Starting phenix.real_space_refine on Fri Jul 25 11:20:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hc7_34654/07_2025/8hc7_34654.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hc7_34654/07_2025/8hc7_34654.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hc7_34654/07_2025/8hc7_34654.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hc7_34654/07_2025/8hc7_34654.map" model { file = "/net/cci-nas-00/data/ceres_data/8hc7_34654/07_2025/8hc7_34654.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hc7_34654/07_2025/8hc7_34654.cif" } resolution = 4.54 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= 0.001 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 29 5.16 5 C 4730 2.51 5 N 1229 2.21 5 O 1385 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 7373 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 3480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3480 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 24, 'TRANS': 405} Chain breaks: 6 Chain: "A" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2134 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 15, 'TRANS': 251} Chain: "H" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 868 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "L" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 793 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.62, per 1000 atoms: 0.63 Number of scatterers: 7373 At special positions: 0 Unit cell: (95.7, 105.6, 132, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 29 16.00 O 1385 8.00 N 1229 7.00 C 4730 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 343 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 343 " Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 1.1 seconds 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1708 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 19 sheets defined 6.7% alpha, 24.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.838A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 removed outlier: 3.895A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'A' and resid 337 through 342 removed outlier: 4.388A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 337 through 342' Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.685A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 391 removed outlier: 3.563A pdb=" N LEU A 390 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N CYS A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 386 through 391' Processing helix chain 'A' and resid 406 through 411 removed outlier: 3.849A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA A 411 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 removed outlier: 3.513A pdb=" N ASN A 422 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.620A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA C 264 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR C 91 " --> pdb=" O GLY C 268 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU C 189 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.620A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA C 264 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR C 91 " --> pdb=" O GLY C 268 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE C 197 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 49 through 51 removed outlier: 4.039A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU C 277 " --> pdb=" O HIS C 49 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AA5, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AA6, first strand: chain 'C' and resid 119 through 121 removed outlier: 3.994A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 140 through 142 removed outlier: 3.668A pdb=" N PHE C 140 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU C 156 " --> pdb=" O ASP C 142 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 354 through 356 removed outlier: 3.836A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER C 514 " --> pdb=" O TYR C 396 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL C 512 " --> pdb=" O ASP C 398 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 397 through 403 removed outlier: 3.718A pdb=" N ASP A 398 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG A 509 " --> pdb=" O TRP A 436 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.652A pdb=" N ARG A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 539 through 543 removed outlier: 3.569A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 7 removed outlier: 4.258A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN H 81 " --> pdb=" O THR H 68 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 11 removed outlier: 7.098A pdb=" N GLY H 10 " --> pdb=" O THR H 113 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR H 110 " --> pdb=" O TYR H 93 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR H 93 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE H 92 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY H 98 " --> pdb=" O TYR H 33 