Starting phenix.real_space_refine on Thu Feb 5 22:03:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ogd_70462/02_2026/9ogd_70462_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ogd_70462/02_2026/9ogd_70462.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ogd_70462/02_2026/9ogd_70462_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ogd_70462/02_2026/9ogd_70462_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ogd_70462/02_2026/9ogd_70462.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ogd_70462/02_2026/9ogd_70462.map" } resolution = 2.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.008 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: 6 Type Number sf(0) Gaussians S 65 5.16 5 C 6386 2.51 5 N 1676 2.21 5 O 1845 1.98 5 F 6 1.80 5 H 9994 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19972 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 13299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 817, 13299 Classifications: {'peptide': 817} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 785} Chain breaks: 2 Chain: "B" Number of atoms: 3619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 3619 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 224} Chain: "E" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1356 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain breaks: 1 Chain: "F" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1667 Classifications: {'peptide': 106} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 96} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'V6A': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.63, per 1000 atoms: 0.18 Number of scatterers: 19972 At special positions: 0 Unit cell: (70.11, 114.39, 177.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 65 16.00 F 6 9.00 O 1845 8.00 N 1676 7.00 C 6386 6.00 H 9994 1.00 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 - 3.00 Amino acid : True - 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.90 Conformation dependent library (CDL) restraints added in 542.7 milliseconds 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2390 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 2 sheets defined 75.3% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 219 through 233 Processing helix chain 'A' and resid 237 through 243 removed outlier: 3.674A pdb=" N ILE A 241 " --> pdb=" O PRO A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 254 removed outlier: 4.933A pdb=" N ILE A 251 " --> pdb=" O ILE A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 273 removed outlier: 4.313A pdb=" N ASN A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N VAL A 263 " --> pdb=" O MET A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 298 Processing helix chain 'A' and resid 303 through 311 Processing helix chain 'A' and resid 312 through 339 removed outlier: 6.907A pdb=" N GLN A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU A 336 " --> pdb=" O GLU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 358 Processing helix chain 'A' and resid 362 through 384 removed outlier: 3.513A pdb=" N TYR A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 423 removed outlier: 3.759A pdb=" N TYR A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) Proline residue: A 411 - end of helix removed outlier: 4.574A pdb=" N PHE A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LYS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL A 416 " --> pdb=" O MET A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 468 Processing helix chain 'A' and resid 468 through 485 removed outlier: 3.594A pdb=" N THR A 472 " --> pdb=" O ASP A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 504 removed outlier: 3.580A pdb=" N ILE A 504 " --> pdb=" O ALA A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 531 Processing helix chain 'A' and resid 533 through 550 Processing helix chain 'A' and resid 551 through 558 removed outlier: 3.571A pdb=" N LEU A 555 " --> pdb=" O TYR A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 573 Processing helix chain 'A' and resid 579 through 595 Processing helix chain 'A' and resid 596 through 599 Processing helix chain 'A' and resid 609 through 617 removed outlier: 3.858A pdb=" N GLU A 613 " --> pdb=" O PRO A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 622 Processing helix chain 'A' and resid 626 through 643 removed outlier: 3.514A pdb=" N MET A 640 " --> pdb=" O ALA A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 658 Processing helix chain 'A' and resid 658 through 675 Processing helix chain 'A' and resid 676 through 680 Processing