Starting phenix.real_space_refine (version: dev) on Sat Feb 18 08:17:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xos_22278/02_2023/6xos_22278.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xos_22278/02_2023/6xos_22278.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xos_22278/02_2023/6xos_22278.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xos_22278/02_2023/6xos_22278.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xos_22278/02_2023/6xos_22278.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xos_22278/02_2023/6xos_22278.pdb" } resolution = 3.7 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= 0.001 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 Process input model Symmetric amino acids flipped Residue "A GLU 59": "OE1" <-> "OE2" Residue "A ASP 83": "OD1" <-> "OD2" Residue "A ASP 142": "OD1" <-> "OD2" Residue "A TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 165": "OD1" <-> "OD2" Residue "A ASP 176": "OD1" <-> "OD2" Residue "A GLU 185": "OE1" <-> "OE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 339": "OD1" <-> "OD2" Residue "A ASP 373": "OD1" <-> "OD2" Residue "A TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 409": "OD1" <-> "OD2" Residue "A ASP 423": "OD1" <-> "OD2" Residue "A ASP 508": "OD1" <-> "OD2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "A GLU 539": "OE1" <-> "OE2" Residue "A GLU 640": "OE1" <-> "OE2" Residue "A ASP 655": "OD1" <-> "OD2" Residue "A ASP 656": "OD1" <-> "OD2" Residue "A ASP 660": "OD1" <-> "OD2" Residue "A GLU 663": "OE1" <-> "OE2" Residue "A PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 679": "OD1" <-> "OD2" Residue "A GLU 686": "OE1" <-> "OE2" Residue "A GLU 695": "OE1" <-> "OE2" Residue "A GLU 697": "OE1" <-> "OE2" Residue "A GLU 709": "OE1" <-> "OE2" Residue "A ASP 716": "OD1" <-> "OD2" Residue "A GLU 754": "OE1" <-> "OE2" Residue "A ASP 757": "OD1" <-> "OD2" Residue "A ASP 776": "OD1" <-> "OD2" Residue "A PHE 848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 877": "OD1" <-> "OD2" Residue "A GLU 901": "OE1" <-> "OE2" Residue "A ASP 940": "OD1" <-> "OD2" Residue "A ASP 953": "OD1" <-> "OD2" Residue "A GLU 954": "OE1" <-> "OE2" Residue "A ASP 975": "OD1" <-> "OD2" Residue "A ASP 1006": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 7704 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7704 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 966, 7698 Classifications: {'peptide': 966} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 60, 'TRANS': 903} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 966, 7698 Classifications: {'peptide': 966} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 60, 'TRANS': 903} Chain breaks: 1 bond proxies already assigned to first conformer: 7882 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASER A 723 " occ=0.42 ... (10 atoms not shown) pdb=" OG BSER A 723 " occ=0.58 Time building chain proxies: 8.26, per 1000 atoms: 1.07 Number of scatterers: 7704 At special positions: 0 Unit cell: (82.176, 88.168, 95.016, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 1459 8.00 N 1305 7.00 C 4901 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: 2.88 Conformation dependent library (CDL) restraints added in 2.1 seconds 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1826 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 7 sheets defined 53.8% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 32 through 38 removed outlier: 3.757A pdb=" N ARG A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 61 Processing helix chain 'A' and resid 101 through 110 Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 121 through 127 Processing helix chain 'A' and resid 152 through 169 Processing helix chain 'A' and resid 173 through 181 Processing helix chain 'A' and resid 200 through 210 Processing helix chain 'A' and resid 212 through 226 Processing helix chain 'A' and resid 229 through 233 removed outlier: 3.694A pdb=" N VAL A 233 " --> pdb=" O THR A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 245 removed outlier: 3.536A pdb=" N GLU A 244 " --> pdb=" O CYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 258 Processing helix chain 'A' and resid 259 through 261 No H-bonds generated for 'chain 'A' and resid 259 through 261' Processing helix chain 'A' and resid 272 through 284 removed outlier: 3.916A pdb=" N HIS A 276 " --> pdb=" O PRO A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 288 Processing helix chain 'A' and resid 339 through 355 Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 400 through 419 Processing helix chain 'A' and resid 421 through 438 removed outlier: 3.643A pdb=" N ILE A 425 " --> pdb=" O GLU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 457 removed outlier: 4.685A pdb=" N SER A 453 " --> pdb=" O SER A 449 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N CYS A 454 " --> pdb=" O TYR A 450 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N HIS A 457 " --> pdb=" O SER A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 481 removed outlier: 3.585A pdb=" N ASN A 481 " --> pdb=" O CYS A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 494 Processing