Starting phenix.real_space_refine on Thu Jan 18 03:36:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pd8_13331/01_2024/7pd8_13331.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pd8_13331/01_2024/7pd8_13331.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pd8_13331/01_2024/7pd8_13331.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pd8_13331/01_2024/7pd8_13331.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pd8_13331/01_2024/7pd8_13331.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pd8_13331/01_2024/7pd8_13331.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 4936 2.51 5 N 1269 2.21 5 O 1381 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 102": "OE1" <-> "OE2" Residue "A PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 114": "NH1" <-> "NH2" Residue "A PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 117": "NH1" <-> "NH2" Residue "A TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 170": "NH1" <-> "NH2" Residue "A TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 257": "OE1" <-> "OE2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A ASP 322": "OD1" <-> "OD2" Residue "A ARG 340": "NH1" <-> "NH2" Residue "A PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 399": "OD1" <-> "OD2" Residue "A TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 471": "NH1" <-> "NH2" Residue "A ARG 504": "NH1" <-> "NH2" Residue "A ASP 541": "OD1" <-> "OD2" Residue "A GLU 831": "OE1" <-> "OE2" Residue "A PHE 912": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1027": "OD1" <-> "OD2" Residue "A GLU 1070": "OE1" <-> "OE2" Residue "A GLU 1077": "OE1" <-> "OE2" Residue "A TYR 1115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1127": "NH1" <-> "NH2" Residue "A ARG 1148": "NH1" <-> "NH2" Residue "A PHE 1153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1197": "NH1" <-> "NH2" Residue "A ASP 1199": "OD1" <-> "OD2" Residue "A ARG 1206": "NH1" <-> "NH2" Residue "A TYR 1222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 13": "OD1" <-> "OD2" Residue "B ASP 28": "OD1" <-> "OD2" Residue "B TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 72": "OD1" <-> "OD2" Residue "B ASP 81": "OD1" <-> "OD2" Residue "B ARG 89": "NH1" <-> "NH2" Residue "B GLU 97": "OE1" <-> "OE2" Residue "B ASP 105": "OD1" <-> "OD2" Residue "B PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 118": "OD1" <-> "OD2" Residue "B GLU 126": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 7642 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 842, 6676 Classifications: {'peptide': 842} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 821} Chain breaks: 6 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 966 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Time building chain proxies: 4.22, per 1000 atoms: 0.55 Number of scatterers: 7642 At special positions: 0 Unit cell: (93.15, 78.57, 144.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1381 8.00 N 1269 7.00 C 4936 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: 3.15 Conformation dependent library (CDL) restraints added in 1.4 seconds 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1810 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 6 sheets defined 64.2% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 99 through 108 removed outlier: 3.585A pdb=" N ALA A 103 " --> pdb=" O ASN A 99 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N MET A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 136 removed outlier: 3.599A pdb=" N THR A 112 " --> pdb=" O CYS A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 163 Processing helix chain 'A' and resid 171 through 193 removed outlier: 4.020A pdb=" N GLN A 193 " --> pdb=" O ALA A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 236 Processing helix chain 'A' and resid 241 through 260 Processing helix chain 'A' and resid 279 through 336 removed outlier: 3.918A pdb=" N PHE A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 347 Processing helix chain 'A' and resid 402 through 407 Processing helix chain 'A' and resid 413 through 434 removed outlier: 3.796A pdb=" N GLU A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 481 removed outlier: 3.758A pdb=" N GLU A 479 " --> pdb=" O GLN A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 523 removed outlier: 3.781A pdb=" N ASN A 515 " --> pdb=" O SER A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 537 Processing helix chain 'A' and resid 784 through 808 removed outlier: 3.642A pdb=" N LEU A 788 " --> pdb=" O THR A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 844 removed outlier: 3.781A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 857 removed outlier: 3.543A pdb=" N ARG A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 860 No H-bonds generated for 'chain 'A' and resid 858 through 860' Processing helix chain 'A' and resid 861 through 885 removed outlier: 3.599A pdb=" N HIS A 866 " --> pdb=" O TRP A 862 " (cutoff:3.500A) Proline residue: A 876 - end of helix removed outlier: 4.058A pdb=" N HIS A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL A 884 " --> pdb=" O VAL A 880 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR A 885 " --> pdb=" O TYR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 908 removed outlier: 3.647A pdb=" N THR A 895 " --> pdb=" O ASN A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 911 No H-bonds generated for 'chain 'A' and resid 909 through 911' Processing helix chain 'A' and resid 917 through 936 Proline residue: A 931 - end of helix Processing helix chain 'A' and resid 978 through 1037 removed outlier: 4.222A pdb=" N ALA A1015 " --> pdb=" O GLY A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1048 removed outlier: 4.949A pdb=" N GLN A1044 " --> pdb=" O HIS A1040 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU A1045 " --> pdb=" O VAL A1041 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS A1046 " --> pdb=" O ALA A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1072 removed outlier: 4.071A pdb=" N GLU A1070 " --> pdb=" O VAL A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1098 Processing helix chain 'A' and resid 1099 through 1103 Processing helix chain 'A' and resid 1133 through 1157 removed outlier: 4.398A pdb=" N GLN A1137 " --> pdb=" O GLN A1133 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN A1156 " --> pdb=" O ASP A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1201 removed outlier: 4.373A pdb=" N ASN A1193 " --> pdb=" O GLY A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1219 Processing helix chain 'B' and resid 13 through 25 Processing helix chain 'B' and resid 26 through 36 Processing helix chain 'B' and resid 49 through 58 removed outlier: 3.549A pdb=" N PHE B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 70 Processing helix chain 'B' and resid 82 through 89 Processing helix chain 'B' and resid 92 through 102 removed outlier: 3.884A pdb=" N VAL B 98 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU B 99 " --> pdb=" O ILE B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 123 removed outlier: 3.993A pdb=" N LEU B 119 " --> pdb=" O THR B 115 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA B 120 " --> pdb=" O PRO B 116 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE B 121 " --> pdb=" O PHE B 117 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 135 removed outlier: 3.659A pdb=" N VAL B 131 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA B 135 " --> pdb=" O VAL B 131 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 388 through 391 Processing sheet with id=AA2, first strand: chain 'A' and resid 436 through 439 removed outlier: 4.907A pdb=" N LYS A 437 " --> pdb=" O VAL A 448 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N VAL A 448 " --> pdb=" O LYS A 437 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP A 399 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG A 487 " --> pdb=" O ASP A 399 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N HIS A 530 " --> pdb=" O MET A 486 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N VAL A 488 " --> pdb=" O HIS A 530 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N SER A 532 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1052 through 1055 Processing sheet with id=AA4, first strand: chain 'A' and resid 1064 through 1065 removed outlier: 3.749A pdb=" N ARG A1165 " --> pdb=" O SER A1064 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1106 through 1109 removed outlier: 6.949A pdb=" N MET A1116 " --> pdb=" O ILE A1108 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1208 through 1209 removed outlier: 3.585A pdb=" N TYR A1241 " --> pdb=" O VAL A1209 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LEU A1242 " --> pdb=" O TYR A1226 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N TYR A1226 " --> pdb=" O LEU A1242 " (cutoff:3.500A) 476 hydrogen bonds defined for protein. 