helix chain 'A' and resid 681 through 703 Processing helix chain 'A' and resid 706 through 736 removed outlier: 3.564A pdb=" N ARG A 712 " --> pdb=" O ILE A 708 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N LEU A 715 " --> pdb=" O GLY A 711 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ASP A 716 " --> pdb=" O ARG A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 741 Processing helix chain 'A' and resid 742 through 765 removed outlier: 3.705A pdb=" N ARG A 765 " --> pdb=" O GLY A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 776 Processing helix chain 'A' and resid 776 through 791 removed outlier: 5.127A pdb=" N ILE A 786 " --> pdb=" O ASP A 782 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ASP A 787 " --> pdb=" O ALA A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 812 Processing helix chain 'A' and resid 813 through 816 Processing helix chain 'A' and resid 818 through 836 removed outlier: 5.655A pdb=" N GLU A 828 " --> pdb=" O ASP A 824 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N CYS A 829 " --> pdb=" O ALA A 825 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS A 836 " --> pdb=" O ASN A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 859 Processing helix chain 'A' and resid 860 through 866 removed outlier: 4.021A pdb=" N LEU A 864 " --> pdb=" O PHE A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 883 Processing helix chain 'A' and resid 886 through 905 Processing helix chain 'A' and resid 907 through 933 removed outlier: 4.150A pdb=" N GLN A 912 " --> pdb=" O GLU A 908 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N SER A 913 " --> pdb=" O ALA A 909 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N CYS A 920 " --> pdb=" O GLN A 916 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ASP A 921 " --> pdb=" O THR A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 937 No H-bonds generated for 'chain 'A' and resid 935 through 937' Processing helix chain 'A' and resid 938 through 955 removed outlier: 3.520A pdb=" N VAL A 953 " --> pdb=" O MET A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 986 Processing helix chain 'A' and resid 990 through 1004 Processing helix chain 'A' and resid 1007 through 1026 removed outlier: 3.529A pdb=" N ALA A1026 " --> pdb=" O ILE A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1033 No H-bonds generated for 'chain 'A' and resid 1031 through 1033' Processing helix chain 'A' and resid 1034 through 1055 removed outlier: 4.114A pdb=" N ILE A1040 " --> pdb=" O GLU A1036 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N SER A1055 " --> pdb=" O LYS A1051 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 64 Processing helix chain 'B' and resid 65 through 74 removed outlier: 3.501A pdb=" N VAL B 69 " --> pdb=" O ASP B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 97 removed outlier: 3.565A pdb=" N TYR B 92 " --> pdb=" O THR B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 107 removed outlier: 3.575A pdb=" N VAL B 101 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR B 107 " --> pdb=" O VAL B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 129 removed outlier: 3.641A pdb=" N TRP B 124 " --> pdb=" O THR B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 140 Processing helix chain 'B' and resid 153 through 161 removed outlier: 3.716A pdb=" N LYS B 161 " --> pdb=" O TRP B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 173 Processing helix chain 'B' and resid 186 through 197 Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 227 through 232 Processing helix chain 'B' and resid 233 through 246 removed outlier: 3.549A pdb=" N ALA B 246 " --> pdb=" O VAL B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 262 Processing helix chain 'B' and resid 266 through 271 Processing helix chain 'B' and resid 272 through 274 No H-bonds generated for 'chain 'B' and resid 272 through 274' Processing helix chain 'B' and resid 277 through 285 removed outlier: 3.543A pdb=" N LEU B 285 " --> pdb=" O LYS B 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 37 Processing helix chain 'E' and resid 39 through 46 Processing helix chain 'E' and resid 66 through 83 removed outlier: 4.186A pdb=" N LYS E 72 " --> pdb=" O HIS E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 110 removed outlier: 4.524A pdb=" N LEU E 101 " --> pdb=" O PRO E 97 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N GLU E 102 " --> pdb=" O GLU E 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 36 removed outlier: 3.503A pdb=" N LEU F 27 " --> pdb=" O THR F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 