resid 99 through 112 Processing helix chain 'C' and resid 114 through 121 Processing helix chain 'C' and resid 121 through 137 Processing helix chain 'C' and resid 171 through 186 Proline residue: C 182 - end of helix Processing helix chain 'C' and resid 199 through 213 removed outlier: 3.551A pdb=" N LEU C 203 " --> pdb=" O PRO C 199 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY C 213 " --> pdb=" O ILE C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 236 Processing helix chain 'C' and resid 247 through 260 Processing helix chain 'C' and resid 283 through 297 Processing helix chain 'C' and resid 298 through 301 Processing helix chain 'C' and resid 315 through 330 Processing helix chain 'C' and resid 347 through 364 Processing helix chain 'C' and resid 394 through 398 Processing helix chain 'C' and resid 413 through 422 Processing helix chain 'C' and resid 437 through 447 Processing helix chain 'C' and resid 479 through 485 removed outlier: 3.670A pdb=" N GLU C 485 " --> pdb=" O TYR C 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 71 Processing helix chain 'D' and resid 75 through 80 Processing helix chain 'D' and resid 81 through 99 Processing helix chain 'D' and resid 99 through 112 Processing helix chain 'D' and resid 114 through 121 Processing helix chain 'D' and resid 121 through 137 Processing helix chain 'D' and resid 171 through 186 Proline residue: D 182 - end of helix Processing helix chain 'D' and resid 199 through 213 removed outlier: 3.535A pdb=" N LEU D 203 " --> pdb=" O PRO D 199 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY D 213 " --> pdb=" O ILE D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 236 Processing helix chain 'D' and resid 247 through 261 Processing helix chain 'D' and resid 283 through 297 Processing helix chain 'D' and resid 298 through 301 Processing helix chain 'D' and resid 315 through 330 Processing helix chain 'D' and resid 347 through 365 Processing helix chain 'D' and resid 394 through 398 Processing helix chain 'D' and resid 413 through 423 Processing helix chain 'D' and resid 437 through 447 Processing helix chain 'D' and resid 479 through 485 removed outlier: 3.683A pdb=" N GLU D 485 " --> pdb=" O TYR D 481 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 25 Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 42 removed outlier: 6.124A pdb=" N PHE A 38 " --> pdb=" O GLN A 51 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N GLN A 51 " --> pdb=" O PHE A 38 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL A 40 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU A 47 " --> pdb=" O ASN A 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 143 through 145 removed outlier: 4.238A pdb=" N THR A 153 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N VAL B 452 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N THR A 491 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N VAL B 454 " --> pdb=" O THR A 491 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR A 493 " --> pdb=" O VAL B 454 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N SER B 274 " --> pdb=" O ALA B 306 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N SER B 307 " --> pdb=" O VAL B 405 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN B 407 " --> pdb=" O SER B 307 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL B 386 " --> pdb=" O GLU B 369 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 219 through 221 removed outlier: 6.281A pdb=" N CYS A 163 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N LYS A 193 " --> pdb=" O CYS A 163 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLN A 165 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A 268 " --> pdb=" O ASN A 474 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 367 through 370 removed outlier: 6.467A pdb=" N VAL A 386 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N SER A 307 " --> pdb=" O GLN A 407 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N MET A 409 " --> pdb=" O SER A 307 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ILE A 309 " --> pdb=" O MET A 409 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N PHE A 411 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL A 311 " --> pdb=" O PHE A 411 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N SER A 274 " --> pdb=" O ALA A 306 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR B 153 " --> pdb=" O ILE B 145 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 374 through 375 removed outlier: 4.043A pdb=" N PHE A 381 " --> pdb=" O TRP A 375 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 23 through 25 Processing sheet with id=AA8, first strand: chain 'B' and resid 37 through 42 removed outlier: 6.212A pdb=" N PHE B 38 " --> pdb=" O GLN B 51 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLN B 51 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL B 40 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU B 47 " --> pdb=" O ASN B 42 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 219 through 221 removed outlier: 6.329A pdb=" N CYS B 163 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N LYS B 193 " --> pdb=" O CYS B 163 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLN B 165 " --> pdb=" O LYS B 193 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 374 through 375 removed outlier: 4.064A pdb=" N PHE B 381 " --> pdb=" O