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TYR H 33 " --> pdb=" O GLY H 98 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL H 50 " --> pdb=" O PHE H 58 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 10 through 11 removed outlier: 7.098A pdb=" N GLY H 10 " --> pdb=" O THR H 113 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR H 110 " --> pdb=" O TYR H 93 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR H 93 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU H 99 " --> pdb=" O LEU H 103 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LEU H 103 " --> pdb=" O LEU H 99 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AB7, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.683A pdb=" N GLU L 106 " --> pdb=" O VAL L 11 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 45 through 46 removed outlier: 3.792A pdb=" N GLN L 45 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN L 37 " --> pdb=" O GLN L 45 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA L 34 " --> pdb=" O GLN L 89 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR L 36 " --> pdb=" O TYR L 87 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR L 87 " --> pdb=" O TYR L 36 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 48 through 49 removed outlier: 3.877A pdb=" N TYR L 49 " --> pdb=" O THR L 53 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'L' and resid 62 through 65 removed outlier: 3.750A pdb=" N SER L 65 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR L 72 " --> pdb=" O SER L 65 " (cutoff:3.500A) 124 hydrogen bonds defined for protein. 321 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.96 Time building geometry restraints manager: 2.18 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: 2333 1.34 - 1.46: 1956 1.46 - 1.58: 3240 1.58 - 1.70: 0 1.70 - 1.82: 33 Bond restraints: 7562 Sorted by residual: bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.86e+00 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.58e+00 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.52e+00 bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.52e+00 bond pdb=" C1 NAG C1305 " pdb=" O5 NAG C1305 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.46e+00 ... (remaining 7557 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 10084 1.97 - 3.94: 163 3.94 - 5.91: 27 5.91 - 7.88: 2 7.88 - 9.84: 2 Bond angle restraints: 10278 Sorted by residual: angle pdb=" CA PHE C 79 " pdb=" CB PHE C 79 " pdb=" CG PHE C 79 " ideal model delta sigma weight residual 113.80 116.84 -3.04 1.00e+00 1.00e+00 9.27e+00 angle pdb=" C PHE C 79 " pdb=" CA PHE C 79 " pdb=" CB PHE C 79 " ideal model delta sigma weight residual 111.97 117.85 -5.88 1.99e+00 2.53e-01 8.74e+00 angle pdb=" CB GLN L 38 " pdb=" CG GLN L 38 " pdb=" CD GLN L 38 " ideal model delta sigma weight residual 112.60 117.38 -4.78 1.70e+00 3.46e-01 7.92e+00 angle pdb=" CA LEU L 95 " pdb=" CB LEU L 95 " pdb=" CG LEU L 95 " ideal model delta sigma weight residual 116.30 126.14 -9.84 3.50e+00 8.16e-02 7.91e+00 angle pdb=" C PHE A 374 " pdb=" N PHE A 375 " pdb=" CA PHE A 375 " ideal model delta sigma weight residual 121.54 126.81 -5.27 1.91e+00 2.74e-01 7.62e+00 ... (remaining 10273 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 4046 16.66 - 33.31: 387 33.31 - 49.97: 90 49.97 - 66.63: 11 66.63 - 83.28: 10 Dihedral angle restraints: 4544 sinusoidal: 1874 harmonic: 2670 Sorted by residual: dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 525 " pdb=" CB CYS C 525 " ideal model delta sinusoidal sigma weight residual -86.00 -152.66 66.66 1 1.00e+01 1.00e-02 5.80e+01 dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual 93.00 39.64 53.36 1 1.00e+01 1.00e-02 3.87e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 51.05 41.95 1 1.00e+01 1.00e-02 2.46e+01 ... (remaining 4541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 697 0.032 - 0.065: 283 0.065 - 0.097: 102 0.097 - 0.130: 51 0.130 - 0.162: 7 Chirality restraints: 1140 Sorted by residual: chirality pdb=" CB ILE C 95 " pdb=" CA ILE C 95 " pdb=" CG1 ILE C 95 " pdb=" CG2 ILE C 95 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.57e-01 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 122 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" C1 NAG C1303 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG C1303 " pdb=" O5 NAG C1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.36e-01 ... (remaining 1137 not shown) Planarity restraints: 1324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 47 " -0.021 2.00e-02 2.50e+03 1.76e-02 7.73e+00 pdb=" CG TRP H 47 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP H 47 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP H 47 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 47 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP H 47 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 47 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 47 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 47 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP H 