Starting phenix.real_space_refine on Sun Aug 4 06:35:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcs_37448/08_2024/8wcs_37448.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcs_37448/08_2024/8wcs_37448.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcs_37448/08_2024/8wcs_37448.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcs_37448/08_2024/8wcs_37448.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcs_37448/08_2024/8wcs_37448.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcs_37448/08_2024/8wcs_37448.cif" } resolution = 3.1 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= 0.001 sd= 0.077 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 66 5.49 5 Mg 1 5.21 5 S 31 5.16 5 C 6245 2.51 5 N 1692 2.21 5 O 2061 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 17": "OD1" <-> "OD2" Residue "A GLU 25": "OE1" <-> "OE2" Residue "A GLU 54": "OE1" <-> "OE2" Residue "A GLU 63": "OE1" <-> "OE2" Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 180": "OE1" <-> "OE2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "A PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A TYR 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "A PHE 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 720": "OE1" <-> "OE2" Residue "A GLU 800": "OE1" <-> "OE2" Residue "A GLU 848": "OE1" <-> "OE2" Residue "A ASP 933": "OD1" <-> "OD2" Residue "A PHE 1025": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 10096 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1044, 8685 Classifications: {'peptide': 1044} Link IDs: {'PTRANS': 26, 'TRANS': 1017} Chain breaks: 2 Chain: "G" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1410 Classifications: {'RNA': 66} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 10, 'rna3p_pur': 26, 'rna3p_pyr': 19} Link IDs: {'rna2p': 20, 'rna3p': 45} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.89, per 1000 atoms: 0.58 Number of scatterers: 10096 At special positions: 0 Unit cell: (93.5, 86.7, 119.85, 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 31 16.00 P 66 15.00 Mg 1 11.99 O 2061 8.00 N 1692 7.00 C 6245 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.43 Conformation dependent library (CDL) restraints added in 1.7 seconds 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1994 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 3 sheets defined 56.7% alpha, 1.5% beta 8 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 3.21 Creating SS restraints... Processing helix chain 'A' and resid 9 through 30 Processing helix chain 'A' and resid 41 through 50 removed outlier: 3.502A pdb=" N LYS A 44 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU A 45 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLY A 46 " --> pdb=" O ASP A 43 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ASN A 47 " --> pdb=" O LYS A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.873A pdb=" N LYS A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 132 removed outlier: 3.852A pdb=" N LEU A 105 " --> pdb=" O HIS A 101 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 163 removed outlier: 3.513A pdb=" N LEU A 156 " --> pdb=" O GLY A 152 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N PHE A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 177 Processing helix chain 'A' and resid 180 through 204 removed outlier: 4.465A pdb=" N GLU A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 261 removed outlier: 3.666A pdb=" N GLU A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 280 Processing helix chain 'A' and resid 290 through 303 removed outlier: 4.313A pdb=" N ALA A 294 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 316 Processing helix chain 'A' and resid 322 through 324 No H-bonds generated for 'chain 'A' and resid 322 through 324' Processing helix chain 'A' and resid 325 through 334 removed outlier: 4.678A pdb=" N PHE A 332 " --> pdb=" O THR A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 361 Processing helix chain 'A' and resid 371 through 390 removed outlier: 3.826A pdb=" N GLU A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS A 388 " --> pdb=" O SER A 384 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU A 390 " --> pdb=" O SER A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 403 removed outlier: 3.733A pdb=" N GLU A 399 " --> pdb=" O LYS A 395 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS A 