Starting phenix.real_space_refine on Mon Mar 11 14:40:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpi_24615/03_2024/7rpi_24615.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpi_24615/03_2024/7rpi_24615.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpi_24615/03_2024/7rpi_24615.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpi_24615/03_2024/7rpi_24615.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpi_24615/03_2024/7rpi_24615.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpi_24615/03_2024/7rpi_24615.pdb" } resolution = 2.5 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= 0.005 sd= 0.579 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 65 5.16 5 Na 2 4.78 5 C 5741 2.51 5 N 1184 2.21 5 O 1534 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 258": "OE1" <-> "OE2" Residue "A PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 461": "OE1" <-> "OE2" Residue "A GLU 472": "OE1" <-> "OE2" Residue "A GLU 594": "OE1" <-> "OE2" Residue "A GLU 659": "OE1" <-> "OE2" Residue "A ARG 660": "NH1" <-> "NH2" Residue "A GLU 705": "OE1" <-> "OE2" Residue "A GLU 746": "OE1" <-> "OE2" Residue "A GLU 749": "OE1" <-> "OE2" Residue "A ARG 754": "NH1" <-> "NH2" Residue "A GLU 760": "OE1" <-> "OE2" Residue "A ARG 774": "NH1" <-> "NH2" Residue "A GLU 779": "OE1" <-> "OE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A ARG 833": "NH1" <-> "NH2" Residue "A GLU 859": "OE1" <-> "OE2" Residue "A GLU 865": "OE1" <-> "OE2" Residue "A GLU 936": "OE1" <-> "OE2" Residue "A GLU 952": "OE1" <-> "OE2" Residue "A GLU 958": "OE1" <-> "OE2" Residue "A ARG 962": "NH1" <-> "NH2" Residue "A GLU 970": "OE1" <-> "OE2" Residue "A GLU 1036": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8526 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8526 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1004, 8521 Unusual residues: {' NA': 2, 'AV0': 2, 'NAG': 5, 'Y01': 26} Classifications: {'peptide': 926, 'undetermined': 35, 'water': 43} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 885, None: 78} Not linked: pdbres="PHE A1143 " pdbres="Y01 A2101 " Not linked: pdbres="Y01 A2101 " pdbres="Y01 A2102 " Not linked: pdbres="Y01 A2102 " pdbres="Y01 A2103 " Not linked: pdbres="Y01 A2103 " pdbres="Y01 A2104 " Not linked: pdbres="Y01 A2104 " pdbres="Y01 A2105 " ... (remaining 73 not shown) Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Conformer: "B" Number of residues, atoms: 1004, 8521 Unusual residues: {' NA': 2, 'AV0': 2, 'NAG': 5, 'Y01': 26} Classifications: {'peptide': 926, 'undetermined': 35, 'water': 43} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 885, None: 78} Not linked: pdbres="PHE A1143 " pdbres="Y01 A2101 " Not linked: pdbres="Y01 A2101 " pdbres="Y01 A2102 " Not linked: pdbres="Y01 A2102 " pdbres="Y01 A2103 " Not linked: pdbres="Y01 A2103 " pdbres="Y01 A2104 " Not linked: pdbres="Y01 A2104 " pdbres="Y01 A2105 " ... (remaining 73 not shown) Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 bond proxies already assigned to first conformer: 8752 Time building chain proxies: 9.46, per 1000 atoms: 1.11 Number of scatterers: 8526 At special positions: 0 Unit cell: (86.005, 87.675, 127.755, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 65 16.00 Na 2 11.00 O 1534 8.00 N 1184 7.00 C 5741 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 292 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 366 " distance=2.05 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 347 " distance=2.03 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 397 " - pdb=" SG CYS A 410 " distance=2.03 Simple disulfide: pdb=" SG CYS A 829 " - pdb=" SG CYS A 849 " distance=2.05 Simple disulfide: pdb=" SG CYS A 863 " - pdb=" SG CYS A 872 " distance=2.04 Simple disulfide: pdb=" SG CYS A 871 " - pdb=" SG CYS A 887 " distance=2.04 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 Links applied NAG-ASN " NAG A2129 " - " ASN A 915 " " NAG A2130 " - " ASN A 834 " " NAG A2131 " - " ASN A 475 " " NAG A2132 " - " ASN A 390 " " NAG A2133 " - " ASN A 362 " Time building additional restraints: 3.22 Conformation dependent library (CDL) restraints added in 2.5 seconds 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1766 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 2 sheets defined 66.1% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 