helix chain 'A' and resid 509 through 527 Processing helix chain 'A' and resid 530 through 550 Processing helix chain 'A' and resid 561 through 565 Processing helix chain 'A' and resid 608 through 613 removed outlier: 3.669A pdb=" N ARG A 612 " --> pdb=" O GLU A 609 " (cutoff:3.500A) Proline residue: A 613 - end of helix Processing helix chain 'A' and resid 614 through 622 Processing helix chain 'A' and resid 631 through 642 Processing helix chain 'A' and resid 676 through 690 Processing helix chain 'A' and resid 695 through 713 removed outlier: 3.618A pdb=" N PHE A 699 " --> pdb=" O GLU A 695 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A 701 " --> pdb=" O GLU A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 727 Processing helix chain 'A' and resid 731 through 742 Processing helix chain 'A' and resid 742 through 755 removed outlier: 3.743A pdb=" N VAL A 746 " --> pdb=" O GLY A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 763 Processing helix chain 'A' and resid 763 through 773 removed outlier: 4.229A pdb=" N ARG A 767 " --> pdb=" O ARG A 763 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N HIS A 771 " --> pdb=" O ARG A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 802 Processing helix chain 'A' and resid 878 through 894 removed outlier: 4.407A pdb=" N SER A 882 " --> pdb=" O PRO A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 901 Processing helix chain 'A' and resid 928 through 945 Processing helix chain 'A' and resid 948 through 964 Processing helix chain 'A' and resid 968 through 972 removed outlier: 3.834A pdb=" N LYS A 972 " --> pdb=" O PRO A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 979 removed outlier: 3.987A pdb=" N PHE A 977 " --> pdb=" O GLY A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 996 Processing helix chain 'A' and resid 997 through 1008 Processing helix chain 'A' and resid 1025 through 1030 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 46 removed outlier: 5.856A pdb=" N VAL A 51 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N THR A 68 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ARG A 75 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N THR A 267 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU A 77 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 134 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 removed outlier: 5.856A pdb=" N VAL A 51 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N THR A 68 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ARG A 75 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N THR A 267 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU A 77 " --> pdb=" O THR A 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 183 through 186 Processing sheet with id=AA4, first strand: chain 'A' and resid 307 through 313 removed outlier: 3.516A pdb=" N CYS A 313 " --> pdb=" O ARG A 505 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL A 328 " --> pdb=" O GLN A 394 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N GLN A 394 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N VAL A 330 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N GLY A 392 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N PHE A 332 " --> pdb=" O SER A 390 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N SER A 390 " --> pdb=" O PHE A 332 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU A 334 " --> pdb=" O TYR A 388 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N TYR A 388 " --> pdb=" O LEU A 334 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASP A 336 " --> pdb=" O GLU A 386 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLU A 386 " --> pdb=" O ASP A 336 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP A 373 " --> pdb=" O GLN A 394 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 307 through 313 removed outlier: 3.516A pdb=" N CYS A 313 " --> pdb=" O ARG A 505 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL A 328 " --> pdb=" O GLN A 394 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N GLN A 394 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N VAL A 330 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N GLY A 392 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N PHE A 332 " --> pdb=" O SER A 390 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N SER A 390 " --> pdb=" O PHE A 332 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU A 334 " --> pdb=" O TYR A 388 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N TYR A 388 " --> pdb=" O LEU A 334 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASP A 336 " --> pdb=" O GLU A 386 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLU A 386 " --> pdb=" O ASP A 336 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 575 through 579 removed outlier: 8.040A pdb=" N VAL A 782 " --> pdb=" O PRO A 584 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLN A 586 " --> pdb=" O VAL A 782 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ALA A 784 " --> pdb=" O GLN A 586 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N CYS A 588 " --> pdb=" O ALA A 784 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 671 " --> pdb=" O