Starting phenix.real_space_refine on Sun Apr 7 07:01:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8buz_16252/04_2024/8buz_16252_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8buz_16252/04_2024/8buz_16252.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8buz_16252/04_2024/8buz_16252.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8buz_16252/04_2024/8buz_16252.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8buz_16252/04_2024/8buz_16252_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8buz_16252/04_2024/8buz_16252_neut_updated.pdb" } resolution = 3.5 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 61 5.16 5 C 6344 2.51 5 N 1702 2.21 5 O 1810 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9921 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 890, 7120 Classifications: {'peptide': 890} Link IDs: {'PTRANS': 19, 'TRANS': 870} Chain breaks: 3 Chain: "B" Number of atoms: 2739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2739 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 13, 'TRANS': 319} Chain breaks: 1 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'FOK': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.84, per 1000 atoms: 0.59 Number of scatterers: 9921 At special positions: 0 Unit cell: (151.8, 115.5, 129.36, 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 61 16.00 P 3 15.00 Mg 1 11.99 O 1810 8.00 N 1702 7.00 C 6344 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 457 " - pdb=" SG CYS A 469 " distance=2.04 Simple disulfide: pdb=" SG CYS A 809 " - pdb=" SG CYS A 832 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.28 Conformation dependent library (CDL) restraints added in 1.7 seconds 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2318 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 8 sheets defined 56.7% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.19 Creating SS restraints... Processing helix chain 'A' and resid 166 through 205 removed outlier: 3.659A pdb=" N GLY A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER A 183 " --> pdb=" O GLN A 179 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL A 186 " --> pdb=" O LYS A 182 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 193 " --> pdb=" O VAL A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 237 removed outlier: 3.656A pdb=" N ILE A 216 " --> pdb=" O PRO A 212 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A 218 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU A 225 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL A 226 " --> pdb=" O THR A 222 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL A 233 " --> pdb=" O CYS A 229 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 263 removed outlier: 3.532A pdb=" N VAL A 249 " --> pdb=" O GLN A 245 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE A 259 " --> pdb=" O MET A 255 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU A 260 " --> pdb=" O THR A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 284 removed outlier: 4.041A pdb=" N TYR A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 311 removed outlier: 3.631A pdb=" N LEU A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 323 through 376 removed outlier: 4.142A pdb=" N MET A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN A 334 " --> pdb=" O PHE A 330 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 359 " --> pdb=" O THR A 355 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 375 " --> pdb=" O ARG A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 392 removed outlier: 4.808A pdb=" N GLU A 387 " --> pdb=" O PHE A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 434 through 454 Processing helix chain 'A' and resid 480 through 498 removed outlier: 3.793A pdb=" N CYS A 484 " --> pdb=" O HIS A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 502 No H-bonds generated for 'chain 'A' and resid 500 through 502' Processing helix chain 'A' and resid 534 through 545 Processing helix chain 'A' and resid 555 through 561 removed outlier: 4.419A pdb=" N CYS A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 687 removed outlier: 3.549A pdb=" N SER A 681 " --> pdb=" O ILE A 677 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ARG A 687 " --> pdb=" O ASP A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 707 Processing helix chain 'A' and resid 714 through 733 Processing helix chain 'A' and resid 740 through 761 Processing helix chain 'A' and resid 771 through 782 Processing helix chain 'A' and resid 784 through 808 removed outlier: 3.619A pdb=" N ILE A 790 " --> pdb=" O ALA A 786 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN A 798 " --> pdb=" O SER A 794 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ASN A 805 " --> pdb=" O GLY A 