Starting phenix.real_space_refine on Tue Feb 13 20:52:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xos_22278/02_2024/6xos_22278.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xos_22278/02_2024/6xos_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_2024/6xos_22278.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xos_22278/02_2024/6xos_22278.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xos_22278/02_2024/6xos_22278.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xos_22278/02_2024/6xos_22278.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 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. 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 8.03, per 1000 atoms: 1.04 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: 2.57 Conformation dependent library (CDL) restraints added in 2.7 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: 1.02 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: 3.14 Time building geometry restraints manager: 2.87 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=" C ALA A 580 " pdb=" N GLY A 581 " pdb=" CA GLY A 581 " ideal model delta sigma weight residual 121.70 128.48 -6.78 1.80e+00 3.09e-01 1.42e+01 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 ... (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 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: 1.130 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: 3.980 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 30.300 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 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 : 1.086 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 % Allowed : 2.10 % Favored : 97.90 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 303 HIS 0.011 0.003 HIS A 186 PHE 0.026 0.003 PHE A 389 TYR 0.026 0.004 TYR A 258 ARG 0.006 0.001 ARG A 81 *********************** 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 : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ARG cc_start: 0.8588 (mmp-170) cc_final: 0.8376 (mmm160) REVERT: A 504 MET cc_start: 0.8109 (ttp) cc_final: 0.7886 (ttm) REVERT: A 721 TYR cc_start: 0.8657 (m-80) cc_final: 0.8085 (m-80) REVERT: A 923 TYR cc_start: 0.7822 (t80) cc_final: 0.7255 (t80) REVERT: A 928 THR cc_start: 0.8506 (p) cc_final: 0.8236 (p) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.2338 time to fit residues: 39.9003 Evaluate side-chains 79 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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: 0.8289 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7896 Z= 0.203 Angle : 0.663 12.743 10708 Z= 0.336 Chirality : 0.044 0.239 1174 Planarity : 0.005 0.044 1398 Dihedral : 4.295 20.056 1037 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.70 % Allowed : 10.26 % Favored : 89.04 % 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: 0.40 (0.27), residues: 965 helix: 0.94 (0.24), residues: 469 sheet: 0.54 (0.37), residues: 175 loop : -0.80 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 178 HIS 0.003 0.001 HIS A 511 PHE 0.011 0.001 PHE A 341 TYR 0.018 0.001 TYR A 450 ARG 0.005 0.000 ARG A 924 *********************** 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 101 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 95 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 ASP cc_start: 0.8628 (m-30) cc_final: 0.8424 (p0) REVERT: A 178 TRP cc_start: 0.8058 (m-10) cc_final: 0.7802 (m-10) REVERT: A 215 ARG cc_start: 0.8644 (mmp-170) cc_final: 0.8417 (mmm160) REVERT: A 721 TYR cc_start: 0.8699 (m-80) cc_final: 0.8296 (m-80) outliers start: 6 outliers final: 3 residues processed: 95 average time/residue: 0.1987 time to fit residues: 26.3965 Evaluate side-chains 75 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 72 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 400 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 59 optimal weight: 0.3980 chunk 24 optimal weight: 9.9990 chunk 87 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 70 optimal weight: 7.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 698 HIS A 856 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 7896 Z= 0.382 Angle : 0.754 8.821 10708 Z= 0.377 Chirality : 0.045 0.144 1174 Planarity : 0.005 0.044 1398 Dihedral : 4.447 19.169 1037 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.10 % Allowed : 11.19 % Favored : 86.71 % 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: 0.62 (0.27), residues: 965 helix: 1.19 (0.24), residues: 470 sheet: 0.59 (0.37), residues: 181 loop : -0.80 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 851 HIS 0.005 0.001 HIS A 108 PHE 0.016 0.002 PHE A 361 TYR 0.014 0.002 TYR A 268 ARG 0.005 0.001 ARG A 81 *********************** 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 88 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 70 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ARG cc_start: 0.8738 (mmp-170) cc_final: 0.8446 (mmm160) REVERT: A 721 TYR cc_start: 0.8768 (m-80) cc_final: 0.8281 (m-80) outliers start: 18 outliers final: 15 residues processed: 79 average time/residue: 0.1788 time to fit residues: 20.4015 Evaluate side-chains 77 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 62 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 778 MET Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 964 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 45 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 chunk 83 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 77 optimal weight: 0.0470 overall best weight: 0.6080 ------------------------------------------------------------------------------- 