Starting phenix.real_space_refine on Sat Jul 20 04:25:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcs_37448/07_2024/8wcs_37448_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcs_37448/07_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_37448/07_2024/8wcs_37448.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcs_37448/07_2024/8wcs_37448.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcs_37448/07_2024/8wcs_37448_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcs_37448/07_2024/8wcs_37448_neut.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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 6.02, per 1000 atoms: 0.60 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: 4.09 Conformation dependent library (CDL) restraints added in 1.6 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: 3.06 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: 3.16 Time building geometry restraints manager: 4.43 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 2.440 nonbonded pdb=" O PHE A 325 " pdb=" OG1 THR A 328 " model vdw 2.231 2.440 nonbonded pdb=" OD2 ASP A 673 " pdb=" OH TYR A 753 " model vdw 2.287 2.440 nonbonded pdb=" OD2 ASP A 424 " pdb=" OH TYR A 890 " model vdw 2.304 2.440 ... (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 ========== 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: 1.000 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 30.920 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.530 ------------------------------------------------------------------------------- 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 : 1.117 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: 0.2220 time to fit residues: 34.0496 Evaluate side-chains 92 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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: 0.9980 chunk 46 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1081 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10454 Z= 0.195 Angle : 0.548 5.480 14362 Z= 0.294 Chirality : 0.040 0.200 1589 Planarity : 0.004 0.044 1558 Dihedral : 19.147 167.904 2143 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 3.27 % Allowed : 30.03 % Favored : 66.70 % 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: -1.35 (0.25), residues: 1038 helix: 0.31 (0.21), residues: 561 sheet: -1.89 (0.76), residues: 42 loop : -2.46 (0.26), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 315 HIS 0.004 0.001 HIS A 114 PHE 0.011 0.001 PHE A 506 TYR 0.021 0.001 TYR A 155 ARG 0.003 0.000 ARG A 36 *********************** 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 132 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 101 time to evaluate : 0.951 Fit side-chains revert: symmetry clash REVERT: A 97 MET cc_start: 0.7858 (ptm) cc_final: 0.7614 (ptm) REVERT: A 228 LYS cc_start: 0.5980 (OUTLIER) cc_final: 0.5409 (ptmt) REVERT: A 591 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8504 (tt) outliers start: 31 outliers final: 18 residues processed: 124 average time/residue: 0.2202 time to fit residues: 38.8691 Evaluate side-chains 107 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 87 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 228 LYS 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 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 867 THR Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1027 LYS Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1070 ASP 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: 10.0000 chunk 31 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1081 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10454 Z= 0.181 Angle : 0.536 6.432 14362 Z= 0.286 Chirality : 0.039 0.196 1589 Planarity : 0.003 0.049 1558 Dihedral : 18.956 169.717 2141 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 3.79 % Allowed : 30.66 % Favored : 65.54 % 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: -0.77 (0.26), residues: 1038 helix: 0.90 (0.22), residues: 561 sheet: -2.00 (0.75), residues: 40 loop : -2.33 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 884 HIS 0.003 0.001 HIS A 114 PHE 0.010 0.001 PHE A 676 TYR 0.020 0.001 TYR A 155 ARG 0.002 0.000 ARG A 304 *********************** 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 137 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 101 time to evaluate : 1.140 Fit side-chains revert: symmetry clash REVERT: A 131 TYR cc_start: 0.6567 (t80) cc_final: 0.6355 (t80) REVERT: A 150 LEU cc_start: 0.6546 (mt) cc_final: 0.6220 (mt) REVERT: A 228 LYS cc_start: 0.5920 (OUTLIER) cc_final: 0.5354 (ptmt) REVERT: A 591 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8532 (tt) REVERT: A 791 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.7427 (t80) outliers start: 36 outliers final: 26 residues processed: 130 average time/residue: 0.2299 time to fit residues: 42.2277 Evaluate side-chains 122 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 93 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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 228 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 327 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 669 LEU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 687 HIS 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 780 LEU 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 970 GLN Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1027 LYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 