Starting phenix.real_space_refine on Mon Apr 8 22:35:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhk_24464/04_2024/7rhk_24464_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhk_24464/04_2024/7rhk_24464.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhk_24464/04_2024/7rhk_24464_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhk_24464/04_2024/7rhk_24464_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhk_24464/04_2024/7rhk_24464_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhk_24464/04_2024/7rhk_24464.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhk_24464/04_2024/7rhk_24464.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhk_24464/04_2024/7rhk_24464_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhk_24464/04_2024/7rhk_24464_updated.pdb" } resolution = 3.27 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= 0.005 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 4 5.49 5 S 83 5.16 5 C 9581 2.51 5 N 2389 2.21 5 O 2625 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 464": "OE1" <-> "OE2" Residue "B GLU 933": "OE1" <-> "OE2" Residue "A TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 365": "OE1" <-> "OE2" Residue "D GLU 289": "OE1" <-> "OE2" Residue "D TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 14682 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 3689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3689 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Chain: "B" Number of atoms: 3438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3438 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 14, 'TRANS': 403} Chain breaks: 2 Chain: "A" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3717 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 14, 'TRANS': 439} Chain: "D" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3717 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 14, 'TRANS': 439} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'5H0': 1, 'PCG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.79, per 1000 atoms: 0.53 Number of scatterers: 14682 At special positions: 0 Unit cell: (97.324, 98.163, 119.138, 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 83 16.00 P 4 15.00 O 2625 8.00 N 2389 7.00 C 9581 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.20 Conformation dependent library (CDL) restraints added in 2.7 seconds 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3366 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 9 sheets defined 61.3% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.88 Creating SS restraints... Processing helix chain 'C' and resid 163 through 188 Proline residue: C 175 - end of helix removed outlier: 5.552A pdb=" N ILE C 184 " --> pdb=" O TRP C 180 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA C 185 " --> pdb=" O THR C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 195 Processing helix chain 'C' and resid 197 through 220 removed outlier: 3.787A pdb=" N ILE C 202 " --> pdb=" O GLU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 233 through 241 Processing helix chain 'C' and resid 244 through 252 Processing helix chain 'C' and resid 256 through 263 removed outlier: 3.894A pdb=" N PHE C 261 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU C 263 " --> pdb=" O TYR C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 289 removed outlier: 4.331A pdb=" N ASN C 273 " --> pdb=" O ILE C 270 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG C 274 " --> pdb=" O ARG C 271 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG C 277 " --> pdb=" O ARG C 274 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N SER C 279 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU C 289 " --> pdb=" O GLN C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 325 Processing helix chain 'C' and resid 345 through 361 Processing helix chain 'C' and resid 372 through 423 removed outlier: 5.370A pdb=" N ALA C 406 " --> pdb=" O ASN C 402 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ARG C 407 " --> pdb=" O MET C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 443 Processing helix chain 'C' and resid 450 through 456 removed outlier: 4.638A pdb=" N TYR C 456 " --> pdb=" O GLU C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 474 removed outlier: 5.415A pdb=" N ASP C 472 " --> pdb=" O ASN C 468 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N THR C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 494 Processing helix chain 'C' and resid 546 through 549 No H-bonds generated for 'chain 'C' and resid 546 through 549' Processing helix chain 'C' and resid 578 through 585 Processing helix chain 'C' and resid 589 through 602 removed outlier: 4.037A pdb=" N ILE C 602 " --> pdb=" O LYS C 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 678 removed outlier: 4.505A pdb=" N ILE B 674 " --> pdb=" O ASN B 670 " (cutoff:3.500A) Proline residue: B 675 - end of helix Processing helix chain 'B' and resid 688 through 708 Processing helix chain 'B' and resid 725 through 734 removed outlier: 4.019A pdb=" N ASN B 730 " --> pdb=" O LYS B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 745 removed outlier: 3.511A pdb=" N LEU B 745 " --> pdb=" O ASP B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 767 Proline residue: B 764 - end of helix Processing helix chain 'B' and resid 770 through 782 Processing helix chain 'B' and resid 786 through 814 removed outlier: 3.780A pdb=" N ALA B 814 " --> pdb=" O TYR B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 841 Processing helix chain 'B' and resid 855 through 886 Processing helix chain 'B' and resid 888 through 906 Processing helix chain 'B' and resid 911 through 927 Processing helix chain 'B' and resid 934 through 939 removed outlier: 4.137A pdb=" N GLN B 939 " --> pdb=" O GLU B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 959 removed outlier: 7.370A pdb=" N ASN B 955 " --> pdb=" O ASP B 951 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE B 956 " --> pdb=" O VAL B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 977 Processing helix chain 'B' and resid 1030 through 1034 Processing helix chain 'B' and resid 1059 through 1068 removed outlier: 4.484A pdb=" N HIS B1068 " --> pdb=" O GLU B1064 " (cutoff:3.500A) Processing helix chain 'B' and resid 1070 through 1083 Processing helix chain 'A' and resid 163 through 188 Proline residue: A 175 - end of helix removed outlier: 5.348A pdb=" N ILE A 184 " --> pdb=" O TRP A 180 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ALA A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 197 through 220 Processing helix chain 'A' and resid 233 through 242 Processing helix chain 'A' and resid 244 through 252 Processing helix chain 'A' and resid 256 through 263 removed outlier: 3.685A pdb=" N LEU A 263 " --> pdb=" O TYR A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 291 removed outlier: 4.284A pdb=" N ASN A 273 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 277 " --> pdb=" O ARG A 274 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER A 279 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU A 289 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR A 290 " --> pdb=" O ARG A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 325 Processing helix chain 'A' and resid 345 through 360 Processing helix chain 'A' and resid 372 through 423 removed outlier: 4.316A pdb=" N ALA A 406 " --> pdb=" O ASN A 402 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ARG A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 443 Processing helix chain 'A' and resid 450 through 453 No H-bonds generated for 'chain 'A' and resid 450 through 453' Processing helix chain 'A' and resid 459 through 474 removed outlier: 6.821A pdb=" N ASP A 472 " --> pdb=" O ASN A 468 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N THR A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 494 removed outlier: 3.533A pdb=" N LEU A 493 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS A 494 " --> pdb=" O GLU A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 584 Processing helix chain 'A' and resid 589 through 606 Processing helix chain 'D' and resid 163 through 188 Proline residue: D 175 - end of helix removed outlier: 5.027A pdb=" N ILE D 184 " --> pdb=" O TRP D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 195 Processing helix chain 'D' and resid 197 through 220 Processing helix chain 'D' and resid 233 through 241 Processing helix chain 'D' and resid 244 through 252 Processing helix chain 'D' and resid 257 through 263 Processing helix chain 'D' and resid 268 through 289 removed outlier: 3.724A pdb=" N ARG D 271 " --> pdb=" O PRO D 268 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASN D 273 " --> pdb=" O ILE D 270 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG D 274 " --> pdb=" O ARG D 271 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG D 277 " --> pdb=" O ARG D 274 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N SER D 279 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR D 288 " --> pdb=" O PHE D 285 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU D 289 " --> pdb=" O GLN D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 325 Processing helix chain 'D' and resid 345 through 360 Processing helix chain 'D' and resid 372 through 403 Processing helix chain 'D' and resid 405 through 423 Processing helix chain 'D' and resid 428 through 443 Processing helix chain 