179 through 187 Processing helix chain 'A' and resid 187 through 209 removed outlier: 3.552A pdb=" N VAL A 191 " --> pdb=" O TRP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 242 Processing helix chain 'A' and resid 253 through 262 removed outlier: 3.827A pdb=" N GLU A 259 " --> pdb=" O LYS A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 329 removed outlier: 3.564A pdb=" N CYS A 322 " --> pdb=" O ILE A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 339 removed outlier: 3.630A pdb=" N LEU A 338 " --> pdb=" O GLN A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 361 Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 370 through 390 removed outlier: 5.239A pdb=" N LYS A 386 " --> pdb=" O ARG A 382 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N HIS A 387 " --> pdb=" O THR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 430 Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 463 through 471 Processing helix chain 'A' and resid 490 through 502 removed outlier: 3.827A pdb=" N GLN A 496 " --> pdb=" O HIS A 492 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASP A 497 " --> pdb=" O SER A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 522 Processing helix chain 'A' and resid 523 through 548 removed outlier: 3.653A pdb=" N THR A 527 " --> pdb=" O SER A 523 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A 538 " --> pdb=" O ILE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 559 Processing helix chain 'A' and resid 560 through 569 Processing helix chain 'A' and resid 570 through 587 removed outlier: 3.642A pdb=" N VAL A 575 " --> pdb=" O ASP A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 620 removed outlier: 5.557A pdb=" N LEU A 605 " --> pdb=" O GLN A 601 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N SER A 606 " --> pdb=" O HIS A 602 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR A 614 " --> pdb=" O THR A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 624 Processing helix chain 'A' and resid 626 through 648 Processing helix chain 'A' and resid 649 through 661 Processing helix chain 'A' and resid 661 through 666 Processing helix chain 'A' and resid 682 through 706 removed outlier: 4.586A pdb=" N GLN A 687 " --> pdb=" O ALA A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 715 removed outlier: 3.720A pdb=" N CYS A 710 " --> pdb=" O LYS A 706 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE A 715 " --> pdb=" O ILE A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 736 Processing helix chain 'A' and resid 746 through 750 Processing helix chain 'A' and resid 757 through 765 removed outlier: 3.689A pdb=" N ASP A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 769 Processing helix chain 'A' and resid 770 through 775 Processing helix chain 'A' and resid 818 through 833 Processing helix chain 'A' and resid 849 through 859 removed outlier: 3.608A pdb=" N THR A 853 " --> pdb=" O CYS A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 869 Processing helix chain 'A' and resid 880 through 899 removed outlier: 3.978A pdb=" N LYS A 889 " --> pdb=" O GLU A 885 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP A 896 " --> pdb=" O ILE A 892 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ARG A 897 " --> pdb=" O MET A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 954 Processing helix chain 'A' and resid 969 through 1002 Processing helix chain 'A' and resid 1003 through 1028 Processing helix chain 'A' and resid 1035 through 1061 removed outlier: 3.590A pdb=" N ILE A1040 " --> pdb=" O GLU A1036 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER A1041 " --> pdb=" O SER A1037 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL A1044 " --> pdb=" O ILE A1040 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY A1045 " --> pdb=" O SER A1041 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ASP A1049 " --> pdb=" O GLY A1045 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N PHE A1050 " --> pdb=" O LEU A1046 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1094 removed outlier: 5.434A pdb=" N SER A1079 " --> pdb=" O SER A1075 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ALA A1080 " --> pdb=" O ARG A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1123 Processing helix chain 'A' and resid 1123 through 1133 