400 " --> pdb=" O GLU A 396 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 425 Processing helix chain 'A' and resid 438 through 449 removed outlier: 3.559A pdb=" N ASN A 449 " --> pdb=" O TYR A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 504 removed outlier: 3.506A pdb=" N ARG A 504 " --> pdb=" O LYS A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 536 removed outlier: 3.639A pdb=" N GLY A 535 " --> pdb=" O GLU A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 559 removed outlier: 3.843A pdb=" N LEU A 549 " --> pdb=" O SER A 545 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET A 550 " --> pdb=" O PRO A 546 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS A 551 " --> pdb=" O ASP A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 591 removed outlier: 3.615A pdb=" N ILE A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 647 removed outlier: 3.786A pdb=" N ILE A 627 " --> pdb=" O ASP A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 654 removed outlier: 3.556A pdb=" N ARG A 653 " --> pdb=" O ALA A 650 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE A 654 " --> pdb=" O PRO A 651 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 650 through 654' Processing helix chain 'A' and resid 658 through 677 removed outlier: 3.594A pdb=" N ILE A 663 " --> pdb=" O LYS A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 688 removed outlier: 3.846A pdb=" N ARG A 686 " --> pdb=" O VAL A 682 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A 688 " --> pdb=" O ALA A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 704 Processing helix chain 'A' and resid 711 through 718 removed outlier: 3.864A pdb=" N LYS A 715 " --> pdb=" O THR A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 759 removed outlier: 3.706A pdb=" N ASN A 744 " --> pdb=" O GLU A 740 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N PHE A 745 " --> pdb=" O GLY A 741 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA A 746 " --> pdb=" O VAL A 742 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER A 759 " --> pdb=" O LYS A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 789 removed outlier: 3.588A pdb=" N GLU A 789 " --> pdb=" O GLY A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 817 Processing helix chain 'A' and resid 824 through 836 removed outlier: 3.898A pdb=" N PHE A 828 " --> pdb=" O SER A 824 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG A 836 " --> pdb=" O VAL A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 853 Processing helix chain 'A' and resid 865 through 893 removed outlier: 4.458A pdb=" N VAL A 871 " --> pdb=" O THR A 867 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA A 872 " --> pdb=" O GLN A 868 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASN A 879 " --> pdb=" O ARG A 875 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLU A 885 " --> pdb=" O LEU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 922 Processing helix chain 'A' and resid 922 through 928 Processing helix chain 'A' and resid 962 through 979 removed outlier: 3.837A pdb=" N GLN A 970 " --> pdb=" O GLN A 966 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL A 974 " --> pdb=" O GLN A 970 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ASP A 975 " --> pdb=" O GLU A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1005 removed outlier: 4.221A pdb=" N ARG A1005 " --> pdb=" O ASP A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1023 removed outlier: 3.944A pdb=" N LYS A1023 " --> pdb=" O HIS A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1030 Processing helix chain 'A' and resid 1053 through 1059 Processing helix chain 'A' and resid 1068 through 1082 Processing helix chain 'A' and resid 1087 through 1105 removed outlier: 3.509A pdb=" N TYR A1091 " --> pdb=" O LYS A1087 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN A1105 " --> pdb=" O TYR A1101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 433 through 436 removed outlier: 3.532A pdb=" N LYS A 509 " --> pdb=" O ILE A 433 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 525 through 529 removed outlier: 3.656A pdb=" N PHE A 527 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 954 through 955 382 hydrogen bonds defined for protein. 1119 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 20 hydrogen bonds 36 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 3.26 Time building geometry restraints manager: 4.