'D' and resid 450 through 456 removed outlier: 4.258A pdb=" N TYR D 456 " --> pdb=" O GLU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 474 removed outlier: 5.938A pdb=" N ASP D 472 " --> pdb=" O ASN D 468 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N THR D 473 " --> pdb=" O VAL D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 493 Processing helix chain 'D' and resid 578 through 584 Processing helix chain 'D' and resid 589 through 605 Processing sheet with id= A, first strand: chain 'C' and resid 496 through 500 removed outlier: 6.489A pdb=" N PHE C 574 " --> pdb=" O ILE C 519 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ILE C 519 " --> pdb=" O PHE C 574 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LEU C 576 " --> pdb=" O TYR C 517 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N TYR C 517 " --> pdb=" O LEU C 576 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 536 through 538 removed outlier: 3.849A pdb=" N VAL C 536 " --> pdb=" O VAL C 526 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 715 through 717 Processing sheet with id= D, first strand: chain 'B' and resid 979 through 983 removed outlier: 6.315A pdb=" N PHE B1055 " --> pdb=" O ILE B1002 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ILE B1002 " --> pdb=" O PHE B1055 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N LEU B1057 " --> pdb=" O TYR B1000 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N TYR B1000 " --> pdb=" O LEU B1057 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 987 through 990 removed outlier: 3.888A pdb=" N ASP B 987 " --> pdb=" O ALA B1048 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL B1046 " --> pdb=" O VAL B 989 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASN B1045 " --> pdb=" O LEU B1010 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN B1006 " --> pdb=" O HIS B1049 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLY B1011 " --> pdb=" O VAL B1018 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N VAL B1018 " --> pdb=" O GLY B1011 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 496 through 500 Processing sheet with id= G, first strand: chain 'A' and resid 564 through 567 removed outlier: 3.817A pdb=" N ASN A 564 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL A 536 " --> pdb=" O VAL A 526 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 496 through 500 removed outlier: 6.795A pdb=" N PHE D 574 " --> pdb=" O ILE D 519 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ILE D 519 " --> pdb=" O PHE D 574 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU D 576 " --> pdb=" O TYR D 517 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N TYR D 517 " --> pdb=" O LEU D 576 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 564 through 567 removed outlier: 3.995A pdb=" N ASN D 564 " --> pdb=" O VAL D 527 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL D 536 " --> pdb=" O VAL D 526 " (cutoff:3.500A) 829 hydrogen bonds defined for protein. 2271 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.14 Time building geometry restraints manager: 6.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4527 1.34 - 1.47: 3805 1.47 - 1.59: 6557 1.59 - 1.71: 8 1.71 - 1.84: 140 Bond restraints: 15037 Sorted by residual: bond pdb=" C3' PCG B1301 " pdb=" C4' PCG B1301 " ideal model delta sigma weight residual 1.808 1.495 0.313 2.00e-02 2.50e+03 2.45e+02 bond pdb=" C3' PCG C 701 " pdb=" C4' PCG C 701 " ideal model delta sigma weight residual 1.808 1.495 0.313 2.00e-02 2.50e+03 2.45e+02 bond pdb=" C3' PCG A1101 " pdb=" C4' PCG A1101 " ideal model delta sigma weight residual 1.808 1.495 0.313 2.00e-02 2.50e+03 2.44e+02 bond pdb=" C3' PCG D 701 " pdb=" C4' PCG D 701 " ideal model delta sigma weight residual 1.808 1.496 0.312 2.00e-02 2.50e+03 2.44e+02 bond pdb=" C2' PCG D 701 " pdb=" C3' PCG D 701 " ideal model delta sigma weight residual 1.200 1.507 -0.307 2.00e-02 2.50e+03 2.36e+02 ... (remaining 15032 not shown) Histogram of bond angle deviations from ideal: 98.80 - 105.91: 280 105.91 - 113.02: 8034 113.02 - 120.13: 5518 120.13 - 127.25: 6415 127.25 - 134.36: 146 Bond angle restraints: 20393 Sorted by residual: angle pdb=" C GLY A 558 " pdb=" N ASN A 559 " pdb=" CA ASN A 559 " ideal model delta sigma weight residual 121.54 130.17 -8.63 1.91e+00 2.74e-01 2.04e+01 angle pdb=" N GLU B 922 " pdb=" CA GLU B 922 " pdb=" CB GLU B 922 " ideal model delta sigma weight residual 110.16 116.13 -5.97 1.48e+00 4.57e-01 1.63e+01 angle pdb=" N CYS D 575 " pdb=" CA CYS D 575 " pdb=" C CYS D 575 " ideal model delta sigma weight residual 108.73 115.02 -6.29 1.63e+00 3.76e-01 1.49e+01 angle pdb=" C TYR A 196 " pdb=" N LEU A 197 " pdb=" CA LEU A 197 " ideal model delta sigma