Processing sheet with id=AA1, first strand: chain 'A' and resid 450 through 458 removed outlier: 4.013A pdb=" N SER A 300 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA A 305 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N VAL A 483 " --> pdb=" O ALA A 305 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 909 through 912 removed outlier: 3.577A pdb=" N ALA A 920 " --> pdb=" O ARG A 911 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N LEU A 923 " --> pdb=" O TRP A 789 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N TRP A 789 " --> pdb=" O LEU A 923 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N PHE A 925 " --> pdb=" O VAL A 787 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N VAL A 787 " --> pdb=" O PHE A 925 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N SER A 927 " --> pdb=" O ILE A 785 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ILE A 785 " --> pdb=" O SER A 927 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N PHE A 929 " --> pdb=" O MET A 783 " (cutoff:3.500A) 441 hydrogen bonds defined for protein. 1287 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: 2.49 Time building geometry restraints manager: 3.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1340 1.32 - 1.45: 2192 1.45 - 1.58: 5065 1.58 - 1.70: 69 1.70 - 1.83: 98 Bond restraints: 8764 Sorted by residual: bond pdb=" N MET A 557 " pdb=" CA BMET A 557 " ideal model delta sigma weight residual 1.458 1.357 0.102 1.27e-02 6.20e+03 6.43e+01 bond pdb=" N GLU A1031 " pdb=" CA GLU A1031 " ideal model delta sigma weight residual 1.454 1.400 0.053 1.23e-02 6.61e+03 1.86e+01 bond pdb=" C ASP A 578 " pdb=" O ASP A 578 " ideal model delta sigma weight residual 1.236 1.189 0.047 1.15e-02 7.56e+03 1.66e+01 bond pdb=" CA GLU A1031 " pdb=" CB GLU A1031 " ideal model delta sigma weight residual 1.535 1.462 0.073 1.93e-02 2.68e+03 1.42e+01 bond pdb=" CB THR A1122 " pdb=" OG1 THR A1122 " ideal model delta sigma weight residual 1.433 1.373 0.060 1.60e-02 3.91e+03 1.42e+01 ... (remaining 8759 not shown) Histogram of bond angle deviations from ideal: 93.37 - 101.77: 49 101.77 - 110.16: 2060 110.16 - 118.55: 4927 118.55 - 126.95: 4923 126.95 - 135.34: 103 Bond angle restraints: 12062 Sorted by residual: angle pdb=" N ARG A 341 " pdb=" CA ARG A 341 " pdb=" C ARG A 341 " ideal model delta sigma weight residual 108.76 122.02 -13.26 1.69e+00 3.50e-01 6.16e+01 angle pdb=" N MET A 557 " pdb=" CA BMET A 557 " pdb=" C MET A 557 " ideal model delta sigma weight residual 111.75 120.36 -8.61 1.28e+00 6.10e-01 4.52e+01 angle pdb=" CA PHE A 759 " pdb=" CB PHE A 759 " pdb=" CG PHE A 759 " ideal model delta sigma weight residual 113.80 120.40 -6.60 1.00e+00 1.00e+00 4.36e+01 angle pdb=" CA PHE A 549 " pdb=" CB PHE A 549 " pdb=" CG PHE A 549 " ideal model delta sigma weight residual 113.80 120.17 -6.37 1.00e+00 1.00e+00 4.06e+01 angle pdb=" CA ASP A 293 " pdb=" CB ASP A 293 " pdb=" CG ASP A 293 " ideal model delta sigma weight residual 112.60 118.82 -6.22 1.00e+00 1.00e+00 3.87e+01 ... (remaining 12057 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.89: 6362 26.89 - 53.79: 229 53.79 - 80.68: 41 80.68 - 107.57: 21 107.57 - 134.47: 6 Dihedral angle restraints: 6659 sinusoidal: 3931 harmonic: 2728 Sorted by residual: dihedral pdb=" CA VAL A1048 " pdb=" C VAL A1048 " pdb=" N ASP A1049 " pdb=" CA ASP A1049 " ideal model delta harmonic sigma weight residual 180.00 -150.68 -29.32 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA TYR A 420 " pdb=" C TYR A 420 " pdb=" N ASN A 421 " pdb=" CA ASN A 421 " ideal model delta harmonic sigma weight residual -180.00 -153.68 -26.32 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA TYR A 443 " pdb=" C TYR A 443 " pdb=" N ALA A 444 " pdb=" CA ALA A 444 " ideal model delta harmonic sigma weight residual -180.00 -155.33 -24.67 0 5.00e+00 4.00e-02 2.43e+01 ... (remaining 6656 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 922 0.095 - 0.191: 432 0.191 - 0.286: 69 0.286 - 0.381: 15 0.381 - 0.477: 3 Chirality restraints: 1441 Sorted by residual: chirality pdb=" CA GLU A1031 " pdb=" N GLU A1031 " pdb=" C GLU A1031 " pdb=" CB GLU A1031 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.68e+00 chirality pdb=" CA BMET A 557 " pdb=" N MET A 557 " pdb=" C MET A 557 " pdb=" CB BMET A 557 