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2406 1.33 - 1.45: 2487 1.45 - 1.57: 5374 1.57 - 1.69: 131 1.69 - 1.81: 56 Bond restraints: 10454 Sorted by residual: bond pdb=" CA ASP A1008 " pdb=" C ASP A1008 " ideal model delta sigma weight residual 1.524 1.487 0.037 1.29e-02 6.01e+03 8.22e+00 bond pdb=" CA LEU A 187 " pdb=" C LEU A 187 " ideal model delta sigma weight residual 1.524 1.498 0.026 1.27e-02 6.20e+03 4.12e+00 bond pdb=" N ASP A 721 " pdb=" CA ASP A 721 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.29e-02 6.01e+03 4.09e+00 bond pdb=" C ASP A1008 " pdb=" N ASP A1009 " ideal model delta sigma weight residual 1.335 1.312 0.023 1.31e-02 5.83e+03 3.14e+00 bond pdb=" O3' C G 12 " pdb=" P C G 13 " ideal model delta sigma weight residual 1.607 1.582 0.025 1.50e-02 4.44e+03 2.84e+00 ... (remaining 10449 not shown) Histogram of bond angle deviations from ideal: 98.64 - 105.74: 443 105.74 - 112.83: 5481 112.83 - 119.93: 3864 119.93 - 127.02: 4323 127.02 - 134.12: 251 Bond angle restraints: 14362 Sorted by residual: angle pdb=" N ASP A1008 " pdb=" CA ASP A1008 " pdb=" C ASP A1008 " ideal model delta sigma weight residual 111.36 105.86 5.50 1.09e+00 8.42e-01 2.54e+01 angle pdb=" C ILE A 568 " pdb=" N THR A 569 " pdb=" CA THR A 569 " ideal model delta sigma weight residual 121.54 129.60 -8.06 1.91e+00 2.74e-01 1.78e+01 angle pdb=" C LYS A 574 " pdb=" N ILE A 575 " pdb=" CA ILE A 575 " ideal model delta sigma weight residual 121.97 129.13 -7.16 1.80e+00 3.09e-01 1.58e+01 angle pdb=" C GLU A 178 " pdb=" N THR A 179 " pdb=" CA THR A 179 " ideal model delta sigma weight residual 122.46 127.94 -5.48 1.41e+00 5.03e-01 1.51e+01 angle pdb=" CB GLU A 859 " pdb=" CG GLU A 859 " pdb=" CD GLU A 859 " ideal model delta sigma weight residual 112.60 119.10 -6.50 1.70e+00 3.46e-01 1.46e+01 ... (remaining 14357 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.32: 5900 34.32 - 68.65: 466 68.65 - 102.97: 33 102.97 - 137.29: 0 137.29 - 171.61: 5 Dihedral angle restraints: 6404 sinusoidal: 3308 harmonic: 3096 Sorted by residual: dihedral pdb=" O4' C G -24 " pdb=" C1' C G -24 " pdb=" N1 C G -24 " pdb=" C2 C G -24 " ideal model delta sinusoidal sigma weight residual 200.00 51.20 148.80 1 1.50e+01 4.44e-03 7.92e+01 dihedral pdb=" O4' U G 18 " pdb=" C1' U G 18 " pdb=" N1 U G 18 " pdb=" C2 U G 18 " ideal model delta sinusoidal sigma weight residual 200.00 56.08 143.92 1 1.50e+01 4.44e-03 7.72e+01 dihedral pdb=" O4' C G -8 " pdb=" C1' C G -8 " pdb=" N1 C G -8 " pdb=" C2 C G -8 " ideal model delta sinusoidal sigma weight residual 232.00 62.06 169.94 1 1.70e+01 3.46e-03 6.59e+01 ... (remaining 6401 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1327 0.064 - 0.128: 221 0.128 - 0.193: 34 0.193 - 0.257: 4 0.257 - 0.321: 3 Chirality restraints: 1589 Sorted by residual: chirality pdb=" CB ILE A1044 " pdb=" CA ILE A1044 " pdb=" CG1 ILE A1044 " pdb=" CG2 ILE A1044 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CG LEU A 16 " pdb=" CB LEU A 16 " pdb=" CD1 LEU A 16 " pdb=" CD2 LEU A 16 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CB VAL A1021 " pdb=" CA VAL A1021 " pdb=" CG1 VAL A1021 " pdb=" CG2 VAL A1021 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 1586 not shown) Planarity restraints: 1558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 211 " -0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO A 212 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 212 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 212 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 25 " 0.010 2.00e-02 2.50e+03 2.11e-02 4.46e+00 pdb=" CD GLU A 25 " -0.037 2.00e-02 2.50e+03 pdb=" OE1 GLU A 25 " 0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU A 25 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1007 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.16e+00 pdb=" C LEU A1007 " 0.035 2.00e-02 2.50e+03 pdb=" O LEU A1007 " -0.013 2.00e-02 2.50e+03 pdb=" N ASP A1008 " -0.012 2.00e-02 2.50e+03 ... (remaining 1555 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 364 2.70 - 3.25: 9184 3.25 - 3.80: 16329 3.80 - 4.35: 20398 4.35 - 4.90: 33314 Nonbonded interactions: 79589 Sorted by model distance: nonbonded pdb=" OP1 A G 22 " pdb="MG MG G 101 " model vdw 2.148 2.170 nonbonded pdb=" OH TYR A1006 " pdb=" O ILE A1083 " model vdw 2.211 3.040 nonbonded pdb=" O PHE A 325 " pdb=" OG1 