801 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ILE A 806 " --> pdb=" O ALA A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 851 removed outlier: 3.597A pdb=" N VAL A 839 " --> pdb=" O PRO A 835 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A 841 " --> pdb=" O TYR A 837 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY A 842 " --> pdb=" O PHE A 838 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR A 848 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N CYS A 849 " --> pdb=" O ALA A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 875 removed outlier: 3.519A pdb=" N MET A 867 " --> pdb=" O VAL A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 890 removed outlier: 3.737A pdb=" N TYR A 886 " --> pdb=" O LEU A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 897 No H-bonds generated for 'chain 'A' and resid 895 through 897' Processing helix chain 'A' and resid 900 through 956 removed outlier: 3.584A pdb=" N LEU A 904 " --> pdb=" O LYS A 900 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU A 905 " --> pdb=" O GLU A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 966 Processing helix chain 'A' and resid 991 through 996 removed outlier: 3.775A pdb=" N ALA A 994 " --> pdb=" O PRO A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1025 Processing helix chain 'A' and resid 1060 through 1082 Processing helix chain 'A' and resid 1115 through 1125 Processing helix chain 'B' and resid 53 through 63 Processing helix chain 'B' and resid 89 through 112 removed outlier: 4.171A pdb=" N SER B 111 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 136 removed outlier: 3.705A pdb=" N ASN B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 155 Processing helix chain 'B' and resid 157 through 165 Processing helix chain 'B' and resid 175 through 186 removed outlier: 3.612A pdb=" N LYS B 181 " --> pdb=" O TYR B 177 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE B 182 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ASP B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N VAL B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 198 Processing helix chain 'B' and resid 231 through 237 removed outlier: 4.074A pdb=" N ILE B 235 " --> pdb=" O ARG B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 277 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.511A pdb=" N ALA B 316 " --> pdb=" O PRO B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 351 Processing helix chain 'B' and resid 369 through 387 Processing sheet with id= A, first strand: chain 'A' and resid 410 through 412 Processing sheet with id= B, first strand: chain 'A' and resid 415 through 417 Processing sheet with id= C, first strand: chain 'A' and resid 420 through 422 Processing sheet with id= D, first strand: chain 'A' and resid 976 through 980 removed outlier: 4.287A pdb=" N TYR A 976 " --> pdb=" O VAL A1102 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1090 through 1096 removed outlier: 3.854A pdb=" N LYS A1036 " --> pdb=" O MET A1043 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL A1045 " --> pdb=" O LYS A1034 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LYS A1034 " --> pdb=" O VAL A1045 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 459 through 463 removed outlier: 7.574A pdb=" N TYR A 468 " --> pdb=" O ILE A 460 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE A 462 " --> pdb=" O CYS A 466 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N CYS A 466 " --> pdb=" O ILE A 462 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 41 through 45 Processing sheet with id= H, first strand: chain 'B' and resid 245 through 249 removed outlier: 6.499A pdb=" N ILE B 288 " --> pdb=" O PHE B 246 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N VAL B 248 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE B 290 " --> pdb=" O VAL B 248 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N TYR B 360 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU B 291 " --> pdb=" O TYR B 360 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N HIS B 362 " --> pdb=" O LEU B 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= H 531 hydrogen bonds defined for protein. 1539 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.13 Time building geometry restraints manager: 4.