1401 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.41 Time building geometry restraints manager: 3.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2433 1.34 - 1.46: 1600 1.46 - 1.58: 3684 1.58 - 1.69: 1 1.69 - 1.81: 88 Bond restraints: 7806 Sorted by residual: bond pdb=" CB TRP A 862 " pdb=" CG TRP A 862 " ideal model delta sigma weight residual 1.498 1.620 -0.122 3.10e-02 1.04e+03 1.56e+01 bond pdb=" CB PHE A 232 " pdb=" CG PHE A 232 " ideal model delta sigma weight residual 1.502 1.437 0.065 2.30e-02 1.89e+03 7.87e+00 bond pdb=" CB VAL A 907 " pdb=" CG2 VAL A 907 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.45e+00 bond pdb=" CB VAL A 986 " pdb=" CG1 VAL A 986 " ideal model delta sigma weight residual 1.521 1.439 0.082 3.30e-02 9.18e+02 6.18e+00 bond pdb=" CG1 ILE A 291 " pdb=" CD1 ILE A 291 " ideal model delta sigma weight residual 1.513 1.422 0.091 3.90e-02 6.57e+02 5.50e+00 ... (remaining 7801 not shown) Histogram of bond angle deviations from ideal: 97.63 - 105.18: 109 105.18 - 112.72: 4280 112.72 - 120.27: 3199 120.27 - 127.81: 2904 127.81 - 135.36: 71 Bond angle restraints: 10563 Sorted by residual: angle pdb=" CA TYR A1072 " pdb=" C TYR A1072 " pdb=" O TYR A1072 " ideal model delta sigma weight residual 119.49 113.57 5.92 1.21e+00 6.83e-01 2.39e+01 angle pdb=" N ASN A 356 " pdb=" CA ASN A 356 " pdb=" C ASN A 356 " ideal model delta sigma weight residual 114.31 108.05 6.26 1.29e+00 6.01e-01 2.35e+01 angle pdb=" C ASP A 344 " pdb=" N ASP A 345 " pdb=" CA ASP A 345 " ideal model delta sigma weight residual 120.38 126.61 -6.23 1.37e+00 5.33e-01 2.07e+01 angle pdb=" C SER A 813 " pdb=" N THR A 814 " pdb=" CA THR A 814 " ideal model delta sigma weight residual 120.69 107.60 13.09 2.95e+00 1.15e-01 1.97e+01 angle pdb=" CA LEU A 231 " pdb=" CB LEU A 231 " pdb=" CG LEU A 231 " ideal model delta sigma weight residual 116.30 102.68 13.62 3.50e+00 8.16e-02 1.51e+01 ... (remaining 10558 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 3969 17.11 - 34.23: 513 34.23 - 51.34: 89 51.34 - 68.46: 18 68.46 - 85.57: 6 Dihedral angle restraints: 4595 sinusoidal: 1788 harmonic: 2807 Sorted by residual: dihedral pdb=" CA PRO A 816 " pdb=" C PRO A 816 " pdb=" N PRO A 817 " pdb=" CA PRO A 817 " ideal model delta harmonic sigma weight residual -180.00 -152.46 -27.54 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA LEU A 978 " pdb=" C LEU A 978 " pdb=" N ILE A 979 " pdb=" CA ILE A 979 " ideal model delta harmonic sigma weight residual 180.00 152.68 27.32 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA GLU A1043 " pdb=" C GLU A1043 " pdb=" N GLN A1044 " pdb=" CA GLN A1044 " ideal model delta harmonic sigma weight residual -180.00 -154.54 -25.46 0 5.00e+00 4.00e-02 2.59e+01 ... (remaining 4592 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 672 0.036 - 0.072: 351 0.072 - 0.108: 144 0.108 - 0.144: 29 0.144 - 0.180: 13 Chirality restraints: 1209 Sorted by residual: chirality pdb=" CB ILE A1022 " pdb=" CA ILE A1022 " pdb=" CG1 ILE A1022 " pdb=" CG2 ILE A1022 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 8.10e-01 chirality pdb=" CA LEU A 875 " pdb=" N LEU A 875 " pdb=" C LEU A 875 " pdb=" CB LEU A 875 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.66e-01 chirality pdb=" CA PHE A 987 " pdb=" N PHE A 987 " pdb=" C PHE A 987 " pdb=" CB PHE A 987 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.53e-01 ... (remaining 1206 not shown) Planarity restraints: 1323 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 918 " 0.020 2.00e-02 2.50e+03 1.51e-02 5.67e+00 pdb=" CG TRP A 918 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP A 918 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 918 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 