40 No H-bonds generated for 'chain 'F' and resid 38 through 40' Processing helix chain 'F' and resid 100 through 104 Processing sheet with id=AA1, first strand: chain 'E' and resid 59 through 61 removed outlier: 8.645A pdb=" N VAL E 60 " --> pdb=" O TYR E 18 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LYS E 20 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N LYS E 32 " --> pdb=" O PHE F 15 " (cutoff:3.500A) removed outlier: 11.068A pdb=" N ASP F 17 " --> pdb=" O LYS E 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 59 through 61 removed outlier: 8.645A pdb=" N VAL E 60 " --> pdb=" O TYR E 18 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LYS E 20 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N LYS E 32 " --> pdb=" O PHE F 15 " (cutoff:3.500A) removed outlier: 11.068A pdb=" N ASP F 17 " --> pdb=" O LYS E 32 " (cutoff:3.500A) 666 hydrogen bonds defined for protein. 1959 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.64 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9969 1.03 - 1.23: 47 1.23 - 1.42: 4141 1.42 - 1.62: 5914 1.62 - 1.81: 104 Bond restraints: 20175 Sorted by residual: bond pdb=" C13 V6A A1101 " pdb=" N04 V6A A1101 " ideal model delta sigma weight residual 1.356 1.454 -0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" C14 V6A A1101 " pdb=" N05 V6A A1101 " ideal model delta sigma weight residual 1.372 1.454 -0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" C05 V6A A1101 " pdb=" C09 V6A A1101 " ideal model delta sigma weight residual 1.462 1.523 -0.061 2.00e-02 2.50e+03 9.28e+00 bond pdb=" N04 V6A A1101 " pdb=" N05 V6A A1101 " ideal model delta sigma weight residual 1.360 1.408 -0.048 2.00e-02 2.50e+03 5.79e+00 bond pdb=" C13 V6A A1101 " pdb=" O01 V6A A1101 " ideal model delta sigma weight residual 1.217 1.185 0.032 2.00e-02 2.50e+03 2.60e+00 ... (remaining 20170 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 34836 1.15 - 2.30: 1601 2.30 - 3.46: 80 3.46 - 4.61: 35 4.61 - 5.76: 7 Bond angle restraints: 36559 Sorted by residual: angle pdb=" N VAL A 600 " pdb=" CA VAL A 600 " pdb=" C VAL A 600 " ideal model delta sigma weight residual 112.96 109.93 3.03 1.00e+00 1.00e+00 9.19e+00 angle pdb=" C ASN B 223 " pdb=" CA ASN B 223 " pdb=" CB ASN B 223 " ideal model delta sigma weight residual 110.42 115.90 -5.48 1.99e+00 2.53e-01 7.57e+00 angle pdb=" N ASN B 223 " pdb=" CA ASN B 223 " pdb=" C ASN B 223 " ideal model delta sigma weight residual 110.80 106.12 4.68 2.13e+00 2.20e-01 4.83e+00 angle pdb=" CA PRO A 258 " pdb=" N PRO A 258 " pdb=" CD PRO A 258 " ideal model delta sigma weight residual 112.00 109.14 2.86 1.40e+00 5.10e-01 4.17e+00 angle pdb=" C VAL B 196 " pdb=" CA VAL B 196 " pdb=" CB VAL B 196 " ideal model delta sigma weight residual 112.16 109.00 3.16 1.55e+00 4.16e-01 4.15e+00 ... (remaining 36554 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.37: 8468 17.37 - 34.74: 720 34.74 - 52.10: 207 52.10 - 69.47: 64 69.47 - 86.84: 12 Dihedral angle restraints: 9471 sinusoidal: 5190 harmonic: 4281 Sorted by residual: dihedral pdb=" CA VAL A 826 " pdb=" C VAL A 826 " pdb=" N PHE A 827 " pdb=" CA PHE A 827 " ideal model delta harmonic sigma weight residual 180.00 -158.26 -21.74 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA VAL A 784 " pdb=" C VAL A 784 " pdb=" N LEU A 785 " pdb=" CA LEU A 785 " ideal model delta harmonic sigma weight residual -180.00 -161.17 -18.83 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CG ARG E 63 " pdb=" CD ARG E 63 " pdb=" NE ARG E 63 " pdb=" CZ ARG E 63 " ideal model delta sinusoidal sigma weight residual -90.00 -39.93 -50.07 2 1.50e+01 4.44e-03 1.25e+01 ... (remaining 9468 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1034 0.026 - 0.052: 355 0.052 - 0.079: 124 0.079 - 0.105: 53 0.105 - 0.131: 19 Chirality restraints: 1585 Sorted by residual: chirality pdb=" CA VAL A 257 " pdb=" N VAL A 257 " pdb=" C VAL A 257 " pdb=" CB VAL A 257 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CA ILE E 90 " pdb=" N ILE E 90 " pdb=" C ILE E 90 " pdb=" CB ILE E 90 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 chirality pdb=" CA ILE A 236 " pdb=" N ILE A 236 " pdb=" C ILE A 236 " pdb=" CB ILE A 236 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 ... (remaining 1582 not shown) Planarity restraints: 2949 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 257 " -0.056 5.00e-02 4.00e+02 8.40e-02 1.13e+01 pdb=" N PRO A 258 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 258 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 258 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 63 " -0.133 9.50e-02 