47 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 79 " -0.014 2.00e-02 2.50e+03 2.09e-02 7.62e+00 pdb=" CG PHE C 79 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE C 79 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE C 79 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE C 79 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE C 79 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 79 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 79 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.87e+00 pdb=" C PHE C 79 " -0.024 2.00e-02 2.50e+03 pdb=" O PHE C 79 " 0.009 2.00e-02 2.50e+03 pdb=" N ASP C 80 " 0.008 2.00e-02 2.50e+03 ... (remaining 1321 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1565 2.78 - 3.31: 6064 3.31 - 3.84: 11596 3.84 - 4.37: 12460 4.37 - 4.90: 21732 Nonbonded interactions: 53417 Sorted by model distance: nonbonded pdb=" O ASP H 89 " pdb=" OH TYR H 93 " model vdw 2.255 3.040 nonbonded pdb=" OG1 THR A 333 " pdb=" O ASN A 360 " model vdw 2.266 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.277 3.040 nonbonded pdb=" OG1 THR C 109 " pdb=" OD1 ASP C 111 " model vdw 2.353 3.040 nonbonded pdb=" O PRO C 57 " pdb=" OG SER C 60 " model vdw 2.370 3.040 ... (remaining 53412 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.440 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 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 : 0.003 0.040 7581 Z= 0.140 Angle : 0.609 9.844 10323 Z= 0.296 Chirality : 0.045 0.162 1140 Planarity : 0.004 0.033 1317 Dihedral : 13.294 83.284 2800 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % 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: -1.52 (0.26), residues: 899 helix: -3.58 (0.53), residues: 31 sheet: 0.67 (0.42), residues: 168 loop : -1.44 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP H 47 HIS 0.002 0.000 HIS A 519 PHE 0.047 0.001 PHE C 79 TYR 0.014 0.001 TYR L 49 ARG 0.004 0.000 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00335 ( 7) link_NAG-ASN : angle 1.22643 ( 21) hydrogen bonds : bond 0.31641 ( 106) hydrogen bonds : angle 11.57568 ( 321) SS BOND : bond 0.00170 ( 12) SS BOND : angle 0.52298 ( 24) covalent geometry : bond 0.00282 ( 7562) covalent geometry : angle 0.60762 (10278) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 58 PHE cc_start: 0.7493 (m-10) cc_final: 0.6940 (m-10) REVERT: H 84 SER cc_start: 0.7170 (p) cc_final: 0.6900 (p) REVERT: L 104 LYS cc_start: 0.4952 (tptt) cc_final: 0.4743 (tppt) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.2150 time to fit residues: 18.0657 Evaluate side-chains 37 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 37 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 81 optimal weight: 9.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 GLN C 185 ASN C 188 ASN C 481 ASN A 360 ASN A 414 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.101265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.080475 restraints weight = 34428.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.079972 restraints weight = 26057.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.080444 restraints weight = 24733.697| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 7581 Z= 0.216 Angle : 0.666 9.468 10323 Z= 0.340 Chirality : 0.045 0.206 1140 Planarity : 0.005 0.047 1317 Dihedral : 5.051 39.664 1153 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.25 % Allowed : 6.40 % Favored : 93.35 % 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: -1.29 (0.27), residues: 899 helix: -3.52 (0.53), residues: 37 sheet: 0.54 (0.41), residues: 179 loop : -1.18 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 64 HIS 0.007 0.002 HIS A 519 PHE 0.028 0.002 PHE C 43 TYR 0.020 0.002 TYR H 52 ARG 0.005 0.001 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00436 ( 7) link_NAG-ASN : angle 1.69286 ( 21) hydrogen bonds : bond 0.05251 ( 106) hydrogen bonds : angle 7.18407 ( 321) SS BOND : bond 0.00465 ( 12) SS BOND : angle 1.08188 ( 24) covalent geometry : bond 0.00469 ( 7562) covalent geometry : angle 0.66055 (10278) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.927 Fit side-chains revert: symmetry clash REVERT: A 554 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8350 (mp0) REVERT: A 559 PHE cc_start: 0.6493 (m-80) cc_final: 0.6059 (m-80) REVERT: L 3 GLN cc_start: 0.8354 (pp30) cc_final: 0.7974 (pp30) outliers start: 2 outliers final: 1 residues processed: 56 average time/residue: 0.1921 time to fit residues: 15.5450 Evaluate side-chains 38 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 38 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.100389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.079577 restraints weight = 33106.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.079199 restraints weight = 26165.