918 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 918 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 918 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 918 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 918 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 918 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 994 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.91e+00 pdb=" C VAL A 994 " 0.034 2.00e-02 2.50e+03 pdb=" O VAL A 994 " -0.013 2.00e-02 2.50e+03 pdb=" N TRP A 995 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 987 " -0.014 2.00e-02 2.50e+03 1.33e-02 3.09e+00 pdb=" CG PHE A 987 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE A 987 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 987 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 987 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 987 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 987 " -0.004 2.00e-02 2.50e+03 ... (remaining 1320 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 139 2.58 - 3.16: 7866 3.16 - 3.74: 13057 3.74 - 4.32: 17552 4.32 - 4.90: 26012 Nonbonded interactions: 64626 Sorted by model distance: nonbonded pdb=" O PHE A 912 " pdb=" NH1 ARG A 920 " model vdw 2.003 2.520 nonbonded pdb=" OH TYR A1226 " pdb=" OG1 THR A1229 " model vdw 2.098 2.440 nonbonded pdb=" O SER A 532 " pdb=" OG1 THR A 535 " model vdw 2.123 2.440 nonbonded pdb=" O PRO A1100 " pdb=" OG SER A1103 " model vdw 2.134 2.440 nonbonded pdb=" NE2 GLN A 389 " pdb=" OG1 THR A 494 " model vdw 2.154 2.520 ... (remaining 64621 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.590 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: 5.840 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 24.020 Find NCS groups from input model: 0.220 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: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 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 : 0.009 0.122 7806 Z= 0.586 Angle : 1.080 13.622 10563 Z= 0.612 Chirality : 0.051 0.180 1209 Planarity : 0.005 0.042 1323 Dihedral : 15.646 85.573 2785 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 34.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.22 % Favored : 88.78 % Rotamer: Outliers : 1.09 % Allowed : 13.82 % Favored : 85.09 % 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: -4.82 (0.20), residues: 954 helix: -2.69 (0.16), residues: 569 sheet: -4.06 (0.40), residues: 84 loop : -3.52 (0.29), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP A 918 HIS 0.009 0.002 HIS A 866 PHE 0.030 0.003 PHE A 987 TYR 0.018 0.003 TYR A1185 ARG 0.016 0.001 ARG A 920 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 193 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 MET cc_start: 0.8257 (mmt) cc_final: 0.7691 (mmt) REVERT: A 167 LEU cc_start: 0.8320 (tp) cc_final: 0.7928 (tt) REVERT: A 288 HIS cc_start: 0.7954 (m90) cc_final: 0.7671 (m90) REVERT: A 446 TYR cc_start: 0.7975 (p90) cc_final: 0.7669 (p90) REVERT: A 465 MET cc_start: 0.8638 (ttt) cc_final: 0.8263 (ttt) REVERT: A 793 LEU cc_start: 0.9331 (tp) cc_final: 0.9010 (tp) REVERT: A 798 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.8090 (t80) REVERT: A 1095 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8050 (mt-10) REVERT: A 1107 LYS cc_start: 0.8546 (ttpt) cc_final: 0.8069 (ttmt) REVERT: A 1115 TYR cc_start: 0.7761 (t80) cc_final: 0.6679 (t80) REVERT: A 1147 MET cc_start: 0.9248 (ttm) cc_final: 0.8775 (tmm) outliers start: 9 outliers final: 5 residues processed: 201 average time/residue: 0.1973 time to fit residues: 52.7889 Evaluate side-chains 161 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 155 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 29 optimal weight: 0.0270 chunk 45 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 overall best weight: 1.