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: 0.8336 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7896 Z= 0.162 Angle : 0.621 9.500 10708 Z= 0.306 Chirality : 0.042 0.200 1174 Planarity : 0.004 0.039 1398 Dihedral : 4.093 17.828 1037 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.70 % Allowed : 12.47 % Favored : 86.83 % 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: 1.03 (0.27), residues: 965 helix: 1.57 (0.25), residues: 470 sheet: 0.74 (0.37), residues: 179 loop : -0.66 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 851 HIS 0.004 0.001 HIS A 719 PHE 0.021 0.001 PHE A 123 TYR 0.013 0.001 TYR A 923 ARG 0.007 0.000 ARG A 900 *********************** 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 80 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 74 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 MET cc_start: 0.7617 (mmt) cc_final: 0.7196 (mmt) REVERT: A 215 ARG cc_start: 0.8743 (mmp-170) cc_final: 0.8430 (mmm160) REVERT: A 721 TYR cc_start: 0.8725 (m-80) cc_final: 0.8252 (m-80) REVERT: A 888 ARG cc_start: 0.8335 (tpp-160) cc_final: 0.8132 (tpt170) outliers start: 6 outliers final: 4 residues processed: 75 average time/residue: 0.2022 time to fit residues: 21.4283 Evaluate side-chains 71 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 464 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 83 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7896 Z= 0.269 Angle : 0.641 8.377 10708 Z= 0.318 Chirality : 0.043 0.136 1174 Planarity : 0.004 0.041 1398 Dihedral : 4.091 16.784 1037 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.40 % Allowed : 12.94 % Favored : 85.66 % 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 (0.28), residues: 965 helix: 1.68 (0.25), residues: 470 sheet: 0.80 (0.38), residues: 178 loop : -0.58 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 851 HIS 0.004 0.001 HIS A 719 PHE 0.010 0.001 PHE A 389 TYR 0.014 0.001 TYR A 258 ARG 0.008 0.001 ARG A 900 *********************** 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 80 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 68 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 MET cc_start: 0.7702 (mmt) cc_final: 0.7217 (mmt) REVERT: A 215 ARG cc_start: 0.8761 (mmp-170) cc_final: 0.8430 (mmm160) REVERT: A 721 TYR cc_start: 0.8756 (m-80) cc_final: 0.8233 (m-80) outliers start: 12 outliers final: 5 residues processed: 73 average time/residue: 0.2054 time to fit residues: 20.9786 Evaluate side-chains 70 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 778 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 7 optimal weight: 0.2980 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 89 optimal weight: 0.9980 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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: 0.8392 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7896 Z= 0.216 Angle : 0.657 11.559 10708 Z= 0.316 Chirality : 0.043 0.206 1174 Planarity : 0.004 0.038 1398 Dihedral : 4.064 16.910 1037 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.82 % Allowed : 13.99 % Favored : 85.20 % 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: 1.20 (0.28), residues: 965 helix: 1.68 (0.25), residues: 470 sheet: 0.77 (0.38), residues: 179 loop : -0.49 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 851 HIS 0.005 0.001 HIS A 719 PHE 0.023 0.001 PHE A 123 TYR 0.015 0.001 TYR A 923 ARG 0.008 0.000 ARG A 900 *********************** 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 73 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 MET cc_start: 0.7696 (mmt) cc_final: 0.7298 (mmt) REVERT: A 215 ARG cc_start: 0.8766 (mmp-170) cc_final: 0.8439 (mmm160) REVERT: A 721 TYR cc_start: 0.8740 (m-80) cc_final: 0.8224 (m-80) outliers start: 7 outliers final: 5 residues processed: 68 average time/residue: 0.2135 time to fit residues: 20.3817 Evaluate side-chains 69 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 464 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 78 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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: 0.8370 moved from start: 0.3465 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= 0.178 Angle : 0.638 11.933 10708 Z= 0.305 Chirality : 0.043 0.290 1174 Planarity : 0.004 0.038 1398 Dihedral : 3.947 15.967 1037 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.70 % Allowed : 13.75 % Favored : 85.55 % 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: 1.37 (0.28), residues: 965 helix: 1.83 (0.25), residues: 469 sheet: 0.84 (0.38), residues: 179 loop : -0.39 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 851 HIS 0.005 0.001 HIS A 719 PHE 0.010 0.001 PHE A 389 TYR 0.009 0.001 TYR A 268 ARG 0.009 0.000 ARG A 900 *********************** 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 75 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 MET cc_start: 0.7710 (mmt) cc_final: 0.7380 (mmt) REVERT: A 215 ARG cc_start: 0.8754 (mmp-170) cc_final: 0.8423 (mmm160) REVERT: A 721 TYR cc_start: 0.8739 (m-80) cc_final: 0.8203 (m-80) outliers start: 6 outliers final: 5 residues processed: 70 average time/residue: 0.2131 time to fit residues: 21.0681 Evaluate side-chains 70 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 778 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 0.0000 chunk 72 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.8586 ------------------------------------------------------------------------------- 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: 0.8351 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7896 