TRP B 375 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 426 through 427 removed outlier: 3.735A pdb=" N GLY B 427 " --> pdb=" O PHE B 469 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 466 through 467 Processing sheet with id=AB4, first strand: chain 'C' and resid 23 through 25 Processing sheet with id=AB5, first strand: chain 'C' and resid 37 through 42 removed outlier: 6.346A pdb=" N PHE C 38 " --> pdb=" O GLN C 51 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLN C 51 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL C 40 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU C 47 " --> pdb=" O ASN C 42 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 143 through 145 removed outlier: 4.261A pdb=" N THR C 153 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N VAL D 452 " --> pdb=" O VAL C 489 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N THR C 491 " --> pdb=" O VAL D 452 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N VAL D 454 " --> pdb=" O THR C 491 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N THR C 493 " --> pdb=" O VAL D 454 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N SER D 274 " --> pdb=" O ALA D 306 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N SER D 307 " --> pdb=" O VAL D 405 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN D 407 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL D 386 " --> pdb=" O GLU D 369 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 219 through 221 removed outlier: 6.309A pdb=" N CYS C 163 " --> pdb=" O VAL C 191 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LYS C 193 " --> pdb=" O CYS C 163 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLN C 165 " --> pdb=" O LYS C 193 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 367 through 370 removed outlier: 6.468A pdb=" N VAL C 386 " --> pdb=" O GLU C 369 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N SER C 307 " --> pdb=" O GLN C 407 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N MET C 409 " --> pdb=" O SER C 307 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ILE C 309 " --> pdb=" O MET C 409 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N PHE C 411 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL C 311 " --> pdb=" O PHE C 411 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N SER C 274 " --> pdb=" O ALA C 306 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR D 153 " --> pdb=" O ILE D 145 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 374 through 375 removed outlier: 4.000A pdb=" N PHE C 381 " --> pdb=" O TRP C 375 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 23 through 25 Processing sheet with id=AC2, first strand: chain 'D' and resid 37 through 42 removed outlier: 6.143A pdb=" N PHE D 38 " --> pdb=" O GLN D 51 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLN D 51 " --> pdb=" O PHE D 38 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL D 40 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU D 47 " --> pdb=" O ASN D 42 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 219 through 221 removed outlier: 6.347A pdb=" N CYS D 163 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N LYS D 193 " --> pdb=" O CYS D 163 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLN D 165 " --> pdb=" O LYS D 193 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU D 268 " --> pdb=" O ASN D 474 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 374 through 375 removed outlier: 3.995A pdb=" N PHE D 381 " --> pdb=" O TRP D 375 " (cutoff:3.500A) 797 hydrogen bonds defined for protein. 2283 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.31 Time building geometry restraints manager: 4.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5004 1.34 - 1.46: 3410 1.46 - 1.58: 7214 1.58 - 1.69: 12 1.69 - 1.81: 108 Bond restraints: 15748 Sorted by residual: bond pdb=" C3N NAD C 601 " pdb=" C4N NAD C 601 " ideal model delta sigma weight residual 1.390 1.499 -0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" C3N NAD A 601 " pdb=" C4N NAD A 601 " ideal model delta sigma weight residual 1.390 1.499 -0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C3N NAD D 601 " pdb=" C4N NAD D 601 " ideal model delta sigma weight residual 1.390 1.499 -0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C3N NAD B 601 " pdb=" C4N NAD B 601 " ideal model delta sigma weight residual 1.390 1.498 -0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C4N NAD B 601 " pdb=" C5N NAD B 601 " ideal model delta sigma weight residual 1.384 1.485 -0.101 2.00e-02 2.50e+03 2.54e+01 ... (remaining 15743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 21058 2.06 - 4.11: 254 4.11 - 6.17: 24 6.17 - 8.23: 8 8.23 - 10.28: 8 Bond angle restraints: 21352 Sorted by residual: angle pdb=" PA NAD A 601 " pdb=" O3 NAD A 601 " pdb=" PN NAD A 601 " ideal model delta sigma weight residual 126.50 136.78 -10.28 3.00e+00 1.11e-01 1.17e+01 angle pdb=" PA NAD D 601 " pdb=" O3 NAD D 601 " pdb=" PN NAD D 601 " ideal model delta sigma weight residual 126.50 136.74 -10.24 3.00e+00 1.11e-01 1.17e+01 angle pdb=" PA NAD B 601 " pdb=" O3 NAD B 601 " pdb=" PN NAD B 601 " ideal model delta sigma weight residual 126.50 136.70 -10.20 3.00e+00 1.11e-01 1.16e+01 angle pdb=" PA NAD C 601 " pdb=" O3 NAD C 601 " pdb=" PN NAD C 601 " ideal model delta sigma weight residual 126.50 136.68 -10.18 3.00e+00 