THR A 328 " model vdw 2.231 3.040 nonbonded pdb=" OD2 ASP A 673 " pdb=" OH TYR A 753 " model vdw 2.287 3.040 nonbonded pdb=" OD2 ASP A 424 " pdb=" OH TYR A 890 " model vdw 2.304 3.040 ... (remaining 79584 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: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 32.260 Find NCS groups from input model: 0.080 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 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 : 0.004 0.049 10454 Z= 0.233 Angle : 0.771 9.905 14362 Z= 0.425 Chirality : 0.051 0.321 1589 Planarity : 0.005 0.056 1558 Dihedral : 21.585 171.613 4410 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 0.74 % Allowed : 31.72 % Favored : 67.54 % 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: -2.55 (0.22), residues: 1038 helix: -0.94 (0.19), residues: 557 sheet: -2.54 (0.76), residues: 30 loop : -2.59 (0.25), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 884 HIS 0.004 0.001 HIS A 787 PHE 0.026 0.002 PHE A 331 TYR 0.023 0.002 TYR A 695 ARG 0.010 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 99 time to evaluate : 1.016 Fit side-chains REVERT: A 1006 TYR cc_start: 0.5842 (OUTLIER) cc_final: 0.5537 (t80) outliers start: 7 outliers final: 0 residues processed: 105 average time/residue: 0.2126 time to fit residues: 32.4851 Evaluate side-chains 92 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1006 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.3980 chunk 86 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 GLN A 996 ASN A1081 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10454 Z= 0.144 Angle : 0.531 6.805 14362 Z= 0.285 Chirality : 0.039 0.212 1589 Planarity : 0.003 0.045 1558 Dihedral : 18.996 170.382 2143 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 3.16 % Allowed : 29.40 % Favored : 67.44 % 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: -1.19 (0.25), residues: 1038 helix: 0.40 (0.22), residues: 560 sheet: -1.39 (0.78), residues: 36 loop : -2.36 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 884 HIS 0.003 0.001 HIS A 114 PHE 0.014 0.001 PHE A 110 TYR 0.019 0.001 TYR A 155 ARG 0.004 0.000 ARG A 304 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 106 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: A 97 MET cc_start: 0.7828 (ptm) cc_final: 0.7553 (ptm) REVERT: A 313 LYS cc_start: 0.8198 (pttp) cc_final: 0.7992 (pttp) REVERT: A 329 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.7961 (mp-120) REVERT: A 330 SER cc_start: 0.7985 (m) cc_final: 0.7746 (t) REVERT: A 591 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8446 (tt) outliers start: 30 outliers final: 14 residues processed: 128 average time/residue: 0.2079 time to fit residues: 38.6545 Evaluate side-chains 106 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1102 CYS Chi-restraints excluded: chain A residue 1108 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 89 optimal weight: 7.9990 chunk 99 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A1081 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10454 Z= 0.234 Angle : 0.585 6.596 14362 Z= 0.312 Chirality : 0.041 0.221 1589 Planarity : 0.004 0.049 1558 Dihedral : 18.966 164.976 2141 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 3.06 % Allowed : 29.93 % Favored : 67.02 % 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: -0.87 (0.26), residues: 1038 helix: 0.77 (0.22), residues: 561 sheet: -2.16 (0.72), residues: 40 loop : -2.29 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 234 HIS 0.004 0.001 HIS A 114 PHE 0.012 0.001 PHE A 506 TYR 0.020 0.002 TYR A 155 ARG 0.003 0.000 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 98 time to evaluate : 1.068 Fit side-chains revert: symmetry clash REVERT: A 150 LEU cc_start: 0.6566 (mt) cc_final: 0.6234 (mt) REVERT: A 591 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8558 (tt) outliers start: 29 outliers final: 16 residues processed: 122 average time/residue: 0.2338 time to fit residues: 40.0746 Evaluate side-chains 105 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 88 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1108 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 chunk 52 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1081 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10454 Z= 0.167 Angle : 0.531 6.990 14362 Z= 0.283 Chirality : 0.039 0.189 1589 