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 HIS A 319 HIS A 389 GLN A 883 HIS A1028 GLN A1075 ASN A1135 HIS ** A1137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1155 ASN B 107 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7806 Z= 0.236 Angle : 0.687 9.632 10563 Z= 0.353 Chirality : 0.042 0.185 1209 Planarity : 0.004 0.054 1323 Dihedral : 5.472 25.737 1036 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.24 % Allowed : 5.70 % Favored : 94.06 % 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: -2.41 (0.25), residues: 954 helix: -0.73 (0.19), residues: 588 sheet: -3.53 (0.44), residues: 88 loop : -2.53 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 918 HIS 0.008 0.001 HIS A 530 PHE 0.023 0.002 PHE A 912 TYR 0.016 0.002 TYR A 261 ARG 0.005 0.001 ARG A1165 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 214 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LEU cc_start: 0.8270 (tp) cc_final: 0.7811 (tt) REVERT: A 233 LEU cc_start: 0.9259 (mm) cc_final: 0.8957 (mm) REVERT: A 288 HIS cc_start: 0.7494 (m90) cc_final: 0.7077 (m90) REVERT: A 342 ILE cc_start: 0.9065 (tp) cc_final: 0.8729 (mt) REVERT: A 419 LEU cc_start: 0.9643 (tp) cc_final: 0.9241 (tp) REVERT: A 446 TYR cc_start: 0.7710 (p90) cc_final: 0.7467 (p90) REVERT: A 465 MET cc_start: 0.9106 (ttt) cc_final: 0.8665 (ttp) REVERT: A 1107 LYS cc_start: 0.8241 (ttpt) cc_final: 0.8000 (ttmt) REVERT: A 1147 MET cc_start: 0.9062 (ttm) cc_final: 0.8471 (tmm) REVERT: A 1149 VAL cc_start: 0.9247 (t) cc_final: 0.8937 (t) REVERT: A 1198 MET cc_start: 0.8259 (tpp) cc_final: 0.7757 (tpp) REVERT: B 78 TRP cc_start: 0.7638 (t-100) cc_final: 0.6905 (t-100) outliers start: 2 outliers final: 1 residues processed: 215 average time/residue: 0.1825 time to fit residues: 53.2704 Evaluate side-chains 173 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 172 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 59 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 87 optimal weight: 20.0000 chunk 94 optimal weight: 0.0770 chunk 77 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 overall best weight: 0.7344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 914 GLN A1154 ASN A1237 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7806 Z= 0.183 Angle : 0.644 9.466 10563 Z= 0.329 Chirality : 0.041 0.205 1209 Planarity : 0.004 0.046 1323 Dihedral : 4.984 24.762 1036 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.12 % Allowed : 4.73 % Favored : 95.15 % 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: -1.24 (0.27), residues: 954 helix: 0.23 (0.20), residues: 593 sheet: -3.00 (0.45), residues: 92 loop : -2.20 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1159 HIS 0.004 0.001 HIS A1170 PHE 0.047 0.002 PHE A 184 TYR 0.020 0.001 TYR A1083 ARG 0.004 0.000 ARG A1148 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 211 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LEU cc_start: 0.8285 (tp) cc_final: 0.7841 (tt) REVERT: A 445 TYR cc_start: 0.7565 (t80) cc_final: 0.7102 (t80) REVERT: A 465 MET cc_start: 0.9105 (ttt) cc_final: 0.8616 (ttp) REVERT: A 1085 VAL cc_start: 0.9478 (t) cc_final: 0.9236 (t) REVERT: A 1107 LYS cc_start: 0.8161 (ttpt) cc_final: 0.7706 (ttmt) REVERT: A 1115 TYR cc_start: 0.7418 (t80) cc_final: 0.6613 (t80) REVERT: A 1147 MET cc_start: 0.9022 (ttm) cc_final: 0.8423 (tmm) REVERT: A 1198 MET cc_start: 0.8131 (tpp) cc_final: 0.7664 (tpp) REVERT: B 29 GLU cc_start: 0.8997 (tm-30) cc_final: 0.8429 (pp20) outliers start: 1 outliers final: 1 residues processed: 211 average time/residue: 0.1798 time to fit residues: 52.1372 Evaluate side-chains 168 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 167 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 41 optimal weight: 0.0970 chunk 58 optimal weight: 0.9990 chunk 87 optimal weight: 20.0000 chunk 92 optimal weight: 20.0000 chunk 83 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 77 optimal weight: 0.0770 overall best weight: 0.6342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 GLN ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7806 Z= 0.169 Angle : 0.624 9.511 10563 Z= 0.314 Chirality : 0.040 0.185 1209 Planarity : 0.004 0.039 1323 Dihedral : 4.680 23.828 1036 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % 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: -0.74 (0.27), residues: 954 helix: 0.61 (0.21), residues: 592 sheet: -2.80 (0.46), residues: 93 loop : -1.97 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1159 HIS 0.008 0.001 HIS A 297 PHE 0.049 0.002 PHE A 184 TYR 0.019 0.001 TYR A1083 ARG 0.003 