794 ASN A1081 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10454 Z= 0.258 Angle : 0.590 5.689 14362 Z= 0.313 Chirality : 0.042 0.197 1589 Planarity : 0.004 0.049 1558 Dihedral : 18.933 170.749 2141 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.12 % Favored : 89.79 % Rotamer: Outliers : 5.90 % Allowed : 28.98 % Favored : 65.12 % 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: -0.80 (0.26), residues: 1038 helix: 0.91 (0.22), residues: 567 sheet: -2.44 (0.73), residues: 41 loop : -2.40 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 884 HIS 0.004 0.001 HIS A 114 PHE 0.011 0.002 PHE A 443 TYR 0.022 0.002 TYR A 155 ARG 0.002 0.000 ARG A1005 *********************** 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 152 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 96 time to evaluate : 1.090 Fit side-chains revert: symmetry clash REVERT: A 131 TYR cc_start: 0.6642 (t80) cc_final: 0.6369 (t80) REVERT: A 228 LYS cc_start: 0.5882 (OUTLIER) cc_final: 0.5320 (ptmt) REVERT: A 313 LYS cc_start: 0.8064 (pttp) cc_final: 0.7833 (ptmm) REVERT: A 591 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8557 (tt) REVERT: A 1006 TYR cc_start: 0.6338 (m-80) cc_final: 0.6075 (m-80) outliers start: 56 outliers final: 37 residues processed: 144 average time/residue: 0.2241 time to fit residues: 45.6901 Evaluate side-chains 129 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 90 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 327 SER 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 559 THR Chi-restraints excluded: chain A residue 564 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 687 HIS Chi-restraints excluded: chain A residue 692 ASP 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 780 LEU 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 970 GLN Chi-restraints excluded: chain A residue 1027 LYS Chi-restraints excluded: chain A residue 1044 ILE 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 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: 4.9990 chunk 1 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 0 optimal weight: 9.9990 chunk 54 optimal weight: 0.0040 chunk 95 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 overall best weight: 0.8794 ------------------------------------------------------------------------------- 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 996 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10454 Z= 0.134 Angle : 0.512 8.168 14362 Z= 0.271 Chirality : 0.038 0.191 1589 Planarity : 0.003 0.051 1558 Dihedral : 18.783 169.359 2141 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 4.53 % Allowed : 30.45 % Favored : 65.02 % 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: -0.40 (0.27), residues: 1038 helix: 1.28 (0.22), residues: 566 sheet: -2.06 (0.76), residues: 43 loop : -2.30 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 234 HIS 0.002 0.001 HIS A 114 PHE 0.008 0.001 PHE A 241 TYR 0.017 0.001 TYR A 155 ARG 0.002 0.000 ARG A 653 *********************** 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 147 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 104 time to evaluate : 1.058 Fit side-chains revert: symmetry clash REVERT: A 102 TYR cc_start: 0.8268 (m-80) cc_final: 0.7939 (m-80) REVERT: A 313 LYS cc_start: 0.8097 (pttp) cc_final: 0.7789 (ptmm) REVERT: A 400 LYS cc_start: 0.7476 (OUTLIER) cc_final: 0.7022 (mmtm) REVERT: A 791 PHE cc_start: 0.8562 (OUTLIER) cc_final: 0.7484 (t80) REVERT: A 962 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.7339 (p0) outliers start: 43 outliers final: 29 residues processed: 137 average time/residue: 0.2215 time to fit residues: 43.4217 Evaluate side-chains 129 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 97 time to evaluate : 1.076 ------------------------------------------------------------------------------- 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 169 ASN 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 306 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 579 LEU 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 687 HIS Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 780 LEU 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 962 ASP Chi-restraints excluded: chain A residue 974 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 106 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN A 329 GLN A 449 ASN A 794 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10454 Z= 0.163 Angle : 0.520 8.433 14362 Z= 0.275 Chirality : 0.039 0.196 1589 Planarity : 0.003 0.049 1558 Dihedral : 18.759 169.558 2141 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 5.06 % Allowed : 29.82 % Favored : 65.12 % 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: -0.29 (0.27), residues: 1038 helix: 1.39 (0.23), residues: 566 sheet: -1.96 (0.76), residues: 43 loop : -2.29 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 234 HIS 0.003 0.001 HIS A 114 PHE 0.012 0.001 PHE A 676 TYR 0.019 0.001 TYR A 155 ARG 0.001 0.000 ARG A1095 *********************** 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 147 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 99 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: A 131 TYR cc_start: 0.6432 (t80) cc_final: 0.6166 (t80) REVERT: A 591 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8530 (tt) REVERT: A 791 PHE cc_start: 0.8595 (OUTLIER) cc_final: 0.7479 (t80) REVERT: A 882 MET cc_start: 0.7979 (mmm) cc_final: 0.7519 (tpt) REVERT: A 962 ASP cc_start: 0.7728 (OUTLIER) cc_final: 0.7348 (p0) outliers start: 48 outliers final: 39 residues processed: 138 average time/residue: 0.2207 time to fit residues: 43.7294 Evaluate side-chains 138 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 96 time to evaluate : 1.033 ------------------------------------------------------------------------------- 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 261 GLU Chi-restraints excluded: chain A residue 265 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 327 SER 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 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 687 HIS Chi-restraints excluded: chain A residue 736 LEU 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 780 LEU 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 962 ASP Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1027 LYS 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 1105 ASN 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: 0.8980 chunk 60 optimal weight: 3.9990 chunk 77 optimal weight: 0.0870 chunk 89 optimal weight: 7.9990 chunk 59 optimal weight: 0.7980 chunk 106 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 overall best weight: 1.3562 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10454 Z= 0.157 Angle : 0.516 7.601 14362 Z= 0.274 Chirality : 0.038 0.203 1589 Planarity : 0.003 0.049 1558 Dihedral : 18.732 169.298 2141 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 5.27 % Allowed : 29.61 % Favored : 65.12 % 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: -0.19 (0.27), residues: 1038 helix: 1.48 (0.23), residues: 567 sheet: -1.93 (0.77), residues: 43 loop : -2.27 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 234 HIS 0.002 0.001 HIS A 114 PHE 0.008 0.001 PHE A 676 TYR 0.019 0.001 TYR A 155 ARG 0.002 0.000 ARG A1095 *********************** 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 154 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 104 time to evaluate : 1.130 Fit side-chains revert: symmetry clash REVERT: A 131 TYR cc_start: 0.6436 (t80) cc_final: 0.6195 (t80) REVERT: A 396 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7467 (pp20) REVERT: A 591 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8525 (tt) REVERT: A 791 PHE cc_start: 0.8595 (OUTLIER) cc_final: 0.7467 (t80) REVERT: A 800 GLU cc_start: 0.7879 (pp20) cc_final: 0.7645 (pp20) REVERT: A 882 MET cc_start: 0.7927 (mmm) cc_final: 0.7480 (mmt) REVERT: A 962 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.7356 (p0) outliers start: 50 outliers final: 40 residues processed: 145 average time/residue: 0.2173 time to fit residues: 44.9364 Evaluate side-chains 142 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 98 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 169 ASN Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 265 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 327 SER Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 400 LYS 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 687 HIS Chi-restraints excluded: chain A residue 736 LEU 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 780 LEU 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 1027 LYS Chi-restraints excluded: chain A residue 1039 LEU 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 1108 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 0.0770 chunk 67 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 92 optimal weight: 8.9990 overall best weight: 2.5944 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10454 Z= 0.244 Angle : 0.578 7.037 14362 Z= 0.305 Chirality : 0.041 0.213 1589 Planarity : 0.003 0.047 1558 Dihedral : 18.836 169.853 2141 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 5.27 % Allowed : 30.03 % 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: -0.41 (0.26), residues: 1038 helix: 1.26 (0.22), residues: 572 sheet: -2.18 (0.75), residues: 43 loop : -2.32 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 315 HIS 0.004 0.001 HIS A 114 PHE 0.010 0.001 PHE A 855 TYR 0.020 0.002 TYR A 155 ARG 0.002 0.000 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 151 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 101 time to evaluate : 1.319 Fit side-chains revert: symmetry clash REVERT: A 591 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8517 (tt) REVERT: A 791 PHE cc_start: 0.8673 (OUTLIER) cc_final: 0.7483 (t80) REVERT: A 882 MET cc_start: 0.7745 (mmm) cc_final: 0.7397 (mmt) REVERT: A 962 ASP cc_start: 0.7716 (OUTLIER) cc_final: 0.7383 (p0) outliers start: 50 outliers final: 43 residues processed: 142 average time/residue: 0.2350 time to fit residues: 47.8630 Evaluate side-chains 141 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 95 time to evaluate : 1.107 ------------------------------------------------------------------------------- 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 261 GLU Chi-restraints excluded: chain A residue 265 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 327 SER 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 687 HIS Chi-restraints excluded: chain A residue 692 ASP Chi-restraints excluded: chain A residue 736 LEU 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 780 LEU 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 1027 LYS Chi-restraints excluded: chain A residue 1044 ILE 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 1108 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 43 