GLY A 645 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLY A 645 " --> pdb=" O LEU A 671 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU A 673 " --> pdb=" O THR A 643 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N THR A 643 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 907 through 912 removed outlier: 3.550A pdb=" N VAL A 866 " --> pdb=" O SER A 922 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ASN A 864 " --> pdb=" O ARG A 924 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY A1022 " --> pdb=" O PHE A 857 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LYS A 854 " --> pdb=" O ILE A1035 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ARG A1037 " --> pdb=" O LYS A 854 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N HIS A 856 " --> pdb=" O ARG A1037 " (cutoff:3.500A) 471 hydrogen bonds defined for protein. 1342 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: 3.34 Time building geometry restraints manager: 3.13 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: 2439 1.34 - 1.46: 1434 1.46 - 1.57: 3961 1.57 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 7896 Sorted by residual: bond pdb=" CB ASP A 165 " pdb=" CG ASP A 165 " ideal model delta sigma weight residual 1.516 1.461 0.055 2.50e-02 1.60e+03 4.81e+00 bond pdb=" CG1 ILE A 432 " pdb=" CD1 ILE A 432 " ideal model delta sigma weight residual 1.513 1.433 0.080 3.90e-02 6.57e+02 4.24e+00 bond pdb=" CG LEU A 736 " pdb=" CD2 LEU A 736 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.12e+00 bond pdb=" CB PRO A 103 " pdb=" CG PRO A 103 " ideal model delta sigma weight residual 1.492 1.405 0.087 5.00e-02 4.00e+02 3.03e+00 bond pdb=" C ILE A 242 " pdb=" N PRO A 243 " ideal model delta sigma weight residual 1.337 1.353 -0.017 9.80e-03 1.04e+04 2.94e+00 ... (remaining 7891 not shown) Histogram of bond angle deviations from ideal: 98.29 - 105.72: 225 105.72 - 113.15: 4175 113.15 - 120.57: 3589 120.57 - 128.00: 2645 128.00 - 135.43: 74 Bond angle restraints: 10708 Sorted by residual: angle pdb=" CA PRO A 243 " pdb=" N PRO A 243 " pdb=" CD PRO A 243 " ideal model delta sigma weight residual 112.00 106.95 5.05 1.40e+00 5.10e-01 1.30e+01 angle pdb=" N GLY A 581 " pdb=" CA GLY A 581 " pdb=" C GLY A 581 " ideal model delta sigma weight residual 113.30 103.20 10.10 2.90e+00 1.19e-01 1.21e+01 angle pdb=" C HIS A 229 " pdb=" N THR A 230 " pdb=" CA THR A 230 " ideal model delta sigma weight residual 120.63 126.16 -5.53 1.61e+00 3.86e-01 1.18e+01 angle pdb=" C ASP A 339 " pdb=" N THR A 340 " pdb=" CA THR A 340 " ideal model delta sigma weight residual 120.54 124.96 -4.42 1.35e+00 5.49e-01 1.07e+01 angle pdb=" C LEU A 353 " pdb=" N THR A 354 " pdb=" CA THR A 354 " ideal model delta sigma weight residual 122.08 117.10 4.98 1.53e+00 4.27e-01 1.06e+01 ... (remaining 10703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 4425 17.76 - 35.52: 263 35.52 - 53.28: 61 53.28 - 71.04: 17 71.04 - 88.80: 9 Dihedral angle restraints: 4775 sinusoidal: 1953 harmonic: 2822 Sorted by residual: dihedral pdb=" CA PRO A 170 " pdb=" C PRO A 170 " pdb=" N CYS A 171 " pdb=" CA CYS A 171 " ideal model delta harmonic sigma weight residual 180.00 154.88 25.12 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA PHE A 210 " pdb=" C PHE A 210 " pdb=" N THR A 211 " pdb=" CA THR A 211 " ideal model delta harmonic sigma weight residual 180.00 158.36 21.64 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" C ILE A 242 " pdb=" N ILE A 242 " pdb=" CA ILE A 242 " pdb=" CB ILE A 242 " ideal model delta harmonic sigma weight residual -122.00 -131.59 9.59 0 2.50e+00 1.60e-01 1.47e+01 ... (remaining 4772 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 731 0.053 - 0.106: 330 0.106 - 0.159: 85 0.159 - 0.212: 21 0.212 - 0.265: 7 Chirality restraints: 1174 Sorted by residual: chirality pdb=" CB ILE A 242 " pdb=" CA ILE A 242 " pdb=" CG1 ILE A 242 " pdb=" CG2 ILE A 242 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CG LEU A 895 " pdb=" CB LEU A 895 " pdb=" CD1 LEU A 895 " pdb=" CD2 LEU A 895 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CB VAL A1004 " pdb=" CA VAL A1004 " pdb=" CG1 VAL A1004 " pdb=" CG2 VAL A1004 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 1171 not shown) Planarity restraints: 1398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 899 " 0.018 2.00e-02 2.50e+03 3.50e-02 1.23e+01 pdb=" C ILE A 899 " -0.061 2.00e-02 2.50e+03 pdb=" O ILE A 899 " 0.022 2.00e-02 2.50e+03 pdb=" N ARG A 900 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 34 " 0.014 2.00e-02 2.50e+03 2.78e-02 7.71e+00 pdb=" C CYS A 34 " -0.048 2.00e-02 2.50e+03 pdb=" O CYS A 34 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU A 35 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 896 " 0.013 2.00e-02 2.50e+03 2.70e-02 7.27e+00 pdb=" C HIS A 896 " -0.047 2.00e-02 2.50e+03 pdb=" O HIS A 896 " 0.017 2.00e-02 2.50e+03 pdb=" N THR A 897 " 0.016 2.00e-02 2.50e+03 ... (remaining 1395 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1339 2.76 - 3.30: 7122 3.30 - 3.83: 12843 3.83 - 4.37: 14940 4.37 - 4.90: 26004 Nonbonded interactions: 62248 Sorted by model distance: nonbonded pdb=" OD1 ASP