weight residual 120.82 126.45 -5.63 1.50e+00 4.44e-01 1.41e+01 angle pdb=" O3' PCG C 701 " pdb=" PA PCG C 701 " pdb=" O5' PCG C 701 " ideal model delta sigma weight residual 111.92 101.89 10.03 3.00e+00 1.11e-01 1.12e+01 ... (remaining 20388 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 7953 17.99 - 35.98: 820 35.98 - 53.98: 127 53.98 - 71.97: 21 71.97 - 89.96: 8 Dihedral angle restraints: 8929 sinusoidal: 3681 harmonic: 5248 Sorted by residual: dihedral pdb=" CA GLY C 364 " pdb=" C GLY C 364 " pdb=" N GLU C 365 " pdb=" CA GLU C 365 " ideal model delta harmonic sigma weight residual 180.00 161.13 18.87 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA LEU A 253 " pdb=" C LEU A 253 " pdb=" N ILE A 254 " pdb=" CA ILE A 254 " ideal model delta harmonic sigma weight residual 180.00 162.39 17.61 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA PRO B 681 " pdb=" C PRO B 681 " pdb=" N TYR B 682 " pdb=" CA TYR B 682 " ideal model delta harmonic sigma weight residual 180.00 162.75 17.25 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 8926 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2163 0.093 - 0.186: 105 0.186 - 0.279: 4 0.279 - 0.372: 5 0.372 - 0.465: 4 Chirality restraints: 2281 Sorted by residual: chirality pdb=" C3' PCG B1301 " pdb=" C2' PCG B1301 " pdb=" C4' PCG B1301 " pdb=" O3' PCG B1301 " both_signs ideal model delta sigma weight residual False -2.10 -2.57 0.46 2.00e-01 2.50e+01 5.40e+00 chirality pdb=" C3' PCG D 701 " pdb=" C2' PCG D 701 " pdb=" C4' PCG D 701 " pdb=" O3' PCG D 701 " both_signs ideal model delta sigma weight residual False -2.10 -2.56 0.46 2.00e-01 2.50e+01 5.24e+00 chirality pdb=" C3' PCG C 701 " pdb=" C2' PCG C 701 " pdb=" C4' PCG C 701 " pdb=" O3' PCG C 701 " both_signs ideal model delta sigma weight residual False -2.10 -2.56 0.45 2.00e-01 2.50e+01 5.13e+00 ... (remaining 2278 not shown) Planarity restraints: 2508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 267 " -0.056 5.00e-02 4.00e+02 8.61e-02 1.19e+01 pdb=" N PRO C 268 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO C 268 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 268 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 860 " -0.024 2.00e-02 2.50e+03 2.03e-02 7.19e+00 pdb=" CG PHE B 860 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE B 860 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE B 860 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 860 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 860 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE B 860 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 684 " -0.039 5.00e-02 4.00e+02 5.90e-02 5.58e+00 pdb=" N PRO B 685 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 685 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 685 " -0.033 5.00e-02 4.00e+02 ... (remaining 2505 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3550 2.79 - 3.32: 14170 3.32 - 3.84: 26133 3.84 - 4.37: 29825 4.37 - 4.90: 50941 Nonbonded interactions: 124619 Sorted by model distance: nonbonded pdb=" O LEU D 169 " pdb=" OG1 THR D 173 " model vdw 2.260 2.440 nonbonded pdb=" OG SER C 501 " pdb=" OD2 ASP C 504 " model vdw 2.261 2.440 nonbonded pdb=" OH TYR C 178 " pdb=" OD1 ASP C 204 " model vdw 2.272 2.440 nonbonded pdb=" OH TYR C 334 " pdb=" O PHE C 342 " model vdw 2.283 2.440 nonbonded pdb=" OH TYR B 892 " pdb=" OH TYR A 456 " model vdw 2.283 2.440 ... (remaining 124614 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 156 through 605) selection = (chain 'C' and resid 156 through 605) selection = (chain 'D' and resid 156 through 605) } 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: 1.800 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: 5.940 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 41.190 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.050 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 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 : 0.012 0.313 15037 Z= 0.810 Angle : 0.720 10.028 20393 Z= 0.351 Chirality : 0.052 0.465 2281 Planarity : 0.005 0.086 2508 Dihedral : 14.293 89.961 5563 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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 (0.19), residues: 1764 helix: 0.49 (0.14), residues: 1110 sheet: 0.19 (0.54), residues: 82 loop : 0.27 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 168 HIS 0.010 0.001 HIS A 470 PHE 0.046 0.002 PHE B 860 TYR 0.015 0.001 TYR B 797 ARG 0.009 0.000 ARG A 514 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 1.748 Fit side-chains REVERT: B 728 MET cc_start: 0.7139 (mtm) cc_final: 0.6874 (mtm) REVERT: A 269 GLU cc_start: 0.6106 (mp0) cc_final: 0.5761 (mt-10) REVERT: A 604 MET cc_start: 0.7340 (mtp) cc_final: 0.7108 (mtp) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.2593 time to fit residues: 94.6671 Evaluate side-chains 178 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 chunk 74 optimal weight: 0.1980 chunk 45 optimal weight: 20.0000 chunk 89 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 137 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 159 optimal weight: 6.