1.11e-01 1.15e+01 angle pdb=" C3N NAD C 601 " pdb=" C4N NAD C 601 " pdb=" C5N NAD C 601 " ideal model delta sigma weight residual 119.68 110.28 9.40 3.00e+00 1.11e-01 9.81e+00 ... (remaining 21347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.87: 8304 11.87 - 23.74: 792 23.74 - 35.61: 231 35.61 - 47.48: 98 47.48 - 59.35: 83 Dihedral angle restraints: 9508 sinusoidal: 3908 harmonic: 5600 Sorted by residual: dihedral pdb=" CA THR D 144 " pdb=" C THR D 144 " pdb=" N ILE D 145 " pdb=" CA ILE D 145 " ideal model delta harmonic sigma weight residual 180.00 -160.40 -19.60 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA THR C 144 " pdb=" C THR C 144 " pdb=" N ILE C 145 " pdb=" CA ILE C 145 " ideal model delta harmonic sigma weight residual -180.00 -160.98 -19.02 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA THR A 144 " pdb=" C THR A 144 " pdb=" N ILE A 145 " pdb=" CA ILE A 145 " ideal model delta harmonic sigma weight residual 180.00 -161.82 -18.18 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 9505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1504 0.031 - 0.061: 550 0.061 - 0.092: 159 0.092 - 0.123: 144 0.123 - 0.154: 7 Chirality restraints: 2364 Sorted by residual: chirality pdb=" C2B NAD D 601 " pdb=" C1B NAD D 601 " pdb=" C3B NAD D 601 " pdb=" O2B NAD D 601 " both_signs ideal model delta sigma weight residual False -2.53 -2.69 0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" C2B NAD B 601 " pdb=" C1B NAD B 601 " pdb=" C3B NAD B 601 " pdb=" O2B NAD B 601 " both_signs ideal model delta sigma weight residual False -2.53 -2.68 0.15 2.00e-01 2.50e+01 5.80e-01 chirality pdb=" C2B NAD C 601 " pdb=" C1B NAD C 601 " pdb=" C3B NAD C 601 " pdb=" O2B NAD C 601 " both_signs ideal model delta sigma weight residual False -2.53 -2.68 0.15 2.00e-01 2.50e+01 5.69e-01 ... (remaining 2361 not shown) Planarity restraints: 2736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAD B 601 " -0.025 2.00e-02 2.50e+03 6.53e-02 8.52e+01 pdb=" C2N NAD B 601 " -0.057 2.00e-02 2.50e+03 pdb=" C3N NAD B 601 " -0.059 2.00e-02 2.50e+03 pdb=" C4N NAD B 601 " -0.068 2.00e-02 2.50e+03 pdb=" C5N NAD B 601 " -0.010 2.00e-02 2.50e+03 pdb=" C6N NAD B 601 " 0.109 2.00e-02 2.50e+03 pdb=" C7N NAD B 601 " 0.100 2.00e-02 2.50e+03 pdb=" N1N NAD B 601 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD D 601 " 0.024 2.00e-02 2.50e+03 5.70e-02 6.49e+01 pdb=" C2N NAD D 601 " 0.047 2.00e-02 2.50e+03 pdb=" C3N NAD D 601 " 0.054 2.00e-02 2.50e+03 pdb=" C4N NAD D 601 " 0.051 2.00e-02 2.50e+03 pdb=" C5N NAD D 601 " 0.020 2.00e-02 2.50e+03 pdb=" C6N NAD D 601 " -0.101 2.00e-02 2.50e+03 pdb=" C7N NAD D 601 " -0.084 2.00e-02 2.50e+03 pdb=" N1N NAD D 601 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD A 601 " -0.009 2.00e-02 2.50e+03 4.55e-02 4.14e+01 pdb=" C2N NAD A 601 " 0.056 2.00e-02 2.50e+03 pdb=" C3N NAD A 601 " 0.057 2.00e-02 2.50e+03 pdb=" C4N NAD A 601 " 0.034 2.00e-02 2.50e+03 pdb=" C5N NAD A 601 " -0.009 2.00e-02 2.50e+03 pdb=" C6N NAD A 601 " -0.049 2.00e-02 2.50e+03 pdb=" C7N NAD A 601 " -0.080 2.00e-02 2.50e+03 pdb=" N1N NAD A 601 " -0.000 2.00e-02 2.50e+03 ... (remaining 2733 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3481 2.79 - 3.32: 14534 3.32 - 3.84: 26298 3.84 - 4.37: 32370 4.37 - 4.90: 54688 Nonbonded interactions: 131371 Sorted by model distance: nonbonded pdb=" O SER B 307 " pdb=" NE2 GLN B 407 " model vdw 2.262 3.120 nonbonded pdb=" OD1 ASP C 281 " pdb=" OG1 THR C 434 " model vdw 2.269 3.040 nonbonded pdb=" OD1 ASP A 281 " pdb=" OG1 THR A 434 " model vdw 2.273 3.040 nonbonded pdb=" OG SER B 461 " pdb=" OE1 GLN B 463 " model vdw 2.274 3.040 nonbonded pdb=" O SER A 307 " pdb=" NE2 GLN A 407 " model vdw 2.290 3.120 ... (remaining 131366 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 501 or resid 601)) selection = (chain 'B' and (resid 9 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 501 or resid 601)) selection = chain 'C' selection = (chain 'D' and (resid 9 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 501 or resid 601)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 36.660 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.070 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:16.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 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 : 0.005 0.109 15748 Z= 0.304 Angle : 0.598 10.283 21352 Z= 0.308 Chirality : 0.041 0.154 2364 Planarity : 0.005 0.065 2736 Dihedral : 12.542 59.347 5940 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.15 % Allowed : 6.01 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.20), residues: 1964 helix: 1.11 (0.19), residues: 828 sheet: 0.10 (0.26), residues: 420 loop : -0.39 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 453 HIS 0.002 0.001 HIS D 204 PHE 0.009 0.001 PHE D 290 TYR 0.016 0.001 TYR D 351 ARG 0.004 0.000 ARG D 131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 346 time to evaluate : 2.527 Fit side-chains revert: symmetry clash REVERT: A 13 LEU cc_start: 0.5007 (OUTLIER) cc_final: 0.4634 (pp) REVERT: A 409 MET cc_start: 0.7342 (mtp) cc_final: 0.7068 (mtm) REVERT: A 441 ILE cc_start: 0.7706 (mm) cc_final: 0.7497 (mm) REVERT: B 13 LEU cc_start: 0.4899 (OUTLIER) cc_final: 0.4532 (pp) REVERT: B 341 THR cc_start: 0.7504 (p) cc_final: 0.7219 (p) REVERT: B 441 ILE cc_start: 0.7592 (mm) cc_final: 0.7357 (mm) REVERT: C 13 LEU cc_start: 