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.08e+00 chirality pdb=" CA ASP A 916 " pdb=" N ASP A 916 " pdb=" C ASP A 916 " pdb=" CB ASP A 916 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.86e+00 ... (remaining 1438 not shown) Planarity restraints: 1344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 834 " -0.102 2.00e-02 2.50e+03 1.05e-01 1.37e+02 pdb=" CG ASN A 834 " 0.066 2.00e-02 2.50e+03 pdb=" OD1 ASN A 834 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A 834 " 0.157 2.00e-02 2.50e+03 pdb=" C1 NAG A2130 " -0.125 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 313 " 0.145 2.00e-02 2.50e+03 7.20e-02 1.30e+02 pdb=" CG TRP A 313 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP A 313 " -0.061 2.00e-02 2.50e+03 pdb=" CD2 TRP A 313 " -0.051 2.00e-02 2.50e+03 pdb=" NE1 TRP A 313 " -0.032 2.00e-02 2.50e+03 pdb=" CE2 TRP A 313 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 313 " -0.090 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 313 " 0.084 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 313 " -0.043 2.00e-02 2.50e+03 pdb=" CH2 TRP A 313 " 0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 915 " -0.091 2.00e-02 2.50e+03 1.01e-01 1.28e+02 pdb=" CG ASN A 915 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN A 915 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 915 " 0.164 2.00e-02 2.50e+03 pdb=" C1 NAG A2129 " -0.119 2.00e-02 2.50e+03 ... (remaining 1341 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 140 2.72 - 3.26: 8270 3.26 - 3.81: 12726 3.81 - 4.35: 18480 4.35 - 4.90: 29510 Nonbonded interactions: 69126 Sorted by model distance: nonbonded pdb=" OD1 ASP A1049 " pdb="NA NA A2134 " model vdw 2.170 2.470 nonbonded pdb=" O GLY A1045 " pdb="NA NA A2134 " model vdw 2.205 2.470 nonbonded pdb=" OD1 ASP A 572 " pdb="NA NA A2135 " model vdw 2.213 2.470 nonbonded pdb=" OD2 ASP A 572 " pdb="NA NA A2135 " model vdw 2.245 2.470 nonbonded pdb="NA NA A2135 " pdb=" O HOH A2231 " model vdw 2.261 2.470 ... (remaining 69121 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.720 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: 0.000 Extract box with map and model: 7.140 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 31.770 Find NCS groups from input model: 0.230 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:13.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 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 : 0.016 0.102 8764 Z= 0.968 Angle : 1.818 13.262 12062 Z= 1.185 Chirality : 0.106 0.477 1441 Planarity : 0.014 0.100 1339 Dihedral : 14.731 134.467 4869 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 0.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.12 % Allowed : 1.72 % Favored : 98.16 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.25), residues: 919 helix: -0.43 (0.19), residues: 558 sheet: 0.48 (0.94), residues: 29 loop : -0.29 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.145 0.028 TRP A 313 HIS 0.008 0.003 HIS A 332 PHE 0.063 0.014 PHE A1109 TYR 0.114 0.021 TYR A 635 ARG 0.007 0.001 ARG A 301 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 129 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 TRP cc_start: 0.7100 (m-10) cc_final: 0.6769 (m-10) REVERT: A 194 MET cc_start: 0.5966 (mtp) cc_final: 0.5583 (mmp) REVERT: A 647 MET cc_start: 0.7973 (mmp) cc_final: 0.7606 (mmt) REVERT: A 698 GLU cc_start: 0.6845 (mm-30) cc_final: 0.6555 (mm-30) REVERT: A 700 SER cc_start: 0.7653 (t) cc_final: 0.7056 (m) REVERT: A 701 ARG cc_start: 0.7019 (mmt90) cc_final: 0.6546 (tpm170) REVERT: A 702 ILE cc_start: 0.6853 (mm) cc_final: 0.6584 (mm) REVERT: A 860 ASN cc_start: 0.7009 (m-40) cc_final: 0.6679 (t0) REVERT: A 937 LYS cc_start: 0.7678 (mtmt) cc_final: 0.7445 (mtmm) REVERT: A 943 LYS cc_start: 0.7334 (mtpp) cc_final: 0.6813 (mmmt) REVERT: A 997 MET cc_start: 0.7552 (mtm) cc_final: 0.7263 (mtp) outliers start: 1 outliers final: 0 residues processed: 129 average time/residue: 1.2326 time to fit residues: 169.0825 Evaluate side-chains 87 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 42 optimal weight: 0.0270 chunk 25 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN A 340 GLN A 421 ASN A 465 ASN A 470 ASN A 856 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8764 Z= 0.179 Angle : 0.683 9.522 12062 Z= 0.323 Chirality : 0.042 0.291 1441 Planarity : 0.004 0.034 1339 Dihedral : 11.595 167.433 3198 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.11 % Allowed : 6.76 % Favored : 92.