optimal weight: 8.9990 chunk 77 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 89 optimal weight: 0.0170 chunk 93 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 104 optimal weight: 20.0000 chunk 63 optimal weight: 1.9990 overall best weight: 0.9824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN A 767 ASN A 794 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10454 Z= 0.142 Angle : 0.525 7.295 14362 Z= 0.278 Chirality : 0.038 0.215 1589 Planarity : 0.003 0.051 1558 Dihedral : 18.748 168.382 2141 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 4.21 % Allowed : 31.09 % 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: -0.16 (0.27), residues: 1038 helix: 1.48 (0.23), residues: 573 sheet: -2.01 (0.76), residues: 43 loop : -2.24 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 891 HIS 0.003 0.001 HIS A 114 PHE 0.010 0.001 PHE A 241 TYR 0.019 0.001 TYR A 499 ARG 0.002 0.000 ARG A1095 *********************** 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 145 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 105 time to evaluate : 0.951 Fit side-chains revert: symmetry clash REVERT: A 102 TYR cc_start: 0.8197 (m-80) cc_final: 0.7891 (m-80) REVERT: A 396 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7470 (pp20) REVERT: A 791 PHE cc_start: 0.8609 (OUTLIER) cc_final: 0.7486 (t80) REVERT: A 882 MET cc_start: 0.7725 (mmm) cc_final: 0.7374 (mmt) REVERT: A 962 ASP cc_start: 0.7700 (OUTLIER) cc_final: 0.7351 (p0) outliers start: 40 outliers final: 37 residues processed: 136 average time/residue: 0.2210 time to fit residues: 43.2470 Evaluate side-chains 140 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 100 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 261 GLU 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 327 SER Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 579 LEU 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 687 HIS Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 780 LEU 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 1027 LYS Chi-restraints excluded: chain A residue 1039 LEU 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 1108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 109 optimal weight: 10.9990 chunk 100 optimal weight: 2.9990 chunk 87 optimal weight: 0.0570 chunk 9 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 overall best weight: 1.8106 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10454 Z= 0.191 Angle : 0.545 6.924 14362 Z= 0.289 Chirality : 0.039 0.222 1589 Planarity : 0.003 0.048 1558 Dihedral : 18.774 168.824 2141 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 4.74 % Allowed : 31.09 % 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: -0.20 (0.27), residues: 1038 helix: 1.43 (0.22), residues: 573 sheet: -2.12 (0.74), residues: 43 loop : -2.22 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 891 HIS 0.003 0.001 HIS A 114 PHE 0.010 0.001 PHE A 241 TYR 0.022 0.002 TYR A 499 ARG 0.002 0.000 ARG A1095 ********************** 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 147 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 102 time to evaluate : 1.180 Fit side-chains revert: symmetry clash REVERT: A 102 TYR cc_start: 0.8233 (m-80) cc_final: 0.7917 (m-80) REVERT: A 396 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7458 (pp20) REVERT: A 591 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8493 (tt) REVERT: A 791 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.7455 (t80) REVERT: A 882 MET cc_start: 0.7718 (mmm) cc_final: 0.7362 (mmt) REVERT: A 962 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7377 (p0) outliers start: 45 outliers final: 38 residues processed: 139 average time/residue: 0.2230 time to fit residues: 43.8686 Evaluate side-chains 143 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 101 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 261 GLU 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 327 SER Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 545 SER 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 687 HIS 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 780 LEU 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 1027 LYS Chi-restraints excluded: chain A residue 1039 LEU 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 1108 LEU 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: 10.0000 chunk 24 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 36 optimal weight: 0.1980 chunk 89 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.4043 r_free = 0.4043 target = 0.152956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.127139 restraints weight = 15239.039| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.70 r_work: 0.3651 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10454 Z= 0.165 Angle : 0.536 6.874 14362 Z= 0.283 Chirality : 0.039 0.222 1589 Planarity : 0.003 0.049 1558 Dihedral : 18.753 168.555 2141 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 4.85 % Allowed : 30.87 % Favored : 64.28 % 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: -0.18 (0.27), residues: 1038 helix: 1.44 (0.22), residues: 573 sheet: -2.08 (0.75), residues: 43 loop : -2.21 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 891 HIS 0.002 0.001 HIS A 114 PHE 0.010 0.001 PHE A 241 TYR 0.022 0.001 TYR A 499 ARG 0.002 0.000 ARG A1095 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2064.24 seconds wall clock time: 37 minutes 51.63 seconds (2271.63 seconds total)