Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 08:46:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhk_24464/04_2023/7rhk_24464_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhk_24464/04_2023/7rhk_24464.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhk_24464/04_2023/7rhk_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_2023/7rhk_24464_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhk_24464/04_2023/7rhk_24464_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhk_24464/04_2023/7rhk_24464.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhk_24464/04_2023/7rhk_24464.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhk_24464/04_2023/7rhk_24464_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhk_24464/04_2023/7rhk_24464_updated.pdb" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 8.02, per 1000 atoms: 0.55 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: 5.76 Conformation dependent library (CDL) restraints added in 2.2 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: 1.29 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: 4.02 Time building geometry restraints manager: 6.22 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: 7907 17.99 - 35.98: 815 35.98 - 53.98: 126 53.98 - 71.97: 21 71.97 - 89.96: 8 Dihedral angle restraints: 8877 sinusoidal: 3629 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 8874 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: 0.980 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: 6.430 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 37.700 Find NCS groups from input model: 0.980 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: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.360 ------------------------------------------------------------------------------- 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 : 14.313 89.961 5511 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 % 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 *********************** 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 : 1.731 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.2401 time to fit residues: 87.2023 Evaluate side-chains 177 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 1.763 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3519 ------------------------------------------------------------------------------- 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: 9.9990 chunk 83 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 159 optimal weight: 6.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- 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: 0.8057 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 15037 Z= 0.187 Angle : 0.488 6.885 20393 Z= 0.249 Chirality : 0.039 0.162 2281 Planarity : 0.004 0.048 2508 Dihedral : 4.055 67.953 1988 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer Outliers : 0.62 % 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: 1.13 (0.20), residues: 1764 helix: 1.06 (0.15), residues: 1130 sheet: 0.49 (0.59), residues: 62 loop : 0.38 (0.28), residues: 572 *********************** 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 193 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 183 time to evaluate : 1.785 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 188 average time/residue: 0.2429 time to fit residues: 70.2699 Evaluate side-chains 171 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 165 time to evaluate : 1.632 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1346 time to fit residues: 3.7360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 133 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 160 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 158 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 128 optimal weight: 10.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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: 0.8111 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 15037 Z= 0.209 Angle : 0.483 6.227 20393 Z= 0.248 Chirality : 0.039 0.166 2281 Planarity : 0.003 0.048 2508 Dihedral : 4.000 65.464 1988 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 1.44 % 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: 1.34 (0.20), residues: 1764 helix: 1.23 (0.15), residues: 1137 sheet: 0.49 (0.61), residues: 62 loop : 0.46 (0.28), residues: 565 *********************** 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 201 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 178 time to evaluate : 1.918 Fit side-chains outliers start: 23 outliers final: 14 residues processed: 193 average time/residue: 0.2498 time to fit residues: 74.6901 Evaluate side-chains 183 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 169 time to evaluate : 1.705 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1482 time to fit residues: 6.3018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 7.9990 chunk 120 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 160 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 chunk 152 optimal weight: 0.0020 chunk 45 optimal weight: 20.0000 chunk 141 optimal weight: 4.9990 overall best weight: 1.3996 ------------------------------------------------------------------------------- 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** A 601 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 15037 Z= 0.182 Angle : 0.463 8.241 20393 Z= 0.237 Chirality : 0.038 0.144 2281 Planarity : 0.003 0.047 2508 Dihedral : 3.941 63.906 1988 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 1.00 % 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: 1.46 (0.20), residues: 1764 helix: 1.35 (0.15), residues: 1136 sheet: 0.46 (0.61), residues: 62 loop : 0.46 (0.28), residues: 566 *********************** 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 197 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 181 time to evaluate : 1.805 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 187 average time/residue: 0.2554 time to fit residues: 73.0496 Evaluate side-chains 177 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 169 time to evaluate : 1.741 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1395 time to fit residues: 4.4695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 126 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 chunk 145 optimal weight: 0.7980 chunk 117 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 152 optimal weight: 0.9980 chunk 42 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 A 601 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 15037 Z= 0.171 Angle : 0.456 9.513 20393 Z= 0.235 Chirality : 0.038 0.143 2281 Planarity : 0.003 0.047 2508 Dihedral : 3.906 63.151 1988 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer Outliers : 1.00 % 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: 1.55 (0.20), residues: 1764 helix: 1.42 (0.15), residues: 1137 sheet: 0.42 (0.62), residues: 62 loop : 0.47 (0.28), residues: 565 *********************** 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 195 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 179 time to evaluate : 1.902 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 186 average time/residue: 0.2582 time to fit residues: 74.0834 Evaluate side-chains 176 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 168 time to evaluate : 1.860 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1388 time to fit residues: 4.4801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 41 optimal weight: 8.9990 chunk 