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.66 (0.28), residues: 919 helix: 1.59 (0.21), residues: 568 sheet: 0.33 (0.88), residues: 31 loop : 0.46 (0.37), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 474 HIS 0.006 0.001 HIS A 827 PHE 0.015 0.002 PHE A1123 TYR 0.014 0.002 TYR A 619 ARG 0.003 0.000 ARG A 363 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 0.940 Fit side-chains revert: symmetry clash REVERT: A 194 MET cc_start: 0.5952 (mtp) cc_final: 0.5557 (mmp) REVERT: A 223 GLU cc_start: 0.7660 (tt0) cc_final: 0.6614 (pm20) REVERT: A 340 GLN cc_start: 0.6976 (tt0) cc_final: 0.6771 (mt0) REVERT: A 515 LEU cc_start: 0.6741 (mt) cc_final: 0.6422 (tp) REVERT: A 698 GLU cc_start: 0.6765 (mm-30) cc_final: 0.6196 (mm-30) REVERT: A 700 SER cc_start: 0.7494 (t) cc_final: 0.7002 (m) REVERT: A 701 ARG cc_start: 0.6864 (mmt90) cc_final: 0.6382 (tpm170) REVERT: A 746 GLU cc_start: 0.6832 (mt-10) cc_final: 0.6622 (mm-30) REVERT: A 771 MET cc_start: 0.7390 (mpp) cc_final: 0.7120 (mmp) REVERT: A 887 CYS cc_start: 0.6934 (m) cc_final: 0.6461 (m) REVERT: A 962 ARG cc_start: 0.6741 (OUTLIER) cc_final: 0.6092 (mtm110) outliers start: 9 outliers final: 3 residues processed: 105 average time/residue: 1.2036 time to fit residues: 135.3483 Evaluate side-chains 88 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 962 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 98 optimal weight: 50.0000 chunk 81 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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: 0.6932 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8764 Z= 0.188 Angle : 0.645 8.021 12062 Z= 0.300 Chirality : 0.042 0.372 1441 Planarity : 0.004 0.038 1339 Dihedral : 11.108 179.039 3198 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.60 % Allowed : 9.09 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.28), residues: 919 helix: 1.91 (0.22), residues: 571 sheet: 0.84 (0.93), residues: 29 loop : 0.31 (0.37), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 650 HIS 0.004 0.001 HIS A 827 PHE 0.020 0.002 PHE A 608 TYR 0.015 0.002 TYR A 619 ARG 0.003 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.5850 (mtp) cc_final: 0.5386 (mmp) REVERT: A 223 GLU cc_start: 0.7706 (tt0) cc_final: 0.6711 (pm20) REVERT: A 515 LEU cc_start: 0.6660 (mt) cc_final: 0.6341 (tt) REVERT: A 700 SER cc_start: 0.7534 (t) cc_final: 0.7022 (m) REVERT: A 701 ARG cc_start: 0.6800 (mmt90) cc_final: 0.6320 (tpm170) REVERT: A 771 MET cc_start: 0.7316 (mpp) cc_final: 0.7070 (mmp) REVERT: A 887 CYS cc_start: 0.6873 (m) cc_final: 0.6455 (m) REVERT: A 962 ARG cc_start: 0.6856 (OUTLIER) cc_final: 0.6128 (mtm110) outliers start: 13 outliers final: 6 residues processed: 105 average time/residue: 1.0676 time to fit residues: 120.7525 Evaluate side-chains 96 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 89 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 475 ASN Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 962 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 96 optimal weight: 50.0000 chunk 86 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 968 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8764 Z= 0.187 Angle : 0.617 7.414 12062 Z= 0.289 Chirality : 0.042 0.374 1441 Planarity : 0.004 0.038 1339 Dihedral : 10.717 174.150 3198 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.97 % Allowed : 9.46 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.28), residues: 919 helix: 2.01 (0.22), residues: 569 sheet: 0.94 (0.92), residues: 29 loop : 0.14 (0.36), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 650 HIS 0.003 0.001 HIS A 827 PHE 0.019 0.002 PHE A 608 TYR 0.014 0.002 TYR A 619 ARG 0.004 0.000 ARG A 774 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.5764 (mtp) cc_final: 0.5317 (mmp) REVERT: A 223 GLU cc_start: 0.7657 (tt0) cc_final: 0.6679 (pm20) REVERT: A 515 LEU cc_start: 0.6665 (mt) cc_final: 0.6368 (tt) REVERT: A 659 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6340 (tt0) REVERT: A 700 SER cc_start: 0.7491 (t) cc_final: 0.6972 (m) REVERT: A 701 ARG cc_start: 0.6736 (mmt90) cc_final: 0.6242 (tpm170) REVERT: A 771 MET cc_start: 0.7282 (mpp) cc_final: 