A 98 " pdb=" OG1 THR A 100 " model vdw 2.225 2.440 nonbonded pdb=" OE1 GLN A 737 " pdb=" OG SER A 741 " model vdw 2.314 2.440 nonbonded pdb=" O SER A 190 " pdb=" OH TYR A 538 " model vdw 2.330 2.440 nonbonded pdb=" O SER A 351 " pdb=" OG SER A 355 " model vdw 2.341 2.440 nonbonded pdb=" NH2 ARG A 36 " pdb=" O ASN A 270 " model vdw 2.374 2.520 ... (remaining 62243 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 4901 2.51 5 N 1305 2.21 5 O 1459 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.42 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 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: 4.240 Check model and map are aligned: 0.110 Process input model: 29.180 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.090 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 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 : 0.009 0.087 7896 Z= 0.567 Angle : 1.085 10.429 10708 Z= 0.593 Chirality : 0.065 0.265 1174 Planarity : 0.007 0.053 1398 Dihedral : 13.213 88.800 2949 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -1.45 (0.24), residues: 965 helix: -1.12 (0.20), residues: 462 sheet: 0.49 (0.36), residues: 174 loop : -1.27 (0.33), residues: 329 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.2389 time to fit residues: 40.6356 Evaluate side-chains 76 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.952 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 151 GLN A 179 GLN A 204 ASN ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 HIS A 712 ASN A 852 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 7896 Z= 0.202 Angle : 0.670 12.600 10708 Z= 0.339 Chirality : 0.044 0.248 1174 Planarity : 0.005 0.044 1398 Dihedral : 4.309 19.451 1037 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 0.37 (0.26), residues: 965 helix: 0.90 (0.24), residues: 469 sheet: 0.62 (0.37), residues: 174 loop : -0.83 (0.34), residues: 322 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 90 average time/residue: 0.1703 time to fit residues: 22.7494 Evaluate side-chains 68 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 65 time to evaluate : 0.950 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0794 time to fit residues: 1.7330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 8.9990 chunk 27 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 94 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 698 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 7896 Z= 0.269 Angle : 0.686 9.415 10708 Z= 0.339 Chirality : 0.043 0.140 1174 Planarity : 0.004 0.043 1398 Dihedral : 4.215 18.425 1037 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 0.82 (0.27), residues: 965 helix: 1.36 (0.24), residues: 468 sheet: 0.76 (0.38), residues: 179 loop : -0.75 (0.34), residues: 318 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 70 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 76 average time/residue: 0.1801 time to fit residues: 20.3143 Evaluate side-chains 66 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.937 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0724 time to fit residues: 2.2521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 41 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 77 optimal weight: 0.0370 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 GLN A1016 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 7896 Z= 0.160 Angle : 0.626 9.680 10708 Z= 0.304 Chirality : 0.042 0.234 1174 Planarity : 0.004 0.040 1398 Dihedral : 4.016 17.609 1037 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 1.12 (0.27), residues: 965 helix: 1.64 (0.25), residues: 469 sheet: 0.72 (0.37), residues: 181 loop : -0.56 (0.35), residues: 315 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 74 time to evaluate : 0.972 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 75 average time/residue: 0.1605 time to fit residues: 18.5866 Evaluate side-chains 66 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 62 time to evaluate : 1.019 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0852 time to fit residues: 2.0316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 79 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 7896 Z= 0.355 Angle : 0.711 8.609 10708 Z= 0.357 Chirality : 0.045 0.215 1174 Planarity : 0.004 0.043 1398 Dihedral : 4.235 18.570 1037 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.27), residues: 965 helix: 1.59 (0.25), residues: 470 sheet: 0.71 (0.37), residues: 181 loop : -0.57 (0.35), residues: 314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 66 average time/residue: 0.1565 time to fit residues: 16.1451 Evaluate side-chains 65 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 60 time to evaluate : 0.932 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0721 time to fit residues: 1.7077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 54 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 89 optimal weight: 5.