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.080201 restraints weight = 20388.966| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7581 Z= 0.155 Angle : 0.550 8.813 10323 Z= 0.284 Chirality : 0.043 0.178 1140 Planarity : 0.003 0.027 1317 Dihedral : 4.728 38.131 1153 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % 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: -1.15 (0.27), residues: 899 helix: -3.06 (0.69), residues: 31 sheet: 0.48 (0.40), residues: 185 loop : -1.09 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 36 HIS 0.003 0.001 HIS A 519 PHE 0.016 0.002 PHE C 43 TYR 0.013 0.001 TYR C 279 ARG 0.005 0.000 ARG C 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00341 ( 7) link_NAG-ASN : angle 1.35403 ( 21) hydrogen bonds : bond 0.04433 ( 106) hydrogen bonds : angle 6.93962 ( 321) SS BOND : bond 0.00395 ( 12) SS BOND : angle 0.98203 ( 24) covalent geometry : bond 0.00330 ( 7562) covalent geometry : angle 0.54558 (10278) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.876 Fit side-chains revert: symmetry clash REVERT: L 3 GLN cc_start: 0.8455 (pp30) cc_final: 0.8105 (pp30) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.2221 time to fit residues: 15.6605 Evaluate side-chains 36 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 6 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 2 optimal weight: 0.0970 chunk 16 optimal weight: 0.8980 chunk 71 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.100192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.078607 restraints weight = 33850.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.078736 restraints weight = 23406.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.079456 restraints weight = 17957.923| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7581 Z= 0.104 Angle : 0.502 7.885 10323 Z= 0.254 Chirality : 0.042 0.164 1140 Planarity : 0.003 0.030 1317 Dihedral : 4.350 35.090 1153 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % 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: -1.07 (0.27), residues: 899 helix: -2.91 (0.73), residues: 31 sheet: 0.60 (0.39), residues: 193 loop : -1.08 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.012 0.001 PHE C 79 TYR 0.013 0.001 TYR C 453 ARG 0.004 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00273 ( 7) link_NAG-ASN : angle 1.32771 ( 21) hydrogen bonds : bond 0.03599 ( 106) hydrogen bonds : angle 6.55720 ( 321) SS BOND : bond 0.00293 ( 12) SS BOND : angle 0.81320 ( 24) covalent geometry : bond 0.00232 ( 7562) covalent geometry : angle 0.49770 (10278) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.844 Fit side-chains REVERT: A 465 GLU cc_start: 0.7457 (tm-30) cc_final: 0.7084 (tm-30) REVERT: L 3 GLN cc_start: 0.8655 (pp30) cc_final: 0.8220 (pp30) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.2004 time to fit residues: 14.2358 Evaluate side-chains 38 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 23 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 17 optimal weight: 0.0980 chunk 51 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.099780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.079324 restraints weight = 36305.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.079145 restraints weight = 29339.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.079577 restraints weight = 25657.813| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7581 Z= 0.112 Angle : 0.506 7.375 10323 Z= 0.254 Chirality : 0.042 0.163 1140 Planarity : 0.003 0.030 1317 Dihedral : 4.340 34.723 1153 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.27), residues: 899 helix: -2.78 (0.75), residues: 31 sheet: 0.57 (0.41), residues: 185 loop : -1.04 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 106 HIS 0.002 0.001 HIS H 35 PHE 0.012 0.001 PHE C 79 TYR 0.010 0.001 TYR C 453 ARG 0.004 0.000 ARG C 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00417 ( 7) link_NAG-ASN : angle 1.93999 ( 21) hydrogen bonds : bond 0.03592 ( 106) hydrogen bonds : angle 6.37998 ( 321) SS BOND : bond 0.00266 ( 12) SS BOND : angle 0.70682 ( 24) covalent geometry : bond 0.00250 ( 7562) covalent geometry : angle 0.49804 (10278) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 223 LEU cc_start: 0.7925 (tp) cc_final: 0.7713 (mt) REVERT: C 273 ARG cc_start: 0.4028 (ttt180) cc_final: 0.3503 (ttt-90) REVERT: H 93 TYR cc_start: 0.8080 (m-10) cc_final: 0.7861 (m-10) REVERT: L 3 GLN cc_start: 0.8658 (pp30) cc_final: 0.8261 (pp30) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.2078 time to fit residues: 15.3193 Evaluate side-chains 34 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 52 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 1 optimal weight: 0.0270 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.8440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 409 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.097949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.076686 restraints weight = 35720.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.076324 restraints weight = 25787.