0.7052 (mmp) REVERT: A 887 CYS cc_start: 0.6944 (m) cc_final: 0.6493 (m) REVERT: A 943 LYS cc_start: 0.7286 (OUTLIER) cc_final: 0.7012 (mtpp) outliers start: 16 outliers final: 7 residues processed: 103 average time/residue: 1.1393 time to fit residues: 126.1586 Evaluate side-chains 101 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 475 ASN Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 943 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 968 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8764 Z= 0.202 Angle : 0.625 7.567 12062 Z= 0.292 Chirality : 0.042 0.370 1441 Planarity : 0.004 0.039 1339 Dihedral : 10.701 171.878 3198 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.72 % Allowed : 10.81 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.28), residues: 919 helix: 1.98 (0.22), residues: 573 sheet: 0.94 (0.91), residues: 29 loop : 0.01 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 650 HIS 0.002 0.001 HIS A 827 PHE 0.019 0.002 PHE A 608 TYR 0.013 0.002 TYR A 644 ARG 0.003 0.000 ARG A 774 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 0.816 Fit side-chains revert: symmetry clash REVERT: A 194 MET cc_start: 0.5734 (mtp) cc_final: 0.5265 (mmp) REVERT: A 223 GLU cc_start: 0.7652 (tt0) cc_final: 0.6811 (pm20) REVERT: A 347 CYS cc_start: 0.6587 (m) cc_final: 0.6242 (m) REVERT: A 515 LEU cc_start: 0.6593 (mt) cc_final: 0.6279 (tt) REVERT: A 659 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6344 (tt0) REVERT: A 700 SER cc_start: 0.7486 (t) cc_final: 0.6963 (m) REVERT: A 701 ARG cc_start: 0.6657 (mmt90) cc_final: 0.6182 (tpm170) REVERT: A 771 MET cc_start: 0.7258 (mpp) cc_final: 0.7040 (mmp) REVERT: A 887 CYS cc_start: 0.6931 (m) cc_final: 0.6499 (m) REVERT: A 937 LYS cc_start: 0.7213 (OUTLIER) cc_final: 0.6456 (mmpt) REVERT: A 943 LYS cc_start: 0.7294 (OUTLIER) cc_final: 0.6676 (tptt) outliers start: 14 outliers final: 8 residues processed: 102 average time/residue: 1.0601 time to fit residues: 116.2802 Evaluate side-chains 102 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain A residue 754 ARG Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 937 LYS Chi-restraints excluded: chain A residue 943 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 23 optimal weight: 0.0020 chunk 96 optimal weight: 50.0000 chunk 80 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 968 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8764 Z= 0.158 Angle : 0.579 8.502 12062 Z= 0.269 Chirality : 0.040 0.344 1441 Planarity : 0.004 0.041 1339 Dihedral : 10.398 169.015 3198 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.60 % Allowed : 11.18 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.28), residues: 919 helix: 2.12 (0.22), residues: 571 sheet: 1.00 (0.93), residues: 29 loop : 0.01 (0.36), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 650 HIS 0.002 0.000 HIS A 827 PHE 0.015 0.001 PHE A 608 TYR 0.011 0.001 TYR A 545 ARG 0.003 0.000 ARG A 774 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.5788 (mtp) cc_final: 0.5391 (mmp) REVERT: A 223 GLU cc_start: 0.7579 (tt0) cc_final: 0.6789 (pm20) REVERT: A 515 LEU cc_start: 0.6582 (mt) cc_final: 0.6329 (tt) REVERT: A 700 SER cc_start: 0.7468 (t) cc_final: 0.6946 (m) REVERT: A 701 ARG cc_start: 0.6692 (mmt90) cc_final: 0.6193 (tpm170) REVERT: A 745 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.6684 (pt) REVERT: A 887 CYS cc_start: 0.6914 (m) cc_final: 0.6470 (m) REVERT: A 937 LYS cc_start: 0.7201 (OUTLIER) cc_final: 0.6459 (mmpt) REVERT: A 943 LYS cc_start: 0.7267 (OUTLIER) cc_final: 0.6668 (tptt) outliers start: 13 outliers final: 4 residues processed: 101 average time/residue: 1.1134 time to fit residues: 121.0210 Evaluate side-chains 98 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 91 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 475 ASN Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 937 LYS Chi-restraints excluded: chain A residue 943 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 chunk 96 optimal weight: 50.0000 chunk 60 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 968 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8764 Z= 0.166 Angle : 0.585 8.862 12062 Z= 0.272 Chirality : 0.041 0.336 1441 Planarity : 0.004 0.041 1339 Dihedral : 10.392 167.523 3198 