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 730 ASN A 243 ASN A 601 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15037 Z= 0.184 Angle : 0.485 6.974 20393 Z= 0.248 Chirality : 0.038 0.161 2281 Planarity : 0.004 0.048 2508 Dihedral : 4.404 63.517 2040 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.62 % Allowed : 7.44 % Favored : 91.94 % 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 (0.20), residues: 1764 helix: 1.08 (0.15), residues: 1130 sheet: 0.49 (0.59), residues: 62 loop : 0.39 (0.28), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 168 HIS 0.005 0.001 HIS A 470 PHE 0.013 0.001 PHE A 298 TYR 0.022 0.001 TYR B 787 ARG 0.002 0.000 ARG B 834 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 185 time to evaluate : 1.690 Fit side-chains REVERT: B 728 MET cc_start: 0.7066 (mtm) cc_final: 0.6843 (mtm) REVERT: A 269 GLU cc_start: 0.6952 (mp0) cc_final: 0.6316 (mt-10) REVERT: A 604 MET cc_start: 0.7345 (mtp) cc_final: 0.7140 (mtp) REVERT: D 234 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8208 (mp) outliers start: 10 outliers final: 6 residues processed: 190 average time/residue: 0.2533 time to fit residues: 73.3336 Evaluate side-chains 174 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 167 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 582 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 0.7980 chunk 49 optimal weight: 0.1980 chunk 133 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 158 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 chunk 128 optimal weight: 9.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 864 ASN A 601 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15037 Z= 0.145 Angle : 0.447 6.641 20393 Z= 0.230 Chirality : 0.038 0.173 2281 Planarity : 0.003 0.046 2508 Dihedral : 4.202 59.690 2040 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.31 % Allowed : 9.44 % Favored : 89.25 % 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: 1.48 (0.20), residues: 1764 helix: 1.31 (0.15), residues: 1142 sheet: 0.33 (0.56), residues: 82 loop : 0.60 (0.29), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 168 HIS 0.005 0.001 HIS A 470 PHE 0.014 0.001 PHE A 298 TYR 0.016 0.001 TYR B 787 ARG 0.006 0.000 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 183 time to evaluate : 1.461 Fit side-chains REVERT: C 202 ILE cc_start: 0.7680 (OUTLIER) cc_final: 0.7083 (mp) REVERT: B 728 MET cc_start: 0.7035 (mtm) cc_final: 0.6835 (mtm) REVERT: A 269 GLU cc_start: 0.7124 (mp0) cc_final: 0.6340 (mt-10) REVERT: D 234 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8192 (mp) outliers start: 21 outliers final: 11 residues processed: 196 average time/residue: 0.2455 time to fit residues: 74.2260 Evaluate side-chains 186 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 173 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 864 ASN Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 516 MET Chi-restraints excluded: chain D residue 582 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 160 optimal weight: 5.9990 chunk 170 optimal weight: 9.9990 chunk 152 optimal weight: 0.0020 chunk 45 optimal weight: 0.0870 chunk 141 optimal weight: 4.9990 overall best weight: 2.4172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 730 ASN B 864 ASN A 601 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15037 Z= 0.263 Angle : 0.499 8.421 20393 Z= 0.257 Chirality : 0.040 0.152 2281 Planarity : 0.003 0.047 2508 Dihedral : 4.292 61.089 2040 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.06 % Allowed : 10.88 % Favored : 87.06 % 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 (0.20), residues: 1764 helix: 1.28 (0.15), residues: 1137 sheet: 0.26 (0.61), residues: 67 loop : 0.46 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 168 HIS 0.007 0.001 HIS A 470 PHE 0.019 0.002 PHE A 298 TYR 0.021 0.001 TYR D 349 ARG 0.004 0.000 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 177 time to evaluate : 1.543 Fit side-chains REVERT: C 202 ILE cc_start: 0.7848 (OUTLIER) cc_final: 0.7252 (mp) REVERT: B 897 MET cc_start: 0.7548 (ttt) cc_final: 0.7285 (ttt) REVERT: B 1078 LYS cc_start: 0.7378 (tttt) cc_final: 0.6517 (mtpt) REVERT: A 269 GLU cc_start: 0.7590 (mp0) cc_final: 0.6554 (mt-10) REVERT: D 234 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8243 (mp) outliers start: 33 outliers