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.076937 restraints weight = 21869.191| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7581 Z= 0.123 Angle : 0.530 9.734 10323 Z= 0.265 Chirality : 0.042 0.166 1140 Planarity : 0.003 0.030 1317 Dihedral : 4.405 35.426 1153 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % 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: -1.15 (0.27), residues: 899 helix: -3.13 (0.62), residues: 38 sheet: 0.66 (0.41), residues: 188 loop : -1.12 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 36 HIS 0.003 0.001 HIS A 519 PHE 0.013 0.001 PHE C 79 TYR 0.011 0.001 TYR C 279 ARG 0.003 0.000 ARG H 97 Details of bonding type rmsd link_NAG-ASN : bond 0.00264 ( 7) link_NAG-ASN : angle 1.47349 ( 21) hydrogen bonds : bond 0.03495 ( 106) hydrogen bonds : angle 6.22999 ( 321) SS BOND : bond 0.00320 ( 12) SS BOND : angle 0.72684 ( 24) covalent geometry : bond 0.00278 ( 7562) covalent geometry : angle 0.52529 (10278) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 223 LEU cc_start: 0.7958 (tp) cc_final: 0.7661 (tp) REVERT: L 3 GLN cc_start: 0.8517 (pp30) cc_final: 0.8121 (pp30) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.2535 time to fit residues: 17.0429 Evaluate side-chains 39 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 71 optimal weight: 20.0000 chunk 46 optimal weight: 3.9990 chunk 1 optimal weight: 0.0670 chunk 33 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.097599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.076946 restraints weight = 36859.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.075324 restraints weight = 32390.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.075800 restraints weight = 28093.975| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7581 Z= 0.133 Angle : 0.539 8.575 10323 Z= 0.272 Chirality : 0.043 0.274 1140 Planarity : 0.003 0.027 1317 Dihedral : 4.512 36.181 1153 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % 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: -1.00 (0.28), residues: 899 helix: -2.77 (0.77), residues: 31 sheet: 0.80 (0.41), residues: 187 loop : -1.06 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 106 HIS 0.001 0.001 HIS C 505 PHE 0.012 0.001 PHE C 79 TYR 0.012 0.001 TYR A 489 ARG 0.003 0.000 ARG A 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00269 ( 7) link_NAG-ASN : angle 1.43523 ( 21) hydrogen bonds : bond 0.03521 ( 106) hydrogen bonds : angle 6.22074 ( 321) SS BOND : bond 0.00417 ( 12) SS BOND : angle 0.97981 ( 24) covalent geometry : bond 0.00300 ( 7562) covalent geometry : angle 0.53455 (10278) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.921 Fit side-chains REVERT: L 3 GLN cc_start: 0.8591 (pp30) cc_final: 0.8179 (pp30) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1921 time to fit residues: 14.1488 Evaluate side-chains 34 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 9 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 121 ASN A 414 GLN A 580 GLN L 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.095037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.072575 restraints weight = 35087.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.072572 restraints weight = 23473.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.073458 restraints weight = 17871.409| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.5159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7581 Z= 0.175 Angle : 0.589 7.679 10323 Z= 0.303 Chirality : 0.044 0.236 1140 Planarity : 0.004 0.067 1317 Dihedral : 5.087 39.726 1153 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.38 % Allowed : 1.63 % Favored : 97.99 % 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: -1.35 (0.28), residues: 899 helix: -3.25 (0.60), residues: 39 sheet: 0.38 (0.41), residues: 190 loop : -1.21 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP H 36 HIS 0.003 0.001 HIS A 519 PHE 0.014 0.002 PHE C 79 TYR 0.014 0.002 TYR C 204 ARG 0.007 0.001 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00255 ( 7) link_NAG-ASN : angle 1.61980 ( 21) hydrogen bonds : bond 0.03865 ( 106) hydrogen bonds : angle 6.32425 ( 321) SS BOND : bond 0.00431 ( 12) SS BOND : angle 0.94534 ( 24) covalent geometry : bond 0.00389 ( 7562) covalent geometry : angle 0.58427 (10278) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 1.076 Fit side-chains REVERT: C 273 ARG cc_start: 0.5034 (ttt180) cc_final: 0.4824 (ttt180) REVERT: C 489 TYR cc_start: 0.6838 (p90) cc_final: 0.6537 (p90) REVERT: H 36 TRP cc_start: 0.7519 (m100) cc_final: 0.6956 (t-100) REVERT: H 38 ARG cc_start: 0.8881 (tmm160) cc_final: 0.8481 (tmm-80) REVERT: L 3 GLN cc_start: 0.8473 (pp30) cc_final: 0.8007 (pp30) REVERT: L 89 GLN cc_start: 0.4842 (OUTLIER) cc_final: 0.4461 (tp-100) outliers start: 3 outliers final: 2 residues processed: 48 average time/residue: 0.2567 time to fit residues: 17.7631 Evaluate side-chains 34 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 16 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 ASN A 422 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.095946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.073077 restraints weight = 34757.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.073764 restraints weight = 21201.