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.47 % Allowed : 11.06 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.28), residues: 919 helix: 2.13 (0.22), residues: 571 sheet: 1.01 (0.92), residues: 29 loop : -0.03 (0.36), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 650 HIS 0.002 0.000 HIS A 827 PHE 0.016 0.001 PHE A 608 TYR 0.012 0.001 TYR A 644 ARG 0.001 0.000 ARG A 363 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: A 194 MET cc_start: 0.5771 (mtp) cc_final: 0.5332 (mmp) REVERT: A 223 GLU cc_start: 0.7589 (tt0) cc_final: 0.6778 (pm20) REVERT: A 515 LEU cc_start: 0.6559 (mt) cc_final: 0.6297 (tt) REVERT: A 700 SER cc_start: 0.7468 (t) cc_final: 0.6946 (m) REVERT: A 701 ARG cc_start: 0.6686 (mmt90) cc_final: 0.6180 (tpm170) REVERT: A 858 MET cc_start: 0.7492 (tpt) cc_final: 0.7266 (tpt) REVERT: A 887 CYS cc_start: 0.6863 (m) cc_final: 0.6289 (m) REVERT: A 937 LYS cc_start: 0.7176 (OUTLIER) cc_final: 0.6436 (mmpt) REVERT: A 943 LYS cc_start: 0.7279 (OUTLIER) cc_final: 0.6670 (tptt) REVERT: A 1036 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7025 (mt-10) outliers start: 12 outliers final: 7 residues processed: 98 average time/residue: 1.0391 time to fit residues: 110.1257 Evaluate side-chains 101 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 91 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 937 LYS Chi-restraints excluded: chain A residue 943 LYS Chi-restraints excluded: chain A residue 1036 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 47 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 92 optimal weight: 9.9990 chunk 84 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 968 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8764 Z= 0.166 Angle : 0.582 9.099 12062 Z= 0.271 Chirality : 0.040 0.331 1441 Planarity : 0.004 0.042 1339 Dihedral : 10.343 165.857 3198 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.60 % Allowed : 11.30 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.28), residues: 919 helix: 2.11 (0.22), residues: 572 sheet: 0.94 (0.91), residues: 29 loop : -0.02 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 650 HIS 0.002 0.000 HIS A 428 PHE 0.022 0.001 PHE A 585 TYR 0.011 0.001 TYR A 644 ARG 0.001 0.000 ARG A 363 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: A 194 MET cc_start: 0.5750 (mtp) cc_final: 0.5320 (mmp) REVERT: A 223 GLU cc_start: 0.7599 (tt0) cc_final: 0.6809 (pm20) REVERT: A 515 LEU cc_start: 0.6609 (mt) cc_final: 0.6336 (tt) REVERT: A 700 SER cc_start: 0.7467 (t) cc_final: 0.6944 (m) REVERT: A 701 ARG cc_start: 0.6677 (mmt90) cc_final: 0.6166 (tpm170) REVERT: A 887 CYS cc_start: 0.6887 (m) cc_final: 0.6407 (m) REVERT: A 937 LYS cc_start: 0.7172 (OUTLIER) cc_final: 0.6438 (mmpt) REVERT: A 943 LYS cc_start: 0.7266 (OUTLIER) cc_final: 0.6665 (tptt) REVERT: A 1036 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.6986 (mt-10) outliers start: 13 outliers final: 7 residues processed: 94 average time/residue: 1.0449 time to fit residues: 106.3153 Evaluate side-chains 97 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 937 LYS Chi-restraints excluded: chain A residue 943 LYS Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1036 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 84 optimal weight: 0.3980 chunk 89 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 94 optimal weight: 9.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 860 ASN A 968 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8764 Z= 0.180 Angle : 0.597 9.137 12062 Z= 0.278 Chirality : 0.041 0.327 1441 Planarity : 0.004 0.042 1339 Dihedral : 10.300 164.975 3198 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.47 % Allowed : 11.55 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.28), residues: 919 helix: 2.09 (0.22), residues: 573 sheet: 0.93 (0.90), residues: 29 loop : -0.06 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 650 HIS 0.002 0.001 HIS A 428 PHE 0.017 0.001 PHE A 608 TYR 0.012 0.001 TYR A 644 ARG 0.001 0.000 ARG A 363 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 89 time to evaluate : 0.885 Fit side-chains revert: symmetry clash REVERT: A 194 MET cc_start: 0.5753 (mtp) cc_final: 0.5302 (mmp) REVERT: A 223 GLU cc_start: 0.7613 (tt0) cc_final: 0.6815 (pm20) REVERT: A 363 ARG cc_start: 0.7002 (mpt90) cc_final: 0.6762 (mtt-85) REVERT: A 515 