Planarity : 0.003 0.050 1558 Dihedral : 18.823 168.781 2141 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 3.90 % Allowed : 28.87 % Favored : 67.23 % 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: -0.57 (0.26), residues: 1038 helix: 1.08 (0.22), residues: 567 sheet: -2.02 (0.73), residues: 42 loop : -2.30 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 822 HIS 0.003 0.001 HIS A 114 PHE 0.008 0.001 PHE A 506 TYR 0.018 0.001 TYR A 155 ARG 0.002 0.000 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 94 time to evaluate : 1.101 Fit side-chains revert: symmetry clash REVERT: A 150 LEU cc_start: 0.6505 (mt) cc_final: 0.6195 (mt) REVERT: A 400 LYS cc_start: 0.7504 (OUTLIER) cc_final: 0.7064 (mmtm) REVERT: A 591 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8515 (tt) outliers start: 37 outliers final: 30 residues processed: 122 average time/residue: 0.2225 time to fit residues: 38.9070 Evaluate side-chains 122 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 90 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 791 PHE Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1044 ILE Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1070 ASP Chi-restraints excluded: chain A residue 1108 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 73 optimal weight: 0.0060 chunk 0 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 overall best weight: 2.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 970 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10454 Z= 0.258 Angle : 0.591 7.674 14362 Z= 0.313 Chirality : 0.042 0.200 1589 Planarity : 0.004 0.051 1558 Dihedral : 18.901 163.821 2141 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 4.74 % Allowed : 28.98 % Favored : 66.28 % 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: -0.66 (0.26), residues: 1038 helix: 0.98 (0.22), residues: 572 sheet: -2.61 (0.70), residues: 41 loop : -2.27 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 315 HIS 0.003 0.001 HIS A 114 PHE 0.012 0.001 PHE A 443 TYR 0.020 0.002 TYR A 155 ARG 0.003 0.000 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 100 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: A 150 LEU cc_start: 0.6581 (mt) cc_final: 0.6269 (mt) REVERT: A 591 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8564 (tt) REVERT: A 962 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7400 (p0) REVERT: A 1050 ASP cc_start: 0.7613 (OUTLIER) cc_final: 0.7252 (p0) outliers start: 45 outliers final: 31 residues processed: 136 average time/residue: 0.2267 time to fit residues: 43.9856 Evaluate side-chains 126 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 92 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 791 PHE Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain A residue 962 ASP Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1044 ILE Chi-restraints excluded: chain A residue 1050 ASP Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1067 PHE Chi-restraints excluded: chain A residue 1070 ASP Chi-restraints excluded: chain A residue 1105 ASN Chi-restraints excluded: chain A residue 1108 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 88 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 970 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10454 Z= 0.187 Angle : 0.552 6.360 14362 Z= 0.293 Chirality : 0.040 0.197 1589 Planarity : 0.003 0.053 1558 Dihedral : 18.834 166.722 2141 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 4.64 % Allowed : 29.61 % Favored : 65.75 % 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: -0.55 (0.26), residues: 1038 helix: 1.11 (0.22), residues: 576 sheet: -2.45 (0.71), residues: 43 loop : -2.32 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 822 HIS 0.003 0.001 HIS A 114 PHE 0.008 0.001 PHE A 506 TYR 0.018 0.001 TYR A 155 ARG 0.002 0.000 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 104 time to evaluate : 1.052 Fit side-chains revert: symmetry clash REVERT: A 36 ARG cc_start: 0.7663 (ptt90) cc_final: 0.7396 (ptm160) REVERT: A 102 TYR cc_start: 0.8278 (m-80) cc_final: 0.7951 (m-80) REVERT: A 591 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8491 (tt) REVERT: A 962 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7374 (p0) REVERT: A 1050 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.7249 (p0) outliers start: 44 outliers final: 34 residues processed: 139 average time/residue: 0.2139 time to fit residues: 42.5966 Evaluate side-chains 134 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 97 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 791 PHE Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain A residue 962 ASP Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1044 ILE Chi-restraints excluded: chain A residue 1050 ASP Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1070 ASP Chi-restraints excluded: chain A residue 1108 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 65 optimal weight: 0.0000 chunk 42 optimal weight: 3.9990 overall best weight: 1.