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1642 1.32 - 1.45: 2690 1.45 - 1.57: 5688 1.57 - 1.69: 5 1.69 - 1.82: 95 Bond restraints: 10120 Sorted by residual: bond pdb=" N VAL A 253 " pdb=" CA VAL A 253 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.21e+00 bond pdb=" N MET A 255 " pdb=" CA MET A 255 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.65e+00 bond pdb=" N THR A 256 " pdb=" CA THR A 256 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.64e+00 bond pdb=" N TRP A 252 " pdb=" CA TRP A 252 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.19e-02 7.06e+03 5.62e+00 bond pdb=" N THR A 257 " pdb=" CA THR A 257 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.40e+00 ... (remaining 10115 not shown) Histogram of bond angle deviations from ideal: 98.82 - 105.91: 147 105.91 - 112.99: 5545 112.99 - 120.08: 3604 120.08 - 127.17: 4316 127.17 - 134.26: 93 Bond angle restraints: 13705 Sorted by residual: angle pdb=" CA LEU A 418 " pdb=" CB LEU A 418 " pdb=" CG LEU A 418 " ideal model delta sigma weight residual 116.30 128.68 -12.38 3.50e+00 8.16e-02 1.25e+01 angle pdb=" CB MET A 741 " pdb=" CG MET A 741 " pdb=" SD MET A 741 " ideal model delta sigma weight residual 112.70 122.84 -10.14 3.00e+00 1.11e-01 1.14e+01 angle pdb=" C ASN B 239 " pdb=" N ASP B 240 " pdb=" CA ASP B 240 " ideal model delta sigma weight residual 121.54 127.68 -6.14 1.91e+00 2.74e-01 1.03e+01 angle pdb=" CA GLN A1145 " pdb=" CB GLN A1145 " pdb=" CG GLN A1145 " ideal model delta sigma weight residual 114.10 120.33 -6.23 2.00e+00 2.50e-01 9.72e+00 angle pdb=" CA GLU A 950 " pdb=" CB GLU A 950 " pdb=" CG GLU A 950 " ideal model delta sigma weight residual 114.10 120.29 -6.19 2.00e+00 2.50e-01 9.58e+00 ... (remaining 13700 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 5226 17.56 - 35.12: 653 35.12 - 52.68: 206 52.68 - 70.24: 31 70.24 - 87.80: 15 Dihedral angle restraints: 6131 sinusoidal: 2551 harmonic: 3580 Sorted by residual: dihedral pdb=" CA CYS A 469 " pdb=" C CYS A 469 " pdb=" N VAL A 470 " pdb=" CA VAL A 470 " ideal model delta harmonic sigma weight residual 180.00 154.82 25.18 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA MET A1002 " pdb=" C MET A1002 " pdb=" N ASN A1003 " pdb=" CA ASN A1003 " ideal model delta harmonic sigma weight residual 180.00 160.01 19.99 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA CYS A 457 " pdb=" C CYS A 457 " pdb=" N LEU A 458 " pdb=" CA LEU A 458 " ideal model delta harmonic sigma weight residual 180.00 161.54 18.46 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 6128 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1265 0.050 - 0.101: 242 0.101 - 0.151: 41 0.151 - 0.202: 6 0.202 - 0.252: 1 Chirality restraints: 1555 Sorted by residual: chirality pdb=" C8 FOK A1301 " pdb=" C7 FOK A1301 " pdb=" C9 FOK A1301 " pdb=" O1 FOK A1301 " both_signs ideal model delta sigma weight residual False 2.90 2.65 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" C6 FOK A1301 " pdb=" C5 FOK A1301 " pdb=" C7 FOK A1301 " pdb=" O3 FOK A1301 " both_signs ideal model delta sigma weight residual False -2.28 -2.48 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" C7 FOK A1301 " pdb=" C6 FOK A1301 " pdb=" C8 FOK A1301 " pdb=" O4 FOK A1301 " both_signs ideal model delta sigma weight residual False -2.45 -2.64 0.18 2.00e-01 2.50e+01 8.37e-01 ... (remaining 1552 not shown) Planarity restraints: 1733 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 931 " -0.020 2.00e-02 2.50e+03 1.59e-02 6.35e+00 pdb=" CG TRP A 931 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP A 931 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 931 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 931 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 931 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 931 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 931 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 931 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 931 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 834 " 0.032 5.00e-02 4.00e+02 4.89e-02 3.83e+00 pdb=" N PRO A 835 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 835 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 835 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 121 " -0.031 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO B 122 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 122 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 122 " -0.027 5.00e-02 4.00e+02 ... (remaining 1730 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 71 2.51 - 3.11: 7504 3.11 - 3.71: 16038 3.71 - 4.30: 21602 4.30 - 4.90: 35178 Nonbonded interactions: 80393 Sorted by model distance: nonbonded pdb=" O2B GSP B 501 " pdb="MG MG B 502 " model vdw 1.915 2.170 nonbonded pdb=" O2G GSP B 501 " pdb="MG MG B 502 " model vdw 2.018 2.170 nonbonded pdb=" O VAL A 758 " pdb=" OG1 THR A 762 " model vdw 2.211 2.440 nonbonded pdb=" O ASP A 191 " pdb=" OG1 THR A 194 " model vdw 2.237 2.440 nonbonded pdb=" OG1 THR A1000 " pdb=" OD1 ASN A1003 " model vdw 2.252 2.440 ... (remaining 80388 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.050 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: 15.130 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 30.930 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 54.