0.4919 (OUTLIER) cc_final: 0.4543 (pp) REVERT: C 330 TYR cc_start: 0.6776 (OUTLIER) cc_final: 0.5236 (t80) REVERT: C 409 MET cc_start: 0.7381 (mtp) cc_final: 0.7121 (mtm) REVERT: C 441 ILE cc_start: 0.7596 (mm) cc_final: 0.7348 (mm) REVERT: D 330 TYR cc_start: 0.6799 (OUTLIER) cc_final: 0.5385 (t80) REVERT: D 409 MET cc_start: 0.7305 (mtp) cc_final: 0.7051 (mtm) outliers start: 35 outliers final: 12 residues processed: 369 average time/residue: 1.2568 time to fit residues: 513.6257 Evaluate side-chains 249 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 232 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 330 TYR Chi-restraints excluded: chain C residue 469 PHE Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 330 TYR Chi-restraints excluded: chain D residue 370 CYS Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain D residue 469 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 82 optimal weight: 0.1980 chunk 50 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 153 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 177 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS A 299 GLN A 350 GLN A 389 ASN A 474 ASN B 157 HIS B 220 ASN B 299 GLN B 301 GLN B 342 GLN B 389 ASN B 474 ASN C 157 HIS C 299 GLN C 301 GLN C 342 GLN C 350 GLN D 299 GLN D 301 GLN D 342 GLN D 389 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15748 Z= 0.230 Angle : 0.542 6.749 21352 Z= 0.290 Chirality : 0.043 0.160 2364 Planarity : 0.004 0.038 2736 Dihedral : 9.513 57.661 2353 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.23 % Allowed : 14.04 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.20), residues: 1964 helix: 1.29 (0.18), residues: 864 sheet: 0.14 (0.26), residues: 420 loop : -0.42 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 178 HIS 0.008 0.001 HIS C 484 PHE 0.010 0.001 PHE D 290 TYR 0.019 0.002 TYR D 351 ARG 0.003 0.001 ARG C 420 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 247 time to evaluate : 1.703 Fit side-chains revert: symmetry clash REVERT: A 13 LEU cc_start: 0.4983 (OUTLIER) cc_final: 0.4639 (pp) REVERT: A 19 GLN cc_start: 0.6963 (OUTLIER) cc_final: 0.6189 (mm-40) REVERT: A 156 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7658 (mtp85) REVERT: A 329 LYS cc_start: 0.7210 (mtpt) cc_final: 0.6973 (mtpt) REVERT: A 399 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7299 (mt-10) REVERT: A 409 MET cc_start: 0.7450 (mtp) cc_final: 0.7180 (mtm) REVERT: A 481 TYR cc_start: 0.6758 (t80) cc_final: 0.6416 (t80) REVERT: A 485 GLU cc_start: 0.6673 (OUTLIER) cc_final: 0.6172 (mp0) REVERT: B 13 LEU cc_start: 0.4936 (OUTLIER) cc_final: 0.4607 (pp) REVERT: B 19 GLN cc_start: 0.6978 (OUTLIER) cc_final: 0.6365 (mm-40) REVERT: B 329 LYS cc_start: 0.7205 (mtpt) cc_final: 0.6962 (mtpt) REVERT: B 330 TYR cc_start: 0.6936 (OUTLIER) cc_final: 0.6032 (t80) REVERT: B 341 THR cc_start: 0.7219 (p) cc_final: 0.6756 (p) REVERT: C 13 LEU cc_start: 0.4892 (OUTLIER) cc_final: 0.4550 (pp) REVERT: C 19 GLN cc_start: 0.6900 (OUTLIER) cc_final: 0.5841 (mm-40) REVERT: C 156 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7649 (mtp85) REVERT: C 329 LYS cc_start: 0.7221 (mtpt) cc_final: 0.6991 (mtpt) REVERT: C 409 MET cc_start: 0.7502 (mtp) cc_final: 0.7174 (mtm) REVERT: D 19 GLN cc_start: 0.6958 (OUTLIER) cc_final: 0.6280 (mm-40) REVERT: D 102 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7354 (tt) REVERT: D 156 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7634 (mtp85) REVERT: D 329 LYS cc_start: 0.7275 (mtpt) cc_final: 0.7057 (mtpt) REVERT: D 409 MET cc_start: 0.7358 (mtp) cc_final: 0.7004 (mtm) REVERT: D 438 ASP cc_start: 0.5915 (m-30) cc_final: 0.5635 (t0) REVERT: D 441 ILE cc_start: 0.7731 (mm) cc_final: 0.7413 (mm) REVERT: D 481 TYR cc_start: 0.6661 (t80) cc_final: 0.6351 (t80) REVERT: D 485 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.6214 (mp0) outliers start: 69 outliers final: 31 residues processed: 279 average time/residue: 1.2472 time to fit residues: 385.3141 Evaluate side-chains 279 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 233 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 469 PHE Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 469 PHE Chi-restraints excluded: chain D residue 485 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 148 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 178 optimal weight: 0.6980 chunk 192 optimal weight: 0.8980 chunk 158 optimal weight: 0.8980 chunk 176 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 143 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 ASN D 157 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15748 Z= 0.191 Angle : 0.498 6.641 21352 Z= 0.267 Chirality : 0.042 0.160 2364 Planarity : 0.004 0.040 2736 Dihedral : 8.332 58.844 2344 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.05 % Allowed : 16.80 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.20), residues: 1964 helix: 1.46 (0.18), residues: 864 sheet: 0.17 (0.26), residues: 420 loop : -0.44 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 178 HIS 0.009 0.001 HIS C 484 PHE 0.010 0.001 PHE D 290 TYR 0.020 0.002 TYR B 351 ARG 0.006 0.000 ARG D 321 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 246 time to evaluate : 1.739 Fit side-chains REVERT: A 19 GLN cc_start: 0.6945 (OUTLIER) cc_final: 0.6070 (mm-40) REVERT: A 156 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7790 (mtp85) REVERT: A 409 MET cc_start: 0.7413 (mtp) cc_final: 0.7156 (mtm) REVERT: B 13 LEU cc_start: 0.4928 (OUTLIER) cc_final: 0.4596 (pp) REVERT: B 19 GLN cc_start: 0.6926 (OUTLIER) cc_final: 0.6247 (mm-40) REVERT: B 330 TYR cc_start: 0.6928 (OUTLIER) cc_final: 0.6164 (t80) REVERT: B 341 THR cc_start: 0.7175 (p) cc_final: 0.6734 (p) REVERT: B 485 GLU cc_start: 0.6808 (OUTLIER) cc_final: 0.6585 (mm-30) REVERT: C 19 GLN cc_start: 0.6958 (OUTLIER) cc_final: 0.5910 (mm-40) REVERT: C 156 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7745 (mtp85) REVERT: C 329 LYS cc_start: 0.7226 (mtpt) cc_final: 0.6949 (mtpt) REVERT: C 399 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7270 (mt-10) REVERT: C 409 MET cc_start: 0.7464 (mtp) cc_final: 0.7174 (mtm) REVERT: C 481 TYR cc_start: 0.6749 (t80) cc_final: 0.6373 (t80) REVERT: C 485 GLU cc_start: 0.6715 (OUTLIER) cc_final: 0.6235 (mp0) REVERT: D 19 GLN cc_start: 0.6951 (OUTLIER) cc_final: 0.6163 (mm-40) REVERT: D 102 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7400 (tt) REVERT: D 156 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7742 (mtp85) REVERT: D 329 LYS cc_start: 0.7266 (mtpt) cc_final: 0.6991 (mtpt) REVERT: D 409 MET cc_start: 0.7416 (mtp) cc_final: 0.7067 (mtm) REVERT: D 438 ASP cc_start: 0.5915 (m-30) cc_final: 0.5559 (t0) REVERT: D 441 ILE cc_start: 0.7656 (mm) cc_final: 0.7377 (mm) outliers start: 66 outliers final: 40 residues processed: 280 average time/residue: 1.1394 time to fit residues: 355.8789 Evaluate side-chains 281 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 228 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 412 LYS Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 469 PHE Chi-restraints excluded: chain C residue 485 GLU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 464 CYS Chi-restraints excluded: chain D residue 469 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 5.9990 chunk 134 optimal weight: 0.0980 chunk 92 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 178 optimal weight: 0.6980 chunk 189 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 51 optimal weight: 0.0070 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 ASN ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15748 Z= 0.214 Angle : 0.507 5.811 21352 Z= 0.271 Chirality : 0.042 0.158 2364 Planarity : 0.004 0.047 2736 Dihedral : 8.038 58.800 2344 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.35 % Allowed : 17.60 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.20), residues: 1964 helix: 1.45 (0.18), residues: 864 sheet: 0.12 (0.26), residues: 420 loop : -0.41 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 178 HIS 0.009 0.001 HIS A 484 PHE 0.010 0.001 PHE C 290 TYR 0.021 0.002 TYR B 351 ARG 0.009 0.001 ARG C 321 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 232 time to evaluate : 1.714 Fit side-chains REVERT: A 19 GLN cc_start: 0.6962 (OUTLIER) cc_final: 0.6033 (mm-40) REVERT: A 156 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7773 (mtp85) REVERT: A 399 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7283 (mt-10) REVERT: A 409 MET cc_start: 0.7435 (mtp) cc_final: 0.7175 (mtm) REVERT: B 13 LEU cc_start: 0.4955 (OUTLIER) cc_final: 0.4628 (pp) REVERT: B 19 GLN cc_start: 0.6889 (OUTLIER) cc_final: 0.6236 (mm-40) REVERT: B 330 TYR cc_start: 0.6947 (OUTLIER) cc_final: 0.5920 (t80) REVERT: B 341 THR cc_start: 0.7169 (p) cc_final: 0.6643 (p) REVERT: B 485 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.6558 (mm-30) REVERT: C 19 GLN cc_start: 0.6972 (OUTLIER) cc_final: 0.5938 (mm-40) REVERT: C 156 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7732 (mtp85) REVERT: C 399 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7286 (mt-10) REVERT: C 409 MET cc_start: 0.7479 (mtp) cc_final: 0.7161 (mtm) REVERT: D 19 GLN cc_start: 0.6927 (OUTLIER) cc_final: 0.6037 (mm-40) REVERT: D 102 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7431 (tt) REVERT: D 156 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7737 (mtp85) REVERT: D 409 MET cc_start: 0.7494 (mtp) cc_final: 0.7136 (mtm) REVERT: D 441 ILE cc_start: 0.7640 (mm) cc_final: 0.7385 (mm) REVERT: D 485 GLU cc_start: 0.6712 (OUTLIER) cc_final: 0.6200 (mp0) outliers start: 71 outliers final: 43 residues processed: 269 average time/residue: 1.2289 time to fit residues: 367.5362 Evaluate side-chains 281 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 224 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 412 LYS Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 464 CYS Chi-restraints excluded: chain D residue 469 PHE Chi-restraints excluded: chain D residue 485 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 170 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 ASN C 301 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 15748 Z= 0.375 Angle : 0.593 7.244 21352 Z= 0.317 Chirality : 0.045 0.160 2364 Planarity : 0.005 0.051 2736 Dihedral : 8.249 58.703 2342 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.33 % Allowed : 16.98 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.19), residues: 1964 helix: 1.24 (0.18), residues: 856 sheet: -0.16 (0.25), residues: 420 loop : -0.54 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 178 HIS 0.007 0.002 HIS C 484 PHE 0.015 0.002 PHE C 24 TYR 0.024 0.002 TYR B 351 ARG 0.009 0.001 ARG A 321 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 