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN A 970 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10454 Z= 0.176 Angle : 0.548 6.399 14362 Z= 0.292 Chirality : 0.040 0.206 1589 Planarity : 0.003 0.051 1558 Dihedral : 18.768 167.332 2141 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 4.32 % Allowed : 29.93 % Favored : 65.75 % 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: -0.52 (0.26), residues: 1038 helix: 1.17 (0.22), residues: 578 sheet: -2.55 (0.69), residues: 45 loop : -2.37 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 891 HIS 0.003 0.001 HIS A 114 PHE 0.017 0.001 PHE A 676 TYR 0.018 0.001 TYR A 155 ARG 0.002 0.000 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 100 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: A 102 TYR cc_start: 0.8226 (m-80) cc_final: 0.7930 (m-80) REVERT: A 591 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8489 (tt) REVERT: A 962 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7384 (p0) REVERT: A 1050 ASP cc_start: 0.7611 (OUTLIER) cc_final: 0.7239 (p0) outliers start: 41 outliers final: 35 residues processed: 134 average time/residue: 0.2207 time to fit residues: 41.8859 Evaluate side-chains 133 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 95 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 791 PHE Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain A residue 962 ASP Chi-restraints excluded: chain A residue 970 GLN Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1044 ILE Chi-restraints excluded: chain A residue 1050 ASP Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1067 PHE Chi-restraints excluded: chain A residue 1070 ASP Chi-restraints excluded: chain A residue 1105 ASN Chi-restraints excluded: chain A residue 1108 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 ASN A 970 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 10454 Z= 0.405 Angle : 0.724 9.135 14362 Z= 0.381 Chirality : 0.047 0.223 1589 Planarity : 0.004 0.048 1558 Dihedral : 19.018 164.823 2141 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.08 % Favored : 88.92 % Rotamer: Outliers : 4.95 % Allowed : 30.35 % Favored : 64.70 % 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: -1.14 (0.25), residues: 1038 helix: 0.55 (0.21), residues: 578 sheet: -2.86 (0.68), residues: 41 loop : -2.46 (0.27), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 240 HIS 0.005 0.001 HIS A 972 PHE 0.017 0.002 PHE A 443 TYR 0.024 0.003 TYR A 968 ARG 0.004 0.001 ARG A1095 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 94 time to evaluate : 0.966 Fit side-chains REVERT: A 88 TRP cc_start: 0.3048 (OUTLIER) cc_final: 0.2614 (t60) REVERT: A 102 TYR cc_start: 0.8360 (m-80) cc_final: 0.8119 (m-80) REVERT: A 591 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8567 (tt) REVERT: A 1050 ASP cc_start: 0.7710 (OUTLIER) cc_final: 0.7382 (p0) outliers start: 47 outliers final: 35 residues processed: 135 average time/residue: 0.2370 time to fit residues: 45.4605 Evaluate side-chains 126 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 88 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 791 PHE Chi-restraints excluded: chain A residue 792 SER Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain A residue 970 GLN Chi-restraints excluded: chain A residue 1044 ILE Chi-restraints excluded: chain A residue 1050 ASP Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1067 PHE Chi-restraints excluded: chain A residue 1070 ASP Chi-restraints excluded: chain A residue 1105 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 104 optimal weight: 20.0000 chunk 63 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 ASN A 970 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10454 Z= 0.153 Angle : 0.560 9.375 14362 Z= 0.298 Chirality : 0.040 0.215 