final: 22 residues processed: 199 average time/residue: 0.2575 time to fit residues: 78.0780 Evaluate side-chains 194 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 170 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 665 MET Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 864 ASN Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 516 MET Chi-restraints excluded: chain D residue 582 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 chunk 145 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 152 optimal weight: 0.7980 chunk 42 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 864 ASN A 601 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15037 Z= 0.175 Angle : 0.462 9.289 20393 Z= 0.237 Chirality : 0.038 0.165 2281 Planarity : 0.003 0.046 2508 Dihedral : 4.226 58.514 2040 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.19 % Allowed : 11.69 % Favored : 86.12 % 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: 1.51 (0.20), residues: 1764 helix: 1.40 (0.15), residues: 1137 sheet: 0.42 (0.62), residues: 62 loop : 0.47 (0.28), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 168 HIS 0.005 0.001 HIS A 470 PHE 0.020 0.001 PHE D 574 TYR 0.016 0.001 TYR D 349 ARG 0.004 0.000 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 181 time to evaluate : 1.675 Fit side-chains revert: symmetry clash REVERT: C 202 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7329 (mp) REVERT: B 897 MET cc_start: 0.7549 (ttt) cc_final: 0.7299 (ttt) REVERT: B 1078 LYS cc_start: 0.7287 (tttt) cc_final: 0.6415 (mtpt) REVERT: A 269 GLU cc_start: 0.7546 (mp0) cc_final: 0.6561 (mt-10) REVERT: D 234 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8249 (mp) outliers start: 35 outliers final: 25 residues processed: 201 average time/residue: 0.2517 time to fit residues: 78.3196 Evaluate side-chains 198 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 171 time to evaluate : 1.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 286 GLN Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 864 ASN Chi-restraints excluded: chain B residue 904 MET Chi-restraints excluded: chain B residue 922 GLU Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 1021 THR Chi-restraints excluded: chain B residue 1036 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 516 MET Chi-restraints excluded: chain D residue 582 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 chunk 99 optimal weight: 0.1980 chunk 41 optimal weight: 8.9990 chunk 170 optimal weight: 4.9990 chunk 141 optimal weight: 0.9980 chunk 78 optimal weight: 8.9990 chunk 14 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 444 ASN B 864 ASN A 601 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15037 Z= 0.129 Angle : 0.437 6.660 20393 Z= 0.225 Chirality : 0.037 0.151 2281 Planarity : 0.003 0.045 2508 Dihedral : 4.156 53.664 2040 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.31 % Allowed : 12.00 % Favored : 85.69 % 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: 1.71 (0.20), residues: 1764 helix: 1.54 (0.15), residues: 1137 sheet: 0.51 (0.60), residues: 66 loop : 0.56 (0.29), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 168 HIS 0.004 0.001 HIS A 470 PHE 0.027 0.001 PHE D 574 TYR 0.014 0.001 TYR B 787 ARG 0.004 0.000 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 181 time to evaluate : 1.707 Fit side-chains revert: symmetry clash REVERT: C 202 ILE cc_start: 0.7907 (OUTLIER) cc_final: 0.7361 (mp) REVERT: B 897 MET cc_start: 0.7486 (ttt) cc_final: 0.7231 (ttt) REVERT: B 1078 LYS cc_start: 0.7295 (tttt) cc_final: 0.6407 (mtpt) REVERT: A 269 GLU cc_start: 0.7454 (mp0) cc_final: 0.6513 (mt-10) REVERT: D 234 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8247 (mp) REVERT: D 517 TYR cc_start: 0.8510 (m-80) cc_final: 0.8208 (m-80) outliers start: 37 outliers final: 21 residues processed: 203 average time/residue: 0.2415 time to fit residues: 75.7823 Evaluate side-chains 194 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 171 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 851 ASP Chi-restraints excluded: chain B residue 864 ASN Chi-restraints excluded: chain B residue 922 GLU Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 1021 THR Chi-restraints excluded: chain B residue 1036 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 516 MET Chi-restraints excluded: chain D residue 582 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 9.9990 chunk 97 optimal weight: 0.6980 chunk 124 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 chunk 143 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 169 optimal weight: 7.9990 chunk 106 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 104 optimal weight: 