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 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 0.037 10120 Z= 0.181 Angle : 0.620 12.382 13705 Z= 0.312 Chirality : 0.041 0.252 1555 Planarity : 0.003 0.049 1733 Dihedral : 17.226 87.803 3807 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.46 % Allowed : 27.73 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.24), residues: 1211 helix: 1.23 (0.20), residues: 690 sheet: -0.13 (0.48), residues: 108 loop : -1.23 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP A 931 HIS 0.009 0.001 HIS A 399 PHE 0.031 0.002 PHE A 448 TYR 0.020 0.001 TYR A 468 ARG 0.005 0.000 ARG A 496 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 132 time to evaluate : 1.128 Fit side-chains REVERT: A 418 LEU cc_start: 0.8741 (tt) cc_final: 0.8387 (tp) REVERT: B 387 HIS cc_start: 0.5764 (OUTLIER) cc_final: 0.4721 (t70) outliers start: 5 outliers final: 3 residues processed: 135 average time/residue: 0.1982 time to fit residues: 39.4742 Evaluate side-chains 129 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 125 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 ASN Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 387 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 31 optimal weight: 0.0040 chunk 62 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 58 optimal weight: 0.1980 chunk 71 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 GLN ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.0842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10120 Z= 0.178 Angle : 0.563 9.295 13705 Z= 0.287 Chirality : 0.040 0.174 1555 Planarity : 0.003 0.044 1733 Dihedral : 5.154 53.143 1439 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.42 % Allowed : 25.97 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.24), residues: 1211 helix: 1.54 (0.19), residues: 702 sheet: 0.13 (0.48), residues: 107 loop : -1.18 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 931 HIS 0.005 0.001 HIS B 149 PHE 0.015 0.001 PHE A 176 TYR 0.019 0.001 TYR A 468 ARG 0.002 0.000 ARG A 496 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 140 time to evaluate : 1.183 Fit side-chains REVERT: A 732 GLN cc_start: 0.5342 (tm-30) cc_final: 0.5132 (tm-30) outliers start: 37 outliers final: 17 residues processed: 168 average time/residue: 0.1964 time to fit residues: 48.6189 Evaluate side-chains 145 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 727 PHE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 1046 SER Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1151 TYR Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 287 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 75 optimal weight: 0.0980 chunk 30 optimal weight: 0.7980 chunk 110 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10120 Z= 0.174 Angle : 0.552 8.205 13705 Z= 0.280 Chirality : 0.040 0.197 1555 Planarity : 0.003 0.042 1733 Dihedral : 4.411 27.660 1431 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.97 % Allowed : 25.60 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.24), residues: 1211 helix: 1.59 (0.19), residues: 709 sheet: 0.21 (0.49), residues: 107 loop : -1.27 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 931 HIS 0.005 0.001 HIS B 149 PHE 0.027 0.001 PHE A 176 TYR 0.021 0.001 TYR A 468 ARG 0.003 0.000 ARG B 317 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 143 time to evaluate : 1.235 Fit side-chains REVERT: A 406 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8017 (ptm-80) REVERT: A 856 ASN cc_start: 0.7553 (t0) cc_final: 0.7112 (t0) REVERT: A 861 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7734 (tt) outliers start: 43 outliers final: 24 residues processed: 172 average time/residue: 0.1961 time to fit residues: 49.9572 Evaluate side-chains 155 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 129 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 727 PHE Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 1031 ASP Chi-restraints excluded: chain A residue 1046 SER Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1151 TYR Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 203 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 0.3980 chunk 57 optimal weight: 0.8980 chunk 12 optimal weight: 0.0770 chunk 52 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10120 Z= 0.161 Angle : 0.546 7.015 13705 Z= 0.274 Chirality : 0.040 0.201 1555 Planarity : 0.003 0.040 1733 Dihedral : 4.341 27.028 1431 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.25 % Allowed : 26.62 % Favored : 69.