1589 Planarity : 0.003 0.055 1558 Dihedral : 18.852 171.303 2141 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 3.06 % Allowed : 32.77 % Favored : 64.17 % 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: -0.51 (0.26), residues: 1038 helix: 1.16 (0.22), residues: 577 sheet: -2.65 (0.67), residues: 45 loop : -2.33 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 891 HIS 0.009 0.001 HIS A 972 PHE 0.012 0.001 PHE A 676 TYR 0.021 0.001 TYR A1075 ARG 0.002 0.000 ARG A 304 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 106 time to evaluate : 1.126 Fit side-chains revert: symmetry clash REVERT: A 36 ARG cc_start: 0.7645 (ptt90) cc_final: 0.7430 (ptm160) REVERT: A 102 TYR cc_start: 0.8204 (m-80) cc_final: 0.7931 (m-80) REVERT: A 1038 LYS cc_start: 0.6435 (tptp) cc_final: 0.5999 (mmmm) outliers start: 29 outliers final: 21 residues processed: 128 average time/residue: 0.2308 time to fit residues: 41.6550 Evaluate side-chains 119 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 98 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 791 PHE Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain A residue 970 GLN Chi-restraints excluded: chain A residue 1044 ILE Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1067 PHE Chi-restraints excluded: chain A residue 1105 ASN Chi-restraints excluded: chain A residue 1108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 109 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 87 optimal weight: 0.0980 chunk 9 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 92 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN A 794 ASN A 970 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10454 Z= 0.183 Angle : 0.579 10.526 14362 Z= 0.304 Chirality : 0.041 0.223 1589 Planarity : 0.003 0.050 1558 Dihedral : 18.786 166.187 2141 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 2.74 % Allowed : 33.51 % Favored : 63.75 % 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: -0.50 (0.26), residues: 1038 helix: 1.18 (0.22), residues: 578 sheet: -2.60 (0.67), residues: 45 loop : -2.35 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 891 HIS 0.003 0.001 HIS A 114 PHE 0.009 0.001 PHE A 676 TYR 0.019 0.001 TYR A 155 ARG 0.004 0.000 ARG A 304 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 98 time to evaluate : 0.968 Fit side-chains revert: symmetry clash REVERT: A 36 ARG cc_start: 0.7721 (ptt90) cc_final: 0.7508 (ptm160) REVERT: A 102 TYR cc_start: 0.8221 (m-80) cc_final: 0.7929 (m-80) REVERT: A 1038 LYS cc_start: 0.6465 (tptp) cc_final: 0.6106 (mmmm) outliers start: 26 outliers final: 24 residues processed: 119 average time/residue: 0.2191 time to fit residues: 37.1091 Evaluate side-chains 121 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 97 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 TYR Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 791 PHE Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 945 VAL Chi-restraints excluded: chain A residue 970 GLN Chi-restraints excluded: chain A residue 1044 ILE Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1067 PHE Chi-restraints excluded: chain A residue 1070 ASP Chi-restraints excluded: chain A residue 1105 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 87 optimal weight: 0.3980 chunk 36 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN A 794 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.151367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.125892 restraints weight = 14935.897| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.57 r_work: 0.3611 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.120 10454 Z= 0.268 Angle : 0.880 59.199 14362 Z= 0.514 Chirality : 0.043 0.604 1589 Planarity : 0.005 0.147 1558 Dihedral : 18.797 166.223 2141 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.15 % Favored : 90.75 % Rotamer: Outliers : 2.74 % Allowed : 33.40 % Favored : 63.86 % Cbeta Deviations : 0.10 % 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: -0.53 (0.26), residues: 1038 helix: 1.14 (0.22), residues: 578 sheet: -2.59 (0.67), residues: 45 loop : -2.35 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 891 HIS 0.003 0.001 HIS A 114 PHE 0.013 0.001 PHE A 241 TYR 0.019 0.001 TYR A 155 ARG 0.004 0.000 ARG A 304 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1933.44 seconds wall clock time: 35 minutes 45.83 seconds (2145.83 seconds total)