0.4980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 864 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15037 Z= 0.136 Angle : 0.444 11.270 20393 Z= 0.228 Chirality : 0.038 0.169 2281 Planarity : 0.003 0.045 2508 Dihedral : 4.107 50.416 2040 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.25 % Allowed : 12.25 % Favored : 85.50 % 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: 1.76 (0.20), residues: 1764 helix: 1.59 (0.15), residues: 1140 sheet: 0.44 (0.60), residues: 66 loop : 0.56 (0.29), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 168 HIS 0.005 0.001 HIS A 470 PHE 0.032 0.001 PHE D 574 TYR 0.014 0.001 TYR D 588 ARG 0.003 0.000 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 182 time to evaluate : 1.661 Fit side-chains revert: symmetry clash REVERT: C 202 ILE cc_start: 0.7921 (OUTLIER) cc_final: 0.7407 (mp) REVERT: C 351 TYR cc_start: 0.8764 (t80) cc_final: 0.8448 (t80) REVERT: B 897 MET cc_start: 0.7463 (ttt) cc_final: 0.7213 (ttt) REVERT: B 1078 LYS cc_start: 0.7312 (tttt) cc_final: 0.6424 (mtpt) REVERT: A 269 GLU cc_start: 0.7468 (mp0) cc_final: 0.6510 (mt-10) REVERT: D 517 TYR cc_start: 0.8510 (m-80) cc_final: 0.8221 (m-80) outliers start: 36 outliers final: 25 residues processed: 204 average time/residue: 0.2484 time to fit residues: 77.4092 Evaluate side-chains 196 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 170 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 851 ASP Chi-restraints excluded: chain B residue 864 ASN Chi-restraints excluded: chain B residue 881 ASP Chi-restraints excluded: chain B residue 922 GLU Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 1021 THR Chi-restraints excluded: chain B residue 1036 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 516 MET Chi-restraints excluded: chain D residue 582 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 7.9990 chunk 101 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 83 optimal weight: 8.9990 chunk 15 optimal weight: 0.7980 chunk 133 optimal weight: 0.9990 chunk 154 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 864 ASN ** D 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15037 Z= 0.141 Angle : 0.443 9.135 20393 Z= 0.228 Chirality : 0.038 0.208 2281 Planarity : 0.003 0.045 2508 Dihedral : 4.046 49.699 2040 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.12 % Allowed : 12.50 % Favored : 85.38 % 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: 1.85 (0.20), residues: 1764 helix: 1.69 (0.15), residues: 1128 sheet: 0.23 (0.64), residues: 62 loop : 0.59 (0.28), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 168 HIS 0.005 0.001 HIS A 470 PHE 0.026 0.001 PHE D 574 TYR 0.013 0.001 TYR B 787 ARG 0.007 0.000 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 177 time to evaluate : 1.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 202 ILE cc_start: 0.7926 (OUTLIER) cc_final: 0.7456 (mp) REVERT: C 351 TYR cc_start: 0.8781 (t80) cc_final: 0.8462 (t80) REVERT: B 658 LEU cc_start: 0.7563 (tt) cc_final: 0.7355 (tp) REVERT: B 1078 LYS cc_start: 0.7344 (tttt) cc_final: 0.6395 (mtpt) REVERT: A 269 GLU cc_start: 0.7482 (mp0) cc_final: 0.6518 (mt-10) REVERT: D 286 GLN cc_start: 0.6933 (mm-40) cc_final: 0.6526 (mt0) REVERT: D 517 TYR cc_start: 0.8510 (m-80) cc_final: 0.8220 (m-80) outliers start: 34 outliers final: 27 residues processed: 197 average time/residue: 0.2490 time to fit residues: 75.2387 Evaluate side-chains 199 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 171 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 851 ASP Chi-restraints excluded: chain B residue 864 ASN Chi-restraints excluded: chain B residue 881 ASP Chi-restraints excluded: chain B residue 922 GLU Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 1021 THR Chi-restraints excluded: chain B residue 1036 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 516 MET Chi-restraints excluded: chain D residue 582 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 8.9990 chunk 148 optimal weight: 0.0870 chunk 158 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 124 optimal weight: 0.0770 chunk 48 optimal weight: 0.0970 chunk 142 optimal weight: 0.9980 chunk 149 optimal weight: 0.9980 chunk 157 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 overall best weight: 0.4514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 864 ASN ** D 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15037 Z= 0.119 Angle : 0.444 11.298 20393 Z= 0.227 Chirality : 0.038 0.193 2281 Planarity : 0.003 0.045 2508 Dihedral : 3.977 39.129 2040 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.62 % Allowed : 13.12 % Favored : 85.25 % 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: 1.96 (0.20), residues: 1764 helix: 1.76 (0.15), residues: 1127 sheet: 0.21 (0.58), residues: 87 loop : 0.69 (0.29), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 168 HIS 0.005 0.001 HIS A 470 PHE 0.022 0.001 PHE D 574 TYR 0.013 0.001 TYR B 787 ARG 0.007 0.000 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 179 time to evaluate : 1.770 Fit side-chains revert: symmetry clash REVERT: C 202 ILE cc_start: 0.7924 (OUTLIER) cc_final: 0.7445 (mp) REVERT: C 351 TYR cc_start: 0.8721 (t80) cc_final: 0.8435 (t80) REVERT: B 658 LEU cc_start: 0.7578 (tt) cc_final: 0.7373 (tp) REVERT: B 1078 LYS cc_start: 0.7298 (tttt) cc_final: 0.6349 (mtpt) REVERT: A 269 GLU cc_start: 0.7426 (mp0) cc_final: 0.6489 (mt-10) REVERT: A 430 MET cc_start: 0.8975 (tpp) cc_final: 0.8655 (tpp) REVERT: D 286 GLN cc_start: 0.6892 (mm-40) cc_final: 0.6510 (mt0) REVERT: D 517 TYR cc_start: 0.8489 (m-80) cc_final: 0.8201 (m-80) outliers start: 26 outliers final: 22 residues processed: 194 average time/residue: 0.2458 time to fit residues: 73.4431 Evaluate side-chains 194 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 171 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 864 ASN Chi-restraints excluded: chain B residue 881 ASP Chi-restraints excluded: chain B residue 904 MET Chi-restraints excluded: chain B residue 922 GLU Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 1021 THR Chi-restraints excluded: chain B residue 1036 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 516 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 7.9990 chunk 102 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 175 optimal weight: 7.9990 chunk 161 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 864 ASN D 470 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15037 Z= 0.149 Angle : 0.458 11.521 20393 Z= 0.234 Chirality : 0.038 0.277 2281 Planarity : 0.003 0.045 2508 Dihedral : 3.973 40.079 2040 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.56 % Allowed : 13.50 % Favored : 84.94 % 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: 1.94 (0.20), residues: 1764 helix: 1.76 (0.15), residues: 1127 sheet: 0.18 (0.58), residues: 87 loop : 0.67 (0.29), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 168 HIS 0.005 0.001 HIS A 470 PHE 0.022 0.001 PHE D 574 TYR 0.013 0.001 TYR B 787 ARG 0.007 0.000 ARG B 765 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 174 time to evaluate : 1.602 Fit side-chains revert: symmetry clash REVERT: C 202 ILE cc_start: 0.7913 (OUTLIER) cc_final: 0.7469 (mp) REVERT: C 351 TYR cc_start: 0.8731 (t80) cc_final: 0.8446 (t80) REVERT: B 658 LEU cc_start: 0.7603 (tt) cc_final: 0.7394 (tp) REVERT: B 1078 LYS cc_start: 0.7279 (tttt) cc_final: 0.6331 (mtpt) REVERT: A 269 GLU cc_start: 0.7486 (mp0) cc_final: 0.6501 (mt-10) REVERT: D 286 GLN cc_start: 0.6910 (mm-40) cc_final: 0.6525 (mt0) REVERT: D 517 TYR cc_start: 0.8510 (m-80) cc_final: 0.8213 (m-80) REVERT: D 604 MET cc_start: 0.6057 (mpp) cc_final: 0.5178 (mmm) outliers start: 25 outliers final: 22 residues processed: 189 average time/residue: 0.2370 time to fit residues: 69.7051 Evaluate side-chains 195 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 172 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 851 ASP Chi-restraints excluded: chain B residue 864 ASN Chi-restraints excluded: chain B residue 922 GLU Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 1021 THR Chi-restraints excluded: chain B residue 1036 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 516 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 chunk 20 optimal weight: 0.0980 chunk 38 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 58 optimal weight: 0.0000 chunk 143 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 864 ASN D 470 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.132997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.109253 restraints weight = 19955.504| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.38 r_work: 0.3168 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15037 Z= 0.141 Angle : 0.456 10.698 20393 Z= 0.234 Chirality : 0.038 0.251 2281 Planarity : 0.003 0.044 2508 Dihedral : 3.962 43.448 2040 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.55 % Favored : 97.39 % Rotamer: Outliers : 1.88 % Allowed : 13.31 % Favored : 84.81 % 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: 1.97 (0.20), residues: 1764 helix: 1.79 (0.15), residues: 1126 sheet: 0.17 (0.58), residues: 87 loop : 0.67 (0.29), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 168 HIS 0.005 0.001 HIS A 470 PHE 0.020 0.001 PHE D 574 TYR 0.013 0.001 TYR B 787 ARG 0.007 0.000 ARG B 765 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3107.38 seconds wall clock time: 57 minutes 59.46 seconds (3479.46 seconds total)