1.11e+02 4.44e-02 2.37e+00 pdb=" NE ARG E 63 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG E 63 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG E 63 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG E 63 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG E 63 " 0.004 2.00e-02 2.50e+03 pdb="HH12 ARG E 63 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG E 63 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG E 63 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 819 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO A 820 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 820 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 820 " -0.022 5.00e-02 4.00e+02 ... (remaining 2946 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.21: 1367 2.21 - 2.81: 42300 2.81 - 3.41: 55847 3.41 - 4.00: 72638 4.00 - 4.60: 113485 Nonbonded interactions: 285637 Sorted by model distance: nonbonded pdb=" O LEU A 355 " pdb=" HG SER A 358 " model vdw 1.615 2.450 nonbonded pdb=" HG1 THR F 23 " pdb=" OE1 GLU F 26 " model vdw 1.625 2.450 nonbonded pdb=" O THR B 241 " pdb=" HG SER B 245 " model vdw 1.630 2.450 nonbonded pdb=" OD1 ASP B 115 " pdb=" H ASP B 119 " model vdw 1.641 2.450 nonbonded pdb="HH21 ARG F 37 " pdb=" OE1 GLU F 41 " model vdw 1.648 2.450 ... (remaining 285632 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.530 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: 0.120 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.980 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 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 : 0.003 0.098 10182 Z= 0.150 Angle : 0.491 5.759 13804 Z= 0.256 Chirality : 0.034 0.131 1585 Planarity : 0.004 0.084 1767 Dihedral : 16.072 86.838 3801 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.54 % Allowed : 14.76 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.25), residues: 1230 helix: 1.65 (0.19), residues: 851 sheet: 0.26 (0.76), residues: 42 loop : 0.81 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 63 TYR 0.012 0.001 TYR E 79 PHE 0.019 0.001 PHE A 882 TRP 0.014 0.001 TRP A 762 HIS 0.002 0.001 HIS A 481 Details of bonding type rmsd covalent geometry : bond 0.00328 (10181) covalent geometry : angle 0.49062 (13804) hydrogen bonds : bond 0.13325 ( 646) hydrogen bonds : angle 6.27284 ( 1959) Misc. bond : bond 0.00028 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 76 average time/residue: 1.2559 time to fit residues: 103.5469 Evaluate side-chains 75 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 84 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 117 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3451 r_free = 0.3451 target = 0.085536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.058519 restraints weight = 61794.854| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.70 r_work: 0.2834 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.0509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 10182 Z= 0.155 Angle : 0.494 5.331 13804 Z= 0.267 Chirality : 0.036 0.133 1585 Planarity : 0.004 0.061 1767 Dihedral : 6.416 72.059 1359 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.00 % Allowed : 13.95 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.53 (0.24), residues: 1230 helix: 2.20 (0.18), residues: 856 sheet: -0.05 (0.74), residues: 42 loop : 0.66 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 63 TYR 0.015 0.001 TYR E 79 PHE 0.022 0.001 PHE A 882 TRP 0.013 0.001 TRP A 762 HIS 0.004 0.001 HIS E 68 Details of bonding type rmsd covalent geometry : bond 0.00353 (10181) covalent geometry : angle 0.49416 (13804) hydrogen bonds : bond 0.05060 ( 646) hydrogen bonds : angle 4.49842 ( 1959) Misc. bond : bond 0.00056 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.7342 (mpm) cc_final: 0.7006 (mpm) outliers start: 11 outliers final: 3 residues processed: 80 average time/residue: 1.2442 time to fit residues: 108.3615 Evaluate side-chains 70 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain F residue 84 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 48 optimal weight: 0.6980 chunk 115 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 67 optimal weight: 0.2980 chunk 105 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3455 r_free = 0.3455 target = 0.085838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.058965 restraints weight = 61984.179| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.70 r_work: 0.2854 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.0727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10182 Z= 0.123 Angle : 0.464 5.380 13804 