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.24), residues: 1211 helix: 1.64 (0.19), residues: 706 sheet: 0.15 (0.49), residues: 107 loop : -1.23 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 931 HIS 0.005 0.001 HIS A 399 PHE 0.026 0.001 PHE A 799 TYR 0.021 0.001 TYR A 468 ARG 0.003 0.000 ARG B 317 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 142 time to evaluate : 1.182 Fit side-chains revert: symmetry clash REVERT: A 406 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.8010 (ptm-80) REVERT: A 856 ASN cc_start: 0.7560 (t0) cc_final: 0.7159 (t0) REVERT: A 861 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7786 (tt) REVERT: A 952 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.7282 (ttm) outliers start: 46 outliers final: 32 residues processed: 176 average time/residue: 0.1896 time to fit residues: 49.8709 Evaluate side-chains 166 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 131 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 1031 ASP Chi-restraints excluded: chain A residue 1046 SER Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1151 TYR Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 294 GLN Chi-restraints excluded: chain B residue 379 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 39 optimal weight: 0.0970 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10120 Z= 0.286 Angle : 0.617 8.485 13705 Z= 0.312 Chirality : 0.042 0.195 1555 Planarity : 0.004 0.040 1733 Dihedral : 4.673 33.680 1431 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 6.28 % Allowed : 25.69 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.24), residues: 1211 helix: 1.39 (0.19), residues: 711 sheet: 0.14 (0.48), residues: 108 loop : -1.25 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1113 HIS 0.005 0.001 HIS A 410 PHE 0.024 0.002 PHE A 799 TYR 0.024 0.002 TYR A 468 ARG 0.003 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 126 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 406 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7990 (ptm-80) REVERT: A 787 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7200 (ptp-170) REVERT: A 856 ASN cc_start: 0.7617 (t0) cc_final: 0.7173 (t0) REVERT: A 861 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7827 (tt) REVERT: A 952 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.7492 (ttm) REVERT: A 1139 TYR cc_start: 0.5938 (OUTLIER) cc_final: 0.5272 (p90) REVERT: B 310 ASP cc_start: 0.7200 (OUTLIER) cc_final: 0.6997 (m-30) outliers start: 68 outliers final: 41 residues processed: 176 average time/residue: 0.1842 time to fit residues: 48.4159 Evaluate side-chains 170 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 123 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 566 ASN Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 727 PHE Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 787 ARG Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 972 ASN Chi-restraints excluded: chain A residue 1031 ASP Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1046 SER Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1139 TYR Chi-restraints excluded: chain A residue 1151 TYR Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 294 GLN Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 310 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 29 optimal weight: 0.5980 chunk 118 optimal weight: 0.0000 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10120 Z= 0.164 Angle : 0.561 9.003 13705 Z= 0.281 Chirality : 0.040 0.202 1555 Planarity : 0.003 0.039 1733 Dihedral : 4.478 31.681 1431 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.34 % Allowed : 27.63 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.24), residues: 1211 helix: 1.59 (0.19), residues: 711 sheet: 0.11 (0.47), residues: 113 loop : -1.26 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 931 HIS 0.005 0.001 HIS A 399 PHE 0.028 0.001 PHE A 799 TYR 0.020 0.001 TYR A 468 ARG 0.002 0.000 ARG A1131 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 127 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 406 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.7871 (ptm-80) REVERT: A 856 ASN cc_start: 0.7492 (t0) cc_final: 0.7014 (t0) REVERT: A 861 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7829 (tt) REVERT: A 952 MET cc_start: 0.7677 (OUTLIER) cc_final: 0.7355 (ttm) outliers start: 47 outliers final: 33 residues processed: 160 average time/residue: 0.1830 time to fit residues: 44.8122 Evaluate side-chains 159 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 123 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 1031 ASP Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1046 SER Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1151 TYR Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 294 GLN Chi-restraints excluded: chain B residue 388 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 117 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 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 717 ASN ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10120 Z= 0.185 Angle : 0.569 9.602 13705 Z= 0.284 Chirality : 0.040 0.198 1555 Planarity : 0.003 0.039 1733 Dihedral : 4.449 31.631 1431 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 5.18 % Allowed : 26.89 % Favored : 67.