219 time to evaluate : 1.561 Fit side-chains REVERT: A 19 GLN cc_start: 0.7071 (OUTLIER) cc_final: 0.6137 (mm-40) REVERT: A 156 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7663 (mtp85) REVERT: A 399 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7305 (mt-10) REVERT: A 485 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.6273 (mp0) REVERT: B 19 GLN cc_start: 0.6985 (OUTLIER) cc_final: 0.6176 (mm-40) REVERT: B 330 TYR cc_start: 0.6932 (OUTLIER) cc_final: 0.5622 (t80) REVERT: B 341 THR cc_start: 0.7328 (p) cc_final: 0.6726 (p) REVERT: B 485 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6638 (mm-30) REVERT: C 19 GLN cc_start: 0.7081 (OUTLIER) cc_final: 0.6071 (mm-40) REVERT: C 156 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7629 (mtp85) REVERT: C 399 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7294 (mt-10) REVERT: C 409 MET cc_start: 0.7626 (mtp) cc_final: 0.7296 (mtm) REVERT: D 19 GLN cc_start: 0.7044 (OUTLIER) cc_final: 0.6085 (mm-40) REVERT: D 58 GLU cc_start: 0.6534 (mp0) cc_final: 0.6260 (mp0) REVERT: D 102 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7415 (tt) REVERT: D 156 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7657 (mtp85) REVERT: D 409 MET cc_start: 0.7631 (mtp) cc_final: 0.7274 (mtm) REVERT: D 441 ILE cc_start: 0.7780 (mm) cc_final: 0.7458 (mm) outliers start: 87 outliers final: 43 residues processed: 271 average time/residue: 1.1823 time to fit residues: 356.1921 Evaluate side-chains 270 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 214 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 412 LYS Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 469 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 0.5980 chunk 170 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 111 optimal weight: 0.0870 chunk 46 optimal weight: 7.9990 chunk 189 optimal weight: 0.5980 chunk 157 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 99 optimal weight: 3.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 ASN C 301 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15748 Z= 0.168 Angle : 0.490 6.259 21352 Z= 0.265 Chirality : 0.042 0.156 2364 Planarity : 0.004 0.047 2736 Dihedral : 7.600 57.980 2340 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.99 % Allowed : 18.21 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.20), residues: 1964 helix: 1.48 (0.18), residues: 860 sheet: -0.01 (0.26), residues: 420 loop : -0.47 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 453 HIS 0.007 0.001 HIS A 484 PHE 0.010 0.001 PHE D 411 TYR 0.020 0.001 TYR B 351 ARG 0.012 0.001 ARG C 321 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 227 time to evaluate : 1.827 Fit side-chains REVERT: A 19 GLN cc_start: 0.6997 (OUTLIER) cc_final: 0.6006 (mm-40) REVERT: A 156 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7781 (mtp85) REVERT: A 399 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7283 (mt-10) REVERT: B 19 GLN cc_start: 0.6881 (OUTLIER) cc_final: 0.6096 (mm-40) REVERT: B 58 GLU cc_start: 0.6411 (mp0) cc_final: 0.6102 (mp0) REVERT: B 330 TYR cc_start: 0.6897 (OUTLIER) cc_final: 0.5646 (t80) REVERT: B 341 THR cc_start: 0.7275 (p) cc_final: 0.6571 (p) REVERT: B 485 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.6629 (mp0) REVERT: C 19 GLN cc_start: 0.7012 (OUTLIER) cc_final: 0.5999 (mm-40) REVERT: C 156 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7732 (mtp85) REVERT: C 399 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7277 (mt-10) REVERT: C 409 MET cc_start: 0.7485 (mtp) cc_final: 0.7171 (mtm) REVERT: D 19 GLN cc_start: 0.6984 (OUTLIER) cc_final: 0.6027 (mm-40) REVERT: D 58 GLU cc_start: 0.6497 (mp0) cc_final: 0.6240 (mp0) REVERT: D 102 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7434 (tt) REVERT: D 156 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7730 (mtp85) REVERT: D 409 MET cc_start: 0.7538 (mtp) cc_final: 0.7217 (mtm) REVERT: D 441 ILE cc_start: 0.7675 (mm) cc_final: 0.7396 (mm) outliers start: 65 outliers final: 40 residues processed: 266 average time/residue: 1.1365 time to fit residues: 337.0351 Evaluate side-chains 273 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 221 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 469 PHE Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 469 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 159 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 chunk 115 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 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 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 GLN C 262 ASN C 301 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15748 Z= 0.292 Angle : 0.547 7.524 21352 Z= 0.293 Chirality : 0.043 0.169 2364 Planarity : 0.005 0.058 2736 Dihedral : 7.733 59.419 2340 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.72 % Allowed : 17.78 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.19), residues: 1964 helix: 1.38 (0.18), residues: 856 sheet: -0.11 (0.26), residues: 420 loop : -0.53 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 178 HIS 0.008 0.001 HIS A 484 PHE 0.013 0.002 PHE D 411 TYR 0.022 0.002 TYR B 351 ARG 0.012 0.001 ARG A 321 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 218 time to evaluate : 1.819 Fit side-chains REVERT: A 19 GLN cc_start: 0.7041 (OUTLIER) cc_final: 0.6007 (mm-40) REVERT: A 156 