Z= 0.247 Chirality : 0.035 0.139 1585 Planarity : 0.004 0.050 1767 Dihedral : 5.996 71.761 1353 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.82 % Allowed : 14.04 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.77 (0.24), residues: 1230 helix: 2.42 (0.18), residues: 856 sheet: -0.08 (0.73), residues: 42 loop : 0.62 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 63 TYR 0.014 0.001 TYR E 79 PHE 0.021 0.001 PHE A 882 TRP 0.013 0.001 TRP A 762 HIS 0.004 0.001 HIS A 481 Details of bonding type rmsd covalent geometry : bond 0.00281 (10181) covalent geometry : angle 0.46400 (13804) hydrogen bonds : bond 0.04358 ( 646) hydrogen bonds : angle 4.20580 ( 1959) Misc. bond : bond 0.00051 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: A 362 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7372 (mp0) outliers start: 9 outliers final: 1 residues processed: 74 average time/residue: 1.3440 time to fit residues: 107.4547 Evaluate side-chains 67 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain E residue 46 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 48 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 chunk 55 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 0.3980 chunk 91 optimal weight: 0.4980 chunk 74 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3458 r_free = 0.3458 target = 0.085811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.059030 restraints weight = 61665.278| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.70 r_work: 0.2861 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.0862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10182 Z= 0.119 Angle : 0.458 5.322 13804 Z= 0.243 Chirality : 0.035 0.137 1585 Planarity : 0.004 0.055 1767 Dihedral : 5.794 71.042 1350 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.63 % Allowed : 14.86 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.86 (0.24), residues: 1230 helix: 2.50 (0.18), residues: 856 sheet: -0.10 (0.73), residues: 42 loop : 0.63 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 63 TYR 0.015 0.001 TYR E 79 PHE 0.021 0.001 PHE A 882 TRP 0.012 0.001 TRP A 762 HIS 0.003 0.001 HIS A 481 Details of bonding type rmsd covalent geometry : bond 0.00274 (10181) covalent geometry : angle 0.45846 (13804) hydrogen bonds : bond 0.04052 ( 646) hydrogen bonds : angle 4.08700 ( 1959) Misc. bond : bond 0.00050 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.549 Fit side-chains revert: symmetry clash REVERT: B 282 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8225 (tt0) REVERT: F 26 GLU cc_start: 0.8872 (mp0) cc_final: 0.8236 (mp0) outliers start: 7 outliers final: 1 residues processed: 79 average time/residue: 1.4920 time to fit residues: 126.4965 Evaluate side-chains 69 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain E residue 46 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 50 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 95 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3452 r_free = 0.3452 target = 0.085680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.058844 restraints weight = 61768.462| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.70 r_work: 0.2849 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10182 Z= 0.134 Angle : 0.465 6.079 13804 Z= 0.246 Chirality : 0.035 0.136 1585 Planarity : 0.004 0.055 1767 Dihedral : 5.791 70.584 1350 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.63 % Allowed : 15.13 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.89 (0.24), residues: 1230 helix: 2.53 (0.18), residues: 856 sheet: -0.11 (0.74), residues: 42 loop : 0.62 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 63 TYR 0.015 0.001 TYR E 79 PHE 0.021 0.001 PHE A 882 TRP 0.012 0.001 TRP A 762 HIS 0.004 0.001 HIS A 481 Details of bonding type rmsd covalent geometry : bond 0.00316 (10181) covalent geometry : angle 0.46506 (13804) hydrogen bonds : bond 0.04093 ( 646) hydrogen bonds : angle 4.04717 ( 1959) Misc. bond : bond 0.00061 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.7393 (mpm) cc_final: 0.7053 (mpm) REVERT: B 282 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8223 (tt0) REVERT: E 64 GLU cc_start: 0.8763 (mp0) cc_final: 0.8447 (pm20) outliers start: 7 outliers final: 3 residues processed: 75 average time/residue: 1.4417 time to fit residues: 116.1982 Evaluate side-chains 71 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain E residue 46 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 93 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 966 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.085189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.058326 