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 CYS cc_start: 0.8859 (m) cc_final: 0.8351 (p) REVERT: A 167 LEU cc_start: 0.8311 (tp) cc_final: 0.7930 (tt) REVERT: A 446 TYR cc_start: 0.7641 (p90) cc_final: 0.7379 (p90) REVERT: A 465 MET cc_start: 0.9119 (ttt) cc_final: 0.8504 (ttp) REVERT: A 1025 MET cc_start: 0.7997 (tpp) cc_final: 0.7690 (tpp) REVERT: A 1107 LYS cc_start: 0.8099 (ttpt) cc_final: 0.7613 (ttmt) REVERT: A 1115 TYR cc_start: 0.7420 (t80) cc_final: 0.6437 (t80) REVERT: A 1147 MET cc_start: 0.9045 (ttm) cc_final: 0.8504 (tmm) REVERT: A 1148 ARG cc_start: 0.9182 (ptp-110) cc_final: 0.8820 (ptp90) REVERT: A 1198 MET cc_start: 0.7980 (tpp) cc_final: 0.7655 (tpp) REVERT: B 29 GLU cc_start: 0.8982 (tm-30) cc_final: 0.8469 (pp20) REVERT: B 34 MET cc_start: 0.7325 (mtp) cc_final: 0.7074 (mmm) REVERT: B 81 ASP cc_start: 0.8272 (m-30) cc_final: 0.8068 (m-30) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.1738 time to fit residues: 50.4765 Evaluate side-chains 172 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 69 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 64 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 23 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 914 GLN ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 7806 Z= 0.287 Angle : 0.728 9.983 10563 Z= 0.367 Chirality : 0.044 0.175 1209 Planarity : 0.004 0.039 1323 Dihedral : 4.911 21.569 1036 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 19.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.27), residues: 954 helix: 0.29 (0.20), residues: 595 sheet: -2.73 (0.45), residues: 98 loop : -2.12 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 995 HIS 0.012 0.001 HIS A 297 PHE 0.042 0.003 PHE A 184 TYR 0.018 0.002 TYR A1083 ARG 0.003 0.000 ARG A 808 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LEU cc_start: 0.8353 (tp) cc_final: 0.7872 (tt) REVERT: A 446 TYR cc_start: 0.7837 (p90) cc_final: 0.7483 (p90) REVERT: A 465 MET cc_start: 0.9129 (ttt) cc_final: 0.8614 (ttp) REVERT: A 1083 TYR cc_start: 0.8440 (m-80) cc_final: 0.8146 (m-10) REVERT: A 1088 GLU cc_start: 0.8941 (pt0) cc_final: 0.8670 (pt0) REVERT: A 1107 LYS cc_start: 0.8241 (ttpt) cc_final: 0.7898 (ttmt) REVERT: A 1147 MET cc_start: 0.9079 (ttm) cc_final: 0.8615 (tmm) REVERT: A 1148 ARG cc_start: 0.9193 (ptp-110) cc_final: 0.8885 (ptp-170) REVERT: A 1198 MET cc_start: 0.8276 (tpp) cc_final: 0.7941 (tpp) REVERT: B 29 GLU cc_start: 0.9036 (tm-30) cc_final: 0.8665 (pp20) REVERT: B 34 MET cc_start: 0.7417 (mtp) cc_final: 0.6812 (mmm) REVERT: B 78 TRP cc_start: 0.7521 (t-100) cc_final: 0.6870 (t-100) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.1776 time to fit residues: 48.0295 Evaluate side-chains 156 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 chunk 92 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7806 Z= 0.213 Angle : 0.675 9.660 10563 Z= 0.339 Chirality : 0.043 0.211 1209 Planarity : 0.004 0.040 1323 Dihedral : 4.799 21.108 1036 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % 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: -0.82 (0.27), residues: 954 helix: 0.50 (0.20), residues: 595 sheet: -2.65 (0.47), residues: 95 loop : -1.97 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 995 HIS 0.010 0.001 HIS A 297 PHE 0.047 0.002 PHE A 184 TYR 0.023 0.002 TYR A1083 ARG 0.002 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LEU cc_start: 0.8359 (tp) cc_final: 0.7891 (tt) REVERT: A 446 TYR cc_start: 0.7780 (p90) cc_final: 0.7422 (p90) REVERT: A 465 MET cc_start: 0.9132 (ttt) cc_final: 0.8528 (ttp) REVERT: A 1083 TYR cc_start: 0.8422 (m-80) cc_final: 0.8130 (m-80) REVERT: A 1107 LYS cc_start: 0.8139 (ttpt) cc_final: 0.7611 (ttmt) REVERT: A 1115 TYR cc_start: 0.7539 (t80) cc_final: 0.6764 (t80) REVERT: A 1142 PHE cc_start: 0.9177 (t80) cc_final: 0.8887 (t80) REVERT: A 1147 MET cc_start: 0.9098 (ttm) cc_final: 0.8591 (tmm) REVERT: A 1148 ARG cc_start: 0.9174 (ptp-110) cc_final: 0.8827 (ptp90) REVERT: A 1198 MET cc_start: 0.8233 (tpp) cc_final: 0.7950 (tpp) REVERT: B 29 GLU cc_start: 0.9085 (tm-30) cc_final: 0.8747 (pp20) REVERT: B 34 MET cc_start: 0.7476 (mtp) cc_final: 0.6910 (mmm) REVERT: B 78 TRP cc_start: 0.7468 (t-100) cc_final: 0.6667 (t-100) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.1748 time to fit residues: 47.7534 Evaluate side-chains 161 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 GLN ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7806 Z= 0.183 Angle : 0.665 10.355 10563 Z= 0.331 Chirality : 0.042 0.212 1209 Planarity : 0.004 0.039 1323 Dihedral : 4.647 21.158 1036 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % 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: -0.60 (0.27), residues: 954 helix: 0.65 (0.21), residues: 596 sheet: -2.48 (0.48), residues: 88 loop : -1.90 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1159 HIS 0.008 0.001 HIS A 297 PHE 0.045 0.002 PHE A 184 TYR 0.019 0.001 TYR A1083 ARG 0.004 0.000 ARG A 340 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 CYS cc_start: 0.8939 (m) cc_final: 0.8393 (p) REVERT: A 167 LEU cc_start: 0.8364 (tp) cc_final: 0.7926 (tt) REVERT: A 446 TYR cc_start: 0.7761 (p90) cc_final: 0.7412 (p90) REVERT: A 465 MET cc_start: 0.9108 (ttt) cc_final: 0.8534 (ttp) REVERT: A 486 MET cc_start: 0.8251 (tpt) cc_final: 0.8020 (tpt) REVERT: A 875 LEU cc_start: 0.8304 (pp) cc_final: 0.7984 (pp) REVERT: A 1025 MET cc_start: 0.7848 (tpp) cc_final: 0.7204 (tpp) REVERT: A 1083 TYR cc_start: 0.8390 (m-80) cc_final: 0.8160 (m-80) REVERT: A 1088 GLU cc_start: 0.9122 (mt-10) cc_final: 0.8756 (pt0) REVERT: A 1107 LYS cc_start: 0.8090 (ttpt) cc_final: 0.7763 (ttmt) REVERT: A 1147 MET cc_start: 0.9084 (ttm) cc_final: 0.8574 (tmm) REVERT: A 1148 ARG cc_start: 0.9160 (ptp-110) cc_final: 0.8848 (ptp-170) REVERT: B 34 MET cc_start: 0.7705 (mtp) cc_final: 0.7192 (mmm) REVERT: B 78 TRP cc_start: 0.7206 (t-100) cc_final: 0.6708 (t-100) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.1711 time to fit residues: 49.1085 Evaluate side-chains 160 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 GLN B 92 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7806 Z= 0.201 Angle : 0.680 10.001 10563 Z= 0.342 Chirality : 0.043 0.192 1209 Planarity : 0.004 0.040 1323 Dihedral : 4.675 21.214 1036 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.68 (0.27), residues: 954 helix: 0.60 (0.21), residues: 594 sheet: -2.37 (0.47), residues: 99 loop : -1.93 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 995 HIS 0.012 0.001 HIS A 297 PHE 0.028 0.002 PHE A 184 TYR 0.019 0.002 TYR A1083 ARG 0.003 0.000 ARG A1197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 CYS cc_start: 0.9007 (m) cc_final: 0.8464 (p) REVERT: A 167 LEU cc_start: 0.8323 (tp) cc_final: 0.7874 (tt) REVERT: A 335 HIS cc_start: 0.7480 (m170) cc_final: 0.7271 (m170) REVERT: A 465 MET cc_start: 0.9140 (ttt) cc_final: 0.8715 (ttp) REVERT: A 1025 MET cc_start: 0.7879 (tpp) cc_final: 0.7167 (tpp) REVERT: A 1083 TYR cc_start: 0.8430 (m-80) cc_final: 0.8197 (m-80) REVERT: A 1088 GLU cc_start: 0.9179 (mt-10) cc_final: 0.8857 (pt0) REVERT: A 1107 LYS cc_start: 0.8095 (ttpt) cc_final: 0.7775 (ttmt) REVERT: A 1142 PHE cc_start: 0.9223 (t80) cc_final: 0.8755 (t80) REVERT: A 1147 MET cc_start: 0.9112 (ttm) cc_final: 0.8515 (tmm) REVERT: A 1148 ARG cc_start: 0.9157 (ptp-110) cc_final: 0.8831 (ptp-170) REVERT: B 20 GLU cc_start: 0.9321 (pm20) cc_final: 0.9120 (pm20) REVERT: B 23 ARG cc_start: 0.9366 (ttp-110) cc_final: 0.9031 (ttt180) REVERT: B 32 ILE cc_start: 0.9462 (mt) cc_final: 0.9223 (mt) REVERT: B 34 MET cc_start: 0.7771 (mtp) cc_final: 0.7177 (mmm) REVERT: B 78 TRP cc_start: 0.7170 (t-100) cc_final: 0.6766 (t-100) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.1676 time to fit residues: 46.2032 Evaluate side-chains 153 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 20.0000 chunk 88 optimal weight: 10.0000 chunk 51 optimal weight: 0.2980 chunk 37 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 81 optimal weight: 0.2980 chunk 85 optimal weight: 8.9990 chunk 56 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 GLN ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7806 Z= 0.223 Angle : 0.694 9.940 10563 Z= 0.350 Chirality : 0.044 0.192 1209 Planarity : 0.004 0.040 1323 Dihedral : 4.719 21.720 1036 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.27), residues: 954 helix: 0.61 (0.21), residues: 594 sheet: -2.32 (0.46), residues: 