Z= 0.164 Angle : 0.662 11.883 10708 Z= 0.315 Chirality : 0.044 0.328 1174 Planarity : 0.004 0.037 1398 Dihedral : 3.889 15.559 1037 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.70 % Allowed : 13.99 % Favored : 85.31 % 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: 1.49 (0.28), residues: 965 helix: 1.88 (0.25), residues: 468 sheet: 0.91 (0.38), residues: 179 loop : -0.26 (0.37), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1034 HIS 0.004 0.001 HIS A 719 PHE 0.024 0.001 PHE A 123 TYR 0.016 0.001 TYR A 923 ARG 0.009 0.000 ARG A 900 *********************** 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 78 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 72 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 ARG cc_start: 0.8752 (mmp-170) cc_final: 0.8431 (mmm160) REVERT: A 721 TYR cc_start: 0.8748 (m-80) cc_final: 0.8195 (m-80) REVERT: A 789 MET cc_start: 0.8739 (mmm) cc_final: 0.8282 (mmm) outliers start: 6 outliers final: 5 residues processed: 73 average time/residue: 0.2014 time to fit residues: 20.9307 Evaluate side-chains 69 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 464 LEU 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: 8.9990 chunk 26 optimal weight: 0.0370 chunk 77 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 91 optimal weight: 0.1980 overall best weight: 0.8062 ------------------------------------------------------------------------------- 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: 0.8347 moved from start: 0.3740 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= 0.158 Angle : 0.656 11.755 10708 Z= 0.309 Chirality : 0.044 0.337 1174 Planarity : 0.004 0.038 1398 Dihedral : 3.822 15.494 1037 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.58 % Allowed : 14.10 % Favored : 85.31 % 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: 1.56 (0.28), residues: 965 helix: 1.91 (0.25), residues: 470 sheet: 0.99 (0.39), residues: 176 loop : -0.20 (0.37), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1034 HIS 0.004 0.001 HIS A 719 PHE 0.011 0.001 PHE A 389 TYR 0.009 0.001 TYR A 380 ARG 0.009 0.000 ARG A 900 *********************** 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 73 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 ARG cc_start: 0.8756 (mmp-170) cc_final: 0.8438 (mmm160) REVERT: A 709 GLU cc_start: 0.8741 (tp30) cc_final: 0.8513 (tp30) REVERT: A 721 TYR cc_start: 0.8754 (m-80) cc_final: 0.8149 (m-80) outliers start: 5 outliers final: 5 residues processed: 69 average time/residue: 0.1826 time to fit residues: 18.2353 Evaluate side-chains 68 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 63 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 464 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 chunk 88 optimal weight: 8.9990 chunk 76 optimal weight: 0.0470 chunk 7 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 60 optimal weight: 0.0870 chunk 81 optimal weight: 0.7980 overall best weight: 0.5656 ------------------------------------------------------------------------------- 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: 0.8332 moved from start: 0.3834 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= 0.153 Angle : 0.671 12.146 10708 Z= 0.312 Chirality : 0.043 0.341 1174 Planarity : 0.004 0.036 1398 Dihedral : 3.769 14.690 1037 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.58 % Allowed : 14.57 % Favored : 84.85 % 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: 1.62 (0.28), residues: 965 helix: 1.97 (0.25), residues: 469 sheet: 1.00 (0.39), residues: 174 loop : -0.17 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 182 HIS 0.004 0.001 HIS A 719 PHE 0.025 0.001 PHE A 123 TYR 0.017 0.001 TYR A 923 ARG 0.009 0.000 ARG A 900 ********************** 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 76 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ARG cc_start: 0.8754 (mmp-170) cc_final: 0.8506 (mmp80) REVERT: A 607 LEU cc_start: 0.8184 (tt) cc_final: 0.7954 (tt) REVERT: A 709 GLU cc_start: 0.8725 (tp30) cc_final: 0.8504 (tp30) REVERT: A 721 TYR cc_start: 0.8744 (m-80) cc_final: 0.8143 (m-80) outliers start: 5 outliers final: 5 residues processed: 72 average time/residue: 0.1855 time to fit residues: 19.5002 Evaluate side-chains 74 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 69 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 859 MET 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: 4.9990 chunk 11 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 76 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 = 0.3266 r_free = 0.3266 target = 0.064539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.050443 restraints weight = 30732.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.052561 restraints weight = 16316.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.053987 restraints weight = 10607.950| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7896 Z= 0.330 Angle : 0.727 11.503 10708 Z= 0.352 Chirality : 0.045 0.326 1174 Planarity : 0.004 0.042 1398 Dihedral : 3.999 15.234 1037 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.58 % Allowed : 14.69 % Favored : 84.73 % 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: 1.43 (0.28), residues: 965 helix: 1.78 (0.25), residues: 470 sheet: 0.97 (0.38), residues: 180 loop : -0.27 (0.36), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 182 HIS 0.005 0.001 HIS A 719 PHE 0.012 0.002 PHE A 618 TYR 0.013 0.002 TYR A 268 ARG 0.009 0.001 ARG A 900 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1580.29 seconds wall clock time: 29 minutes 48.30 seconds (1788.30 seconds total)