restraints weight = 61868.664| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.71 r_work: 0.2850 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10182 Z= 0.154 Angle : 0.473 5.441 13804 Z= 0.252 Chirality : 0.036 0.136 1585 Planarity : 0.004 0.041 1767 Dihedral : 5.850 70.187 1350 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.72 % Allowed : 15.04 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.85 (0.24), residues: 1230 helix: 2.51 (0.18), residues: 856 sheet: -0.15 (0.74), residues: 42 loop : 0.59 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1043 TYR 0.017 0.001 TYR E 79 PHE 0.022 0.001 PHE A 882 TRP 0.012 0.001 TRP A 762 HIS 0.005 0.001 HIS A 481 Details of bonding type rmsd covalent geometry : bond 0.00368 (10181) covalent geometry : angle 0.47341 (13804) hydrogen bonds : bond 0.04234 ( 646) hydrogen bonds : angle 4.04319 ( 1959) Misc. bond : bond 0.00072 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.7410 (mpm) cc_final: 0.7129 (mpm) REVERT: B 282 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8215 (tt0) outliers start: 8 outliers final: 5 residues processed: 77 average time/residue: 1.4020 time to fit residues: 115.8958 Evaluate side-chains 74 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain F residue 84 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 6 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 91 optimal weight: 0.1980 chunk 99 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 92 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3456 r_free = 0.3456 target = 0.085835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.059082 restraints weight = 61706.194| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.70 r_work: 0.2852 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10182 Z= 0.122 Angle : 0.464 5.692 13804 Z= 0.246 Chirality : 0.035 0.138 1585 Planarity : 0.004 0.066 1767 Dihedral : 5.781 69.601 1350 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.72 % Allowed : 15.40 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.94 (0.24), residues: 1230 helix: 2.57 (0.18), residues: 856 sheet: -0.12 (0.74), residues: 42 loop : 0.64 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 63 TYR 0.015 0.001 TYR E 79 PHE 0.020 0.001 PHE A 882 TRP 0.012 0.001 TRP A 762 HIS 0.004 0.001 HIS A 481 Details of bonding type rmsd covalent geometry : bond 0.00286 (10181) covalent geometry : angle 0.46377 (13804) hydrogen bonds : bond 0.03968 ( 646) hydrogen bonds : angle 3.97466 ( 1959) Misc. bond : bond 0.00059 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.7407 (mpm) cc_final: 0.7148 (mpm) REVERT: B 282 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8197 (tt0) REVERT: E 64 GLU cc_start: 0.8780 (mp0) cc_final: 0.8485 (pm20) outliers start: 8 outliers final: 4 residues processed: 80 average time/residue: 1.2621 time to fit residues: 108.9690 Evaluate side-chains 74 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain E residue 46 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 80 optimal weight: 0.6980 chunk 48 optimal weight: 0.2980 chunk 59 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3455 r_free = 0.3455 target = 0.085793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.059028 restraints weight = 61673.920| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.70 r_work: 0.2853 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10182 Z= 0.130 Angle : 0.467 5.598 13804 Z= 0.247 Chirality : 0.035 0.136 1585 Planarity : 0.004 0.039 1767 Dihedral : 5.763 69.369 1350 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.82 % Allowed : 15.31 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.90 (0.24), residues: 1230 helix: 2.51 (0.18), residues: 864 sheet: -0.13 (0.74), residues: 42 loop : 0.67 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 63 TYR 0.016 0.001 TYR E 79 PHE 0.020 0.001 PHE A 882 TRP 0.012 0.001 TRP A 762 HIS 0.004 0.001 HIS A 481 Details of bonding type rmsd covalent geometry : bond 0.00306 (10181) covalent geometry : angle 0.46747 (13804) hydrogen bonds : bond 0.03972 ( 646) hydrogen bonds : angle 3.96175 ( 1959) Misc. bond : bond 0.00063 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.7446 (mpm) cc_final: 0.7189 (mpm) REVERT: B 282 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8225 (tt0) REVERT: E 64 GLU cc_start: 0.8771 (mp0) cc_final: 0.8484 (pm20) outliers start: 9 outliers final: 5 residues processed: 80 average time/residue: 1.2668 time to fit residues: 109.1597 Evaluate side-chains 76 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain F residue 84 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 28 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3430 r_free = 0.3430 target = 0.084345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.057450 restraints weight = 61732.149| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.70 r_work: 0.2820 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10182 Z= 0.197 Angle : 0.499 5.846 13804 Z= 0.266 Chirality : 0.037 0.136 1585 Planarity : 0.004 0.053 1767 Dihedral : 5.931 69.650 1350 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.72 % Allowed : 15.49 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.76 (0.24), residues: 1230 helix: 2.42 (0.18), residues: 863 sheet: -0.17 (0.75), residues: 42 loop : 0.58 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 63 TYR 0.018 0.002 TYR E 79 PHE 0.023 0.001 PHE A 882 TRP 0.011 0.001 TRP A 762 HIS 0.005 0.001 HIS A 481 Details of bonding type rmsd covalent geometry : bond 0.00476 (10181) covalent geometry : angle 0.49868 (13804) hydrogen bonds : bond 0.04473 ( 646) hydrogen bonds : angle 4.04857 ( 1959) Misc. bond : bond 0.00096 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.7483 (mpm) cc_final: 0.7253 (mpm) REVERT: B 282 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8197 (tt0) REVERT: E 64 GLU cc_start: 0.8816 (mp0) cc_final: 0.8429 (pm20) outliers start: 8 outliers final: 4 residues processed: 81 average time/residue: 1.3302 time to fit residues: 116.1496 Evaluate side-chains 76 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain F residue 84 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 33 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 121 optimal weight: 0.3980 chunk 37 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 120 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3448 r_free = 0.3448 target = 0.085443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.058574 restraints weight = 61762.921| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.71 r_work: 0.2860 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10182 Z= 0.127 Angle : 0.475 5.700 13804 Z= 0.251 Chirality : 0.035 0.139 1585 Planarity : 0.004 0.057 1767 Dihedral : 5.840 69.262 1350 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.54 % Allowed : 15.94 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.86 (0.24), residues: 1230 helix: 2.48 (0.18), residues: 864 sheet: -0.13 (0.74), residues: 42 loop : 0.66 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 63 TYR 0.016 0.001 TYR E 79 PHE 0.019 0.001 PHE A 882 TRP 0.013 0.001 TRP A 762 HIS 0.004 0.001 HIS A 481 Details of bonding type rmsd covalent geometry : bond 0.00298 (10181) covalent geometry : angle 0.47479 (13804) hydrogen bonds : bond 0.04044 ( 646) hydrogen bonds : angle 3.96308 ( 1959) Misc. bond : bond 0.00059 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.592 Fit side-chains revert: symmetry clash REVERT: A 292 MET cc_start: 0.7457 (mpm) cc_final: 0.7220 (mpm) REVERT: B 282 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8205 (tt0) REVERT: E 64 GLU cc_start: 0.8781 (mp0) cc_final: 0.8342 (pm20) outliers start: 6 outliers final: 4 residues processed: 77 average time/residue: 1.3923 time to fit residues: 115.6917 Evaluate side-chains 76 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain E residue 46 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 114 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.3439 r_free = 0.3439 target = 0.084715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.058026 restraints weight = 61937.703| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.71 r_work: 0.2841 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10182 Z= 0.142 Angle : 0.480 5.774 13804 Z= 0.253 Chirality : 0.035 0.137 1585 Planarity : 0.004 0.057 1767 Dihedral : 5.834 69.194 1350 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.45 % Allowed : 16.21 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.86 (0.24), residues: 1230 helix: 2.48 (0.18), residues: 863 sheet: -0.15 (0.74), residues: 42 loop : 0.67 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 63 TYR 0.016 0.001 TYR E 79 PHE 0.021 0.001 PHE A 882 TRP 0.013 0.001 TRP A 762 HIS 0.004 0.001 HIS A 481 Details of bonding type rmsd covalent geometry : bond 0.00337 (10181) covalent geometry : angle 0.47954 (13804) hydrogen bonds : bond 0.04091 ( 646) hydrogen bonds : angle 3.96527 ( 1959) Misc. bond : bond 0.00068 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7639.05 seconds wall clock time: 129 minutes 58.38 seconds (7798.38 seconds total)