103 loop : -1.83 (0.40), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 918 HIS 0.012 0.001 HIS A 297 PHE 0.051 0.002 PHE A 184 TYR 0.029 0.002 TYR A 909 ARG 0.003 0.000 ARG A 340 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 CYS cc_start: 0.8993 (m) cc_final: 0.8413 (p) REVERT: A 167 LEU cc_start: 0.8349 (tp) cc_final: 0.7893 (tt) REVERT: A 465 MET cc_start: 0.9172 (ttt) cc_final: 0.8520 (ttp) REVERT: A 505 PHE cc_start: 0.9214 (p90) cc_final: 0.8813 (p90) REVERT: A 875 LEU cc_start: 0.8401 (pp) cc_final: 0.8110 (pp) REVERT: A 1083 TYR cc_start: 0.8457 (m-80) cc_final: 0.8220 (m-80) REVERT: A 1088 GLU cc_start: 0.9195 (mt-10) cc_final: 0.8714 (mt-10) REVERT: A 1107 LYS cc_start: 0.8113 (ttpt) cc_final: 0.7771 (ttmt) REVERT: A 1148 ARG cc_start: 0.9136 (ptp-110) cc_final: 0.8880 (ptp-110) REVERT: B 34 MET cc_start: 0.7699 (mtp) cc_final: 0.6591 (mmm) REVERT: B 78 TRP cc_start: 0.7214 (t-100) cc_final: 0.6691 (t-100) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.1707 time to fit residues: 46.8646 Evaluate side-chains 152 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 63 optimal weight: 0.1980 chunk 95 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 60 optimal weight: 0.4980 chunk 81 optimal weight: 10.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 GLN A1170 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.5225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7806 Z= 0.199 Angle : 0.687 9.592 10563 Z= 0.341 Chirality : 0.043 0.213 1209 Planarity : 0.004 0.048 1323 Dihedral : 4.640 21.781 1036 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % 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 (0.27), residues: 954 helix: 0.70 (0.21), residues: 594 sheet: -2.18 (0.50), residues: 91 loop : -1.84 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 918 HIS 0.010 0.001 HIS A 297 PHE 0.038 0.002 PHE A 184 TYR 0.041 0.002 TYR A 909 ARG 0.003 0.000 ARG A 340 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 CYS cc_start: 0.8958 (m) cc_final: 0.8338 (p) REVERT: A 167 LEU cc_start: 0.8327 (tp) cc_final: 0.7877 (tt) REVERT: A 446 TYR cc_start: 0.7555 (p90) cc_final: 0.7290 (p90) REVERT: A 465 MET cc_start: 0.9151 (ttt) cc_final: 0.8746 (ttp) REVERT: A 505 PHE cc_start: 0.9175 (p90) cc_final: 0.8756 (p90) REVERT: A 1083 TYR cc_start: 0.8458 (m-80) cc_final: 0.8216 (m-80) REVERT: A 1088 GLU cc_start: 0.9224 (mt-10) cc_final: 0.8785 (mt-10) REVERT: A 1090 ILE cc_start: 0.9204 (mt) cc_final: 0.8960 (mt) REVERT: A 1107 LYS cc_start: 0.8045 (ttpt) cc_final: 0.7535 (ttmt) REVERT: A 1115 TYR cc_start: 0.7466 (t80) cc_final: 0.6624 (t80) REVERT: A 1148 ARG cc_start: 0.9137 (ptp-110) cc_final: 0.8886 (ptp-170) REVERT: B 23 ARG cc_start: 0.9178 (ttp-110) cc_final: 0.8843 (ttt180) REVERT: B 34 MET cc_start: 0.7763 (mtp) cc_final: 0.6696 (mmm) REVERT: B 78 TRP cc_start: 0.7171 (t-100) cc_final: 0.6735 (t-100) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.1664 time to fit residues: 45.1006 Evaluate side-chains 152 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 8.9990 chunk 70 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 7.9990 chunk 76 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.132374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.092261 restraints weight = 19918.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.094534 restraints weight = 12249.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.096124 restraints weight = 8638.185| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.5213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7806 Z= 0.230 Angle : 0.705 9.960 10563 Z= 0.356 Chirality : 0.044 0.184 1209 Planarity : 0.004 0.042 1323 Dihedral : 4.686 22.393 1036 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % 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 (0.27), residues: 954 helix: 0.69 (0.21), residues: 591 sheet: -2.28 (0.50), residues: 91 loop : -1.82 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 56 HIS 0.012 0.001 HIS A 297 PHE 0.027 0.002 PHE A 184 TYR 0.030 0.002 TYR A 909 ARG 0.006 0.000 ARG B 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1952.78 seconds wall clock time: 37 minutes 9.30 seconds (2229.30 seconds total)