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 7896 Z= 0.230 Angle : 0.678 9.585 10708 Z= 0.328 Chirality : 0.044 0.219 1174 Planarity : 0.004 0.037 1398 Dihedral : 4.164 17.068 1037 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 1.16 (0.27), residues: 965 helix: 1.65 (0.24), residues: 468 sheet: 0.73 (0.37), residues: 181 loop : -0.47 (0.35), residues: 316 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 69 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 71 average time/residue: 0.1777 time to fit residues: 18.8568 Evaluate side-chains 64 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 61 time to evaluate : 1.013 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0827 time to fit residues: 1.7811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 92 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 7896 Z= 0.233 Angle : 0.706 12.363 10708 Z= 0.341 Chirality : 0.046 0.322 1174 Planarity : 0.004 0.039 1398 Dihedral : 4.162 22.215 1037 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.27), residues: 965 helix: 1.62 (0.24), residues: 468 sheet: 0.72 (0.37), residues: 181 loop : -0.45 (0.36), residues: 316 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 65 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 68 average time/residue: 0.1744 time to fit residues: 17.8202 Evaluate side-chains 65 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 61 time to evaluate : 0.926 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0806 time to fit residues: 2.0099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 7896 Z= 0.171 Angle : 0.687 10.689 10708 Z= 0.329 Chirality : 0.044 0.301 1174 Planarity : 0.004 0.036 1398 Dihedral : 4.041 20.583 1037 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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 (0.28), residues: 965 helix: 1.81 (0.25), residues: 465 sheet: 0.74 (0.38), residues: 174 loop : -0.31 (0.36), residues: 326 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 73 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 73 average time/residue: 0.1749 time to fit residues: 18.6956 Evaluate side-chains 64 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 62 time to evaluate : 1.010 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0929 time to fit residues: 1.4974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 1.9990 chunk 88 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 77 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 7896 Z= 0.172 Angle : 0.685 11.442 10708 Z= 0.325 Chirality : 0.044 0.329 1174 Planarity : 0.004 0.039 1398 Dihedral : 4.012 20.192 1037 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 1.42 (0.28), residues: 965 helix: 1.87 (0.25), residues: 466 sheet: 0.75 (0.38), residues: 176 loop : -0.24 (0.36), residues: 323 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 1.017 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 58 average time/residue: 0.1562 time to fit residues: 14.5834 Evaluate side-chains 57 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.946 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0771 time to fit residues: 1.4666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 6.9990 chunk 43 optimal weight: 0.3980 chunk 63 optimal weight: 2.9990 chunk 95 optimal weight: 0.0270 chunk 88 optimal weight: 8.9990 chunk 76 optimal weight: 0.7980 chunk 7 optimal weight: 0.0040 chunk 58 optimal weight: 0.0070 chunk 46 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.2468 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 7896 Z= 0.154 Angle : 0.699 11.929 10708 Z= 0.326 Chirality : 0.044 0.337 1174 Planarity : 0.004 0.048 1398 Dihedral : 3.960 20.577 1037 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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 (0.28), residues: 965 helix: 1.89 (0.25), residues: 468 sheet: 0.69 (0.38), residues: 174 loop : -0.17 (0.36), residues: 323 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 0.947 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 67 average time/residue: 0.1699 time to fit residues: 17.3597 Evaluate side-chains 62 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 1.553 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0755 time to fit residues: 1.4645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 21 optimal weight: 0.0980 chunk 76 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 66 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.067863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.053865 restraints weight = 29741.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.056111 restraints weight = 15488.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.057613 restraints weight = 9919.263| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3348 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3348 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 7896 Z= 0.161 Angle : 0.686 11.994 10708 Z= 0.322 Chirality : 0.043 0.330 1174 Planarity : 0.004 0.056 1398 Dihedral : 3.909 20.790 1037 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 1.54 (0.28), residues: 965 helix: 1.98 (0.25), residues: 468 sheet: 0.70 (0.39), residues: 174 loop : -0.14 (0.36), residues: 323 =============================================================================== Job complete usr+sys time: 1523.03 seconds wall clock time: 28 minutes 49.93 seconds (1729.93 seconds total)