170 optimal weight: 0.5980 chunk 141 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 444 ASN ** B 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 15037 Z= 0.160 Angle : 0.445 6.705 20393 Z= 0.230 Chirality : 0.038 0.144 2281 Planarity : 0.003 0.046 2508 Dihedral : 3.867 62.319 1988 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 1.12 % 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: 1.70 (0.20), residues: 1764 helix: 1.55 (0.15), residues: 1126 sheet: 0.58 (0.60), residues: 66 loop : 0.53 (0.28), residues: 572 *********************** 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 198 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 180 time to evaluate : 1.628 Fit side-chains outliers start: 18 outliers final: 5 residues processed: 189 average time/residue: 0.2605 time to fit residues: 75.9850 Evaluate side-chains 174 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 169 time to evaluate : 1.745 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1530 time to fit residues: 4.7958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 7.9990 chunk 97 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 143 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 169 optimal weight: 8.9990 chunk 106 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 104 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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** A 314 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1682 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= 0.140 Angle : 0.445 11.448 20393 Z= 0.228 Chirality : 0.038 0.159 2281 Planarity : 0.003 0.046 2508 Dihedral : 3.930 71.326 1988 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer Outliers : 0.75 % 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: 1.78 (0.20), residues: 1764 helix: 1.63 (0.15), residues: 1125 sheet: 0.55 (0.61), residues: 66 loop : 0.53 (0.28), residues: 573 *********************** 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 189 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 177 time to evaluate : 1.756 Fit side-chains outliers start: 12 outliers final: 3 residues processed: 184 average time/residue: 0.2629 time to fit residues: 73.9156 Evaluate side-chains 173 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 170 time to evaluate : 1.798 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1347 time to fit residues: 3.2297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 51 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 115 optimal weight: 8.9990 chunk 83 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 133 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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** D 286 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 15037 Z= 0.161 Angle : 0.457 10.729 20393 Z= 0.234 Chirality : 0.038 0.204 2281 Planarity : 0.003 0.047 2508 Dihedral : 3.907 70.695 1988 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 0.50 % 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: 1.77 (0.20), residues: 1764 helix: 1.62 (0.15), residues: 1136 sheet: 0.40 (0.64), residues: 62 loop : 0.54 (0.28), residues: 566 *********************** 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 187 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 179 time to evaluate : 1.878 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 185 average time/residue: 0.2674 time to fit residues: 76.4296 Evaluate side-chains 176 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 172 time to evaluate : 1.849 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1397 time to fit residues: 3.6354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 7.9990 chunk 148 optimal weight: 0.7980 chunk 158 optimal weight: 4.9990 chunk 95 optimal weight: 0.5980 chunk 68 optimal weight: 7.9990 chunk 124 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 142 optimal weight: 0.3980 chunk 149 optimal weight: 0.9980 chunk 157 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** D 286 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 15037 Z= 0.137 Angle : 0.449 8.087 20393 Z= 0.230 Chirality : 0.038 0.229 2281 Planarity : 0.003 0.046 2508 Dihedral : 3.765 49.010 1988 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer Outliers : 0.38 % 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: 1.87 (0.20), residues: 1764 helix: 1.73 (0.15), residues: 1125 sheet: 0.40 (0.62), residues: 67 loop : 0.53 (0.28), residues: 572 *********************** 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 182 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 176 time to evaluate : 1.815 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 177 average time/residue: 0.2571 time to fit residues: 70.9003 Evaluate side-chains 173 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 170 time to evaluate : 1.848 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1583 time to fit residues: 3.0718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 116 optimal weight: 0.9990 chunk 175 optimal weight: 0.9980 chunk 161 optimal weight: 20.0000 chunk 139 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 110 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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** A 314 ASN D 286 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1809 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= 0.151 Angle : 0.464 13.605 20393 Z= 0.237 Chirality : 0.038 0.193 2281 Planarity : 0.003 0.046 2508 Dihedral : 3.776 53.974 1988 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 0.25 % 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: 1.87 (0.20), residues: 1764 helix: 1.71 (0.15), residues: 1127 sheet: 0.34 (0.65), residues: 62 loop : 0.56 (0.28), residues: 575 ********************** 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 175 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 171 time to evaluate : 2.082 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 173 average time/residue: 0.2576 time to fit residues: 68.9656 Evaluate side-chains 170 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.717 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.0370 chunk 42 optimal weight: 9.9990 chunk 128 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 143 optimal weight: 0.7980 chunk 17 optimal weight: 0.0040 chunk 25 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 overall best weight: 0.4870 ------------------------------------------------------------------------------- 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** A 314 ASN D 286 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.133308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.107512 restraints weight = 20050.907| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.49 r_work: 0.3132 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1757 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= 0.122 Angle : 0.439 10.889 20393 Z= 0.226 Chirality : 0.037 0.179 2281 Planarity : 0.003 0.046 2508 Dihedral : 3.720 54.921 1988 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.66 % Favored : 97.28 % Rotamer Outliers : 0.31 % 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: 2.00 (0.21), residues: 1764 helix: 1.82 (0.15), residues: 1127 sheet: 0.30 (0.57), residues: 87 loop : 0.63 (0.29), residues: 550 =============================================================================== Job complete usr+sys time: 2812.45 seconds wall clock time: 52 minutes 18.00 seconds (3138.00 seconds total)