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.25), residues: 1211 helix: 1.64 (0.19), residues: 711 sheet: 0.15 (0.48), residues: 113 loop : -1.29 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 931 HIS 0.005 0.001 HIS A 399 PHE 0.029 0.002 PHE A 799 TYR 0.022 0.001 TYR A 468 ARG 0.002 0.000 ARG A 680 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 130 time to evaluate : 1.109 Fit side-chains revert: symmetry clash REVERT: A 406 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7955 (ptm-80) REVERT: A 856 ASN cc_start: 0.7578 (t0) cc_final: 0.7085 (t0) REVERT: A 861 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7802 (tt) REVERT: A 952 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.7378 (ttm) REVERT: A 1139 TYR cc_start: 0.5987 (OUTLIER) cc_final: 0.5245 (p90) outliers start: 56 outliers final: 38 residues processed: 173 average time/residue: 0.1735 time to fit residues: 46.3974 Evaluate side-chains 166 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 124 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 928 ASP Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 972 ASN Chi-restraints excluded: chain A residue 1031 ASP Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1046 SER Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1139 TYR Chi-restraints excluded: chain A residue 1147 PHE Chi-restraints excluded: chain A residue 1151 TYR Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 294 GLN Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 388 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 92 optimal weight: 0.4980 chunk 106 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10120 Z= 0.244 Angle : 0.616 10.903 13705 Z= 0.310 Chirality : 0.042 0.199 1555 Planarity : 0.003 0.039 1733 Dihedral : 4.678 36.409 1431 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 4.99 % Allowed : 27.45 % Favored : 67.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.24), residues: 1211 helix: 1.52 (0.19), residues: 710 sheet: 0.05 (0.47), residues: 113 loop : -1.33 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1113 HIS 0.008 0.001 HIS A 399 PHE 0.028 0.002 PHE A 799 TYR 0.022 0.001 TYR A 468 ARG 0.002 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 120 time to evaluate : 1.189 Fit side-chains revert: symmetry clash REVERT: A 406 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.7948 (ptm-80) REVERT: A 856 ASN cc_start: 0.7609 (t0) cc_final: 0.7111 (t0) REVERT: A 861 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7832 (tt) REVERT: A 952 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.7470 (ttm) REVERT: A 1139 TYR cc_start: 0.6200 (OUTLIER) cc_final: 0.5402 (p90) REVERT: B 310 ASP cc_start: 0.7299 (OUTLIER) cc_final: 0.6571 (m-30) REVERT: B 387 HIS cc_start: 0.5971 (OUTLIER) cc_final: 0.5053 (t70) outliers start: 54 outliers final: 42 residues processed: 162 average time/residue: 0.1701 time to fit residues: 42.9293 Evaluate side-chains 166 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 118 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 566 ASN Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 928 ASP Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 947 GLU Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 972 ASN Chi-restraints excluded: chain A residue 981 ASP Chi-restraints excluded: chain A residue 1031 ASP Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1046 SER Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1139 TYR Chi-restraints excluded: chain A residue 1151 TYR Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 294 GLN Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 387 HIS Chi-restraints excluded: chain B residue 388 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 0.3980 chunk 102 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 99 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10120 Z= 0.185 Angle : 0.581 11.349 13705 Z= 0.289 Chirality : 0.040 0.199 1555 Planarity : 0.003 0.038 1733 Dihedral : 4.542 35.603 1431 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.25 % Allowed : 28.47 % Favored : 67.