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.074372 restraints weight = 15851.153| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.5250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7581 Z= 0.127 Angle : 0.549 7.315 10323 Z= 0.278 Chirality : 0.043 0.189 1140 Planarity : 0.003 0.032 1317 Dihedral : 4.885 37.793 1153 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % 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: -1.38 (0.28), residues: 899 helix: -3.17 (0.62), residues: 38 sheet: 0.37 (0.42), residues: 184 loop : -1.24 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP H 36 HIS 0.001 0.001 HIS C 207 PHE 0.014 0.001 PHE C 374 TYR 0.014 0.001 TYR H 79 ARG 0.002 0.000 ARG C 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00274 ( 7) link_NAG-ASN : angle 1.43630 ( 21) hydrogen bonds : bond 0.03527 ( 106) hydrogen bonds : angle 6.25289 ( 321) SS BOND : bond 0.00374 ( 12) SS BOND : angle 0.88389 ( 24) covalent geometry : bond 0.00289 ( 7562) covalent geometry : angle 0.54447 (10278) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: C 489 TYR cc_start: 0.6828 (p90) cc_final: 0.6392 (p90) REVERT: A 584 ILE cc_start: 0.8308 (mt) cc_final: 0.8063 (mt) REVERT: H 36 TRP cc_start: 0.7498 (m100) cc_final: 0.7075 (m100) REVERT: L 4 MET cc_start: 0.5926 (mmp) cc_final: 0.5114 (mmm) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.2068 time to fit residues: 14.2426 Evaluate side-chains 31 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 72 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 0.3980 chunk 54 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN L 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.095115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.072896 restraints weight = 33672.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.073077 restraints weight = 21288.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.074185 restraints weight = 16679.816| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.5537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7581 Z= 0.136 Angle : 0.560 7.688 10323 Z= 0.285 Chirality : 0.043 0.169 1140 Planarity : 0.003 0.033 1317 Dihedral : 4.936 37.415 1153 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % 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: -1.35 (0.28), residues: 899 helix: -3.16 (0.61), residues: 38 sheet: 0.58 (0.40), residues: 195 loop : -1.31 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 36 HIS 0.003 0.001 HIS C 66 PHE 0.014 0.001 PHE C 79 TYR 0.012 0.001 TYR C 473 ARG 0.003 0.000 ARG A 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00247 ( 7) link_NAG-ASN : angle 1.49167 ( 21) hydrogen bonds : bond 0.03602 ( 106) hydrogen bonds : angle 6.27553 ( 321) SS BOND : bond 0.00405 ( 12) SS BOND : angle 0.80305 ( 24) covalent geometry : bond 0.00311 ( 7562) covalent geometry : angle 0.55604 (10278) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1798 Ramachandran restraints generated. 899 Oldfield, 0 Emsley, 899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.859 Fit side-chains REVERT: H 34 MET cc_start: 0.8238 (mmm) cc_final: 0.7199 (mmm) REVERT: H 36 TRP cc_start: 0.7398 (m100) cc_final: 0.6849 (t-100) REVERT: H 38 ARG cc_start: 0.8883 (tmm160) cc_final: 0.8470 (ttp80) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.2043 time to fit residues: 13.4106 Evaluate side-chains 32 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 4 optimal weight: 0.3980 chunk 35 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 28 optimal weight: 0.0970 chunk 32 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.095264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.073635 restraints weight = 33964.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.073459 restraints weight = 22759.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.074230 restraints weight = 18744.477| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.5658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7581 Z= 0.131 Angle : 0.575 8.479 10323 Z= 0.290 Chirality : 0.044 0.164 1140 Planarity : 0.003 0.034 1317 Dihedral : 4.892 36.257 1153 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 0.13 % Allowed : 0.75 % Favored : 99.12 % 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: -1.41 (0.28), residues: 899 helix: -3.14 (0.61), residues: 38 sheet: 0.39 (0.39), residues: 204 loop : -1.33 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 36 HIS 0.001 0.001 HIS C 207 PHE 0.014 0.001 PHE C 79 TYR 0.014 0.001 TYR C 473 ARG 0.006 0.000 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00265 ( 7) link_NAG-ASN : angle 1.42902 ( 21) hydrogen bonds : bond 0.03734 ( 106) hydrogen bonds : angle 6.33043 ( 321) SS BOND : bond 0.00783 ( 12) SS BOND : angle 0.90171 ( 24) covalent geometry : bond 0.00304 ( 7562) covalent geometry : angle 0.57113 (10278) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2400.07 seconds wall clock time: 42 minutes 47.16 seconds (2567.16 seconds total)