LEU cc_start: 0.6598 (mt) cc_final: 0.6295 (tt) REVERT: A 700 SER cc_start: 0.7472 (t) cc_final: 0.6951 (m) REVERT: A 701 ARG cc_start: 0.6663 (mmt90) cc_final: 0.6147 (tpm170) REVERT: A 887 CYS cc_start: 0.6867 (m) cc_final: 0.6361 (m) REVERT: A 937 LYS cc_start: 0.7200 (OUTLIER) cc_final: 0.6474 (mmpt) REVERT: A 943 LYS cc_start: 0.7279 (OUTLIER) cc_final: 0.6671 (tptt) REVERT: A 1036 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.6925 (mt-10) outliers start: 12 outliers final: 5 residues processed: 95 average time/residue: 1.0495 time to fit residues: 107.5909 Evaluate side-chains 97 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 89 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 937 LYS Chi-restraints excluded: chain A residue 943 LYS Chi-restraints excluded: chain A residue 1036 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 2.9990 chunk 66 optimal weight: 0.1980 chunk 99 optimal weight: 50.0000 chunk 91 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 84 optimal weight: 0.3980 chunk 24 optimal weight: 0.9980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 860 ASN A 968 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8764 Z= 0.157 Angle : 0.576 9.390 12062 Z= 0.267 Chirality : 0.040 0.328 1441 Planarity : 0.004 0.042 1339 Dihedral : 10.142 164.642 3198 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.11 % Allowed : 11.92 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.29), residues: 919 helix: 2.14 (0.22), residues: 572 sheet: 0.94 (0.90), residues: 29 loop : -0.02 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 650 HIS 0.002 0.000 HIS A 827 PHE 0.024 0.001 PHE A 585 TYR 0.011 0.001 TYR A 545 ARG 0.001 0.000 ARG A 341 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1838 Ramachandran restraints generated. 919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 0.830 Fit side-chains revert: symmetry clash REVERT: A 194 MET cc_start: 0.5764 (mtp) cc_final: 0.5384 (mmp) REVERT: A 223 GLU cc_start: 0.7593 (tt0) cc_final: 0.6810 (pm20) REVERT: A 515 LEU cc_start: 0.6593 (mt) cc_final: 0.6325 (tt) REVERT: A 700 SER cc_start: 0.7462 (t) cc_final: 0.6940 (m) REVERT: A 701 ARG cc_start: 0.6702 (mmt90) cc_final: 0.6195 (tpm170) REVERT: A 887 CYS cc_start: 0.6795 (m) cc_final: 0.6373 (m) REVERT: A 937 LYS cc_start: 0.6967 (OUTLIER) cc_final: 0.6248 (mmpt) REVERT: A 943 LYS cc_start: 0.7345 (OUTLIER) cc_final: 0.6748 (tptt) REVERT: A 1036 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.6872 (mt-10) outliers start: 9 outliers final: 6 residues processed: 98 average time/residue: 1.0553 time to fit residues: 111.5836 Evaluate side-chains 99 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 937 LYS Chi-restraints excluded: chain A residue 943 LYS Chi-restraints excluded: chain A residue 1036 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.4980 chunk 11 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 0.0040 chunk 69 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 57 optimal weight: 0.0570 overall best weight: 0.3910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 860 ASN A 968 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.192795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.141420 restraints weight = 11096.239| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.04 r_work: 0.3549 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3388 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3388 r_free = 0.3388 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3388 r_free = 0.3388 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3388 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8764 Z= 0.133 Angle : 0.553 10.556 12062 Z= 0.255 Chirality : 0.039 0.327 1441 Planarity : 0.004 0.043 1339 Dihedral : 9.888 163.803 3198 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.74 % Allowed : 12.41 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.29), residues: 919 helix: 2.25 (0.22), residues: 572 sheet: 1.02 (0.92), residues: 29 loop : 0.01 (0.37), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 650 HIS 0.002 0.000 HIS A 827 PHE 0.010 0.001 PHE A 304 TYR 0.011 0.001 TYR A 498 ARG 0.001 0.000 ARG A 341 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3203.36 seconds wall clock time: 57 minutes 45.66 seconds (3465.66 seconds total)