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.25), residues: 1211 helix: 1.69 (0.19), residues: 711 sheet: 0.08 (0.47), residues: 113 loop : -1.30 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 931 HIS 0.006 0.001 HIS A 399 PHE 0.031 0.002 PHE A 799 TYR 0.020 0.001 TYR A 468 ARG 0.002 0.000 ARG A 680 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 128 time to evaluate : 1.167 Fit side-chains revert: symmetry clash REVERT: A 406 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.7923 (ptm-80) REVERT: A 679 LEU cc_start: 0.6346 (OUTLIER) cc_final: 0.5949 (tp) REVERT: A 856 ASN cc_start: 0.7626 (t0) cc_final: 0.7137 (t0) REVERT: A 861 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7832 (tt) REVERT: A 952 MET cc_start: 0.7685 (OUTLIER) cc_final: 0.7337 (ttm) REVERT: A 1139 TYR cc_start: 0.6231 (OUTLIER) cc_final: 0.5520 (p90) outliers start: 46 outliers final: 39 residues processed: 161 average time/residue: 0.1676 time to fit residues: 42.3792 Evaluate side-chains 170 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 126 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 928 ASP Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 947 GLU Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 972 ASN Chi-restraints excluded: chain A residue 981 ASP Chi-restraints excluded: chain A residue 1031 ASP Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1046 SER Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1139 TYR Chi-restraints excluded: chain A residue 1151 TYR Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 294 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 121 optimal weight: 0.9990 chunk 111 optimal weight: 0.0980 chunk 96 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 74 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 76 optimal weight: 0.0070 chunk 103 optimal weight: 6.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 GLN ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10120 Z= 0.169 Angle : 0.579 12.188 13705 Z= 0.286 Chirality : 0.040 0.201 1555 Planarity : 0.003 0.038 1733 Dihedral : 4.422 32.104 1431 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.88 % Allowed : 29.21 % Favored : 66.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.25), residues: 1211 helix: 1.74 (0.20), residues: 716 sheet: 0.19 (0.48), residues: 108 loop : -1.32 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 931 HIS 0.006 0.001 HIS A 399 PHE 0.031 0.002 PHE A 799 TYR 0.018 0.001 TYR A 468 ARG 0.001 0.000 ARG A 459 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 126 time to evaluate : 1.211 Fit side-chains revert: symmetry clash REVERT: A 406 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7919 (ptm-80) REVERT: A 679 LEU cc_start: 0.6493 (OUTLIER) cc_final: 0.6083 (tp) REVERT: A 856 ASN cc_start: 0.7489 (t0) cc_final: 0.7201 (t0) REVERT: A 861 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7778 (tt) REVERT: A 952 MET cc_start: 0.7648 (OUTLIER) cc_final: 0.7286 (ttm) REVERT: A 1139 TYR cc_start: 0.6287 (OUTLIER) cc_final: 0.5632 (p90) outliers start: 42 outliers final: 33 residues processed: 158 average time/residue: 0.1757 time to fit residues: 43.4754 Evaluate side-chains 162 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 124 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 928 ASP Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 947 GLU Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 972 ASN Chi-restraints excluded: chain A residue 1031 ASP Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1046 SER Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1139 TYR Chi-restraints excluded: chain A residue 1151 TYR Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 294 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.6980 chunk 89 optimal weight: 0.0970 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 99 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 GLN ** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.156328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.122243 restraints weight = 19223.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.123402 restraints weight = 10525.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.124013 restraints weight = 7495.522| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10120 Z= 0.181 Angle : 0.590 11.789 13705 Z= 0.292 Chirality : 0.040 0.198 1555 Planarity : 0.003 0.038 1733 Dihedral : 4.410 31.626 1431 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.16 % Allowed : 29.21 % Favored : 66.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.25), residues: 1211 helix: 1.69 (0.19), residues: 717 sheet: 0.17 (0.47), residues: 113 loop : -1.29 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 931 HIS 0.006 0.001 HIS A 399 PHE 0.030 0.002 PHE A 799 TYR 0.020 0.001 TYR A 468 ARG 0.002 0.000 ARG A 680 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2270.05 seconds wall clock time: 42 minutes 8.42 seconds (2528.42 seconds total)