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7675 (mtp85) REVERT: A 399 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7293 (mt-10) REVERT: A 485 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.6266 (mp0) REVERT: B 19 GLN cc_start: 0.6955 (OUTLIER) cc_final: 0.6116 (mm-40) REVERT: B 330 TYR cc_start: 0.6907 (OUTLIER) cc_final: 0.5472 (t80) REVERT: B 341 THR cc_start: 0.7330 (p) cc_final: 0.6607 (p) REVERT: B 485 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6642 (mp0) REVERT: C 19 GLN cc_start: 0.7062 (OUTLIER) cc_final: 0.6059 (mm-40) REVERT: C 102 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7403 (tt) REVERT: C 156 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7627 (mtp85) REVERT: C 399 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7290 (mt-10) REVERT: C 409 MET cc_start: 0.7609 (mtp) cc_final: 0.7293 (mtm) REVERT: D 19 GLN cc_start: 0.7061 (OUTLIER) cc_final: 0.6057 (mm-40) REVERT: D 58 GLU cc_start: 0.6475 (mp0) cc_final: 0.6173 (mp0) REVERT: D 102 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7455 (tt) REVERT: D 156 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7648 (mtp85) REVERT: D 399 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7327 (mt-10) REVERT: D 409 MET cc_start: 0.7617 (mtp) cc_final: 0.7234 (mtm) REVERT: D 441 ILE cc_start: 0.7705 (mm) cc_final: 0.7402 (mm) outliers start: 77 outliers final: 41 residues processed: 264 average time/residue: 1.2117 time to fit residues: 354.9620 Evaluate side-chains 268 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 212 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 469 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 36 optimal weight: 0.3980 chunk 120 optimal weight: 5.9990 chunk 128 optimal weight: 0.5980 chunk 93 optimal weight: 0.0970 chunk 17 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 GLN C 262 ASN C 301 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15748 Z= 0.187 Angle : 0.506 6.651 21352 Z= 0.272 Chirality : 0.042 0.164 2364 Planarity : 0.004 0.060 2736 Dihedral : 7.529 59.855 2340 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.17 % Allowed : 18.45 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.20), residues: 1964 helix: 1.49 (0.18), residues: 860 sheet: -0.01 (0.26), residues: 420 loop : -0.49 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 178 HIS 0.010 0.001 HIS D 484 PHE 0.011 0.001 PHE B 411 TYR 0.019 0.001 TYR B 351 ARG 0.013 0.001 ARG B 321 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 221 time to evaluate : 2.079 Fit side-chains REVERT: A 19 GLN cc_start: 0.7008 (OUTLIER) cc_final: 0.5975 (mm-40) REVERT: A 156 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7774 (mtp85) REVERT: A 399 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7293 (mt-10) REVERT: B 19 GLN cc_start: 0.6853 (OUTLIER) cc_final: 0.5948 (mm-40) REVERT: B 330 TYR cc_start: 0.6891 (OUTLIER) cc_final: 0.5558 (t80) REVERT: B 341 THR cc_start: 0.7325 (p) cc_final: 0.6597 (p) REVERT: B 485 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6617 (mp0) REVERT: C 19 GLN cc_start: 0.7046 (OUTLIER) cc_final: 0.6042 (mm-40) REVERT: C 58 GLU cc_start: 0.6464 (OUTLIER) cc_final: 0.6217 (pm20) REVERT: C 156 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7699 (mtp85) REVERT: C 349 GLU cc_start: 0.6619 (OUTLIER) cc_final: 0.6300 (mp0) REVERT: C 399 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7280 (mt-10) REVERT: C 409 MET cc_start: 0.7548 (mtp) cc_final: 0.7230 (mtm) REVERT: D 19 GLN cc_start: 0.7046 (OUTLIER) cc_final: 0.6018 (mm-40) REVERT: D 58 GLU cc_start: 0.6411 (mp0) cc_final: 0.6123 (mp0) REVERT: D 102 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7391 (tt) REVERT: D 156 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7721 (mtp85) REVERT: D 409 MET cc_start: 0.7548 (mtp) cc_final: 0.7291 (mtm) REVERT: D 441 ILE cc_start: 0.7630 (mm) cc_final: 0.7387 (mm) outliers start: 68 outliers final: 36 residues processed: 263 average time/residue: 1.1725 time to fit residues: 343.8788 Evaluate side-chains 267 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 217 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 469 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 3.9990 chunk 180 optimal weight: 0.6980 chunk 165 optimal weight: 0.6980 chunk 176 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 76 optimal weight: 0.0870 chunk 138 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 159 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 175 optimal weight: 0.5980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 GLN C 262 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15748 Z= 0.164 Angle : 0.483 6.580 21352 Z= 0.260 Chirality : 0.041 0.161 2364 Planarity : 0.004 0.057 2736 Dihedral : 7.216 58.930 2340 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.80 % Allowed : 19.01 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.20), residues: 1964 helix: 1.61 (0.18), residues: 860 sheet: 0.07 (0.26), residues: 420 loop : -0.44 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 453 HIS 0.010 0.001 HIS D 484 PHE 0.011 0.001 PHE B 411 TYR 0.018 0.001 TYR B 351 ARG 0.015 0.001 ARG A 321 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 227 time to evaluate : 1.940 Fit side-chains REVERT: A 19 GLN cc_start: 0.6984 (OUTLIER) cc_final: 0.5888 (mm-40) REVERT: A 156 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7764 (mtp85) REVERT: A 399 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7285 (mt-10) REVERT: B 19 GLN cc_start: 0.6924 (OUTLIER) cc_final: 0.5889 (mm-40) REVERT: B 330 TYR cc_start: 0.6919 (OUTLIER) cc_final: 0.5533 (t80) REVERT: B 341 THR cc_start: 0.7157 (p) cc_final: 0.6355 (p) REVERT: B 485 GLU cc_start: 0.6770 (mm-30) cc_final: 0.6541 (mp0) REVERT: C 19 GLN cc_start: 0.6894 (OUTLIER) cc_final: 0.5900 (mm-40) REVERT: C 102 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7283 (tt) REVERT: C 156 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7695 (mtp85) REVERT: C 349 GLU cc_start: 0.6595 (OUTLIER) cc_final: 0.6309 (mp0) REVERT: C 399 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7278 (mt-10) REVERT: C 409 MET cc_start: 0.7538 (mtp) cc_final: 0.7220 (mtm) REVERT: D 19 GLN cc_start: 0.6993 (OUTLIER) cc_final: 0.5888 (mm-40) REVERT: D 102 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7372 (tt) REVERT: D 156 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7718 (mtp85) REVERT: D 409 MET cc_start: 0.7519 (mtp) cc_final: 0.7261 (mtm) REVERT: D 441 ILE cc_start: 0.7652 (mm) cc_final: 0.7382 (mm) outliers start: 62 outliers final: 38 residues processed: 264 average time/residue: 1.1477 time to fit residues: 337.2790 Evaluate side-chains 265 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 214 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 469 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 195 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 120 optimal weight: 0.5980 chunk 95 optimal weight: 8.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 GLN B 350 GLN B 474 ASN C 69 GLN C 262 ASN D 69 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.158 15748 Z= 0.319 Angle : 0.908 61.597 21352 Z= 0.439 Chirality : 0.046 0.438 2364 Planarity : 0.005 0.072 2736 Dihedral : 7.232 58.877 2340 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.68 % Allowed : 19.25 % Favored : 77.07 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.20), residues: 1964 helix: 1.56 (0.18), residues: 860 sheet: 0.09 (0.26), residues: 420 loop : -0.45 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 453 HIS 0.011 0.001 HIS D 484 PHE 0.012 0.001 PHE B 411 TYR 0.018 0.002 TYR B 351 ARG 0.013 0.001 ARG B 321 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 214 time to evaluate : 1.679 Fit side-chains REVERT: A 19 GLN cc_start: 0.6998 (OUTLIER) cc_final: 0.5898 (mm-40) REVERT: A 156 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7772 (mtp85) REVERT: A 399 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7292 (mt-10) REVERT: B 19 GLN cc_start: 0.6827 (OUTLIER) cc_final: 0.5819 (mm-40) REVERT: B 330 TYR cc_start: 0.6944 (OUTLIER) cc_final: 0.5554 (t80) REVERT: B 341 THR cc_start: 0.7174 (p) cc_final: 0.6375 (p) REVERT: B 485 GLU cc_start: 0.6781 (mm-30) cc_final: 0.6548 (mp0) REVERT: C 19 GLN cc_start: 0.6905 (OUTLIER) cc_final: 0.5908 (mm-40) REVERT: C 102 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7297 (tt) REVERT: C 156 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7703 (mtp85) REVERT: C 349 GLU cc_start: 0.6606 (OUTLIER) cc_final: 0.6352 (mp0) REVERT: C 399 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7281 (mt-10) REVERT: C 409 MET cc_start: 0.7554 (mtp) cc_final: 0.7235 (mtm) REVERT: D 19 GLN cc_start: 0.7003 (OUTLIER) cc_final: 0.5897 (mm-40) REVERT: D 58 GLU cc_start: 0.6493 (mp0) cc_final: 0.6164 (mp0) REVERT: D 102 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7377 (tt) REVERT: D 156 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7726 (mtp85) REVERT: D 399 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7308 (mt-10) REVERT: D 409 MET cc_start: 0.7530 (mtp) cc_final: 0.7279 (mtm) REVERT: D 441 ILE cc_start: 0.7687 (mm) cc_final: 0.7421 (mm) REVERT: D 485 GLU cc_start: 0.6796 (OUTLIER) cc_final: 0.6185 (mp0) outliers start: 60 outliers final: 38 residues processed: 251 average time/residue: 1.1791 time to fit residues: 328.7792 Evaluate side-chains 265 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 212 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 469 PHE Chi-restraints excluded: chain D residue 485 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 3.9990 chunk 165 optimal weight: 0.2980 chunk 47 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 159 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 GLN B 350 GLN C 69 GLN C 262 ASN D 69 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.157164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.137432 restraints weight = 17877.337| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.03 r_work: 0.3659 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15748 Z= 0.254 Angle : 0.549 7.334 21352 Z= 0.295 Chirality : 0.043 0.172 2364 Planarity : 0.005 0.070 2736 Dihedral : 7.353 57.693 2340 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.92 % Allowed : 18.88 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.20), residues: 1964 helix: 1.45 (0.18), residues: 860 sheet: 0.02 (0.26), residues: 420 loop : -0.49 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 178 HIS 0.013 0.002 HIS D 484 PHE 0.013 0.002 PHE B 411 TYR 0.020 0.002 TYR B 351 ARG 0.014 0.001 ARG B 321 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5871.23 seconds wall clock time: 103 minutes 30.51 seconds (6210.51 seconds total)