Starting phenix.real_space_refine on Wed Mar 12 15:27:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dya_27779/03_2025/8dya_27779.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dya_27779/03_2025/8dya_27779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dya_27779/03_2025/8dya_27779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dya_27779/03_2025/8dya_27779.map" model { file = "/net/cci-nas-00/data/ceres_data/8dya_27779/03_2025/8dya_27779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dya_27779/03_2025/8dya_27779.cif" } resolution = 3.67 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= 0.082 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 36 5.16 5 C 5034 2.51 5 N 1368 2.21 5 O 1458 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7896 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2548 Classifications: {'peptide': 388} Incomplete info: {'truncation_to_alanine': 159} Link IDs: {'PTRANS': 20, 'TRANS': 367} Chain breaks: 4 Unresolved non-hydrogen bonds: 468 Unresolved non-hydrogen angles: 592 Unresolved non-hydrogen dihedrals: 355 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 9, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 227 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Restraints were copied for chains: C, B Time building chain proxies: 4.71, per 1000 atoms: 0.60 Number of scatterers: 7896 At special positions: 0 Unit cell: (87, 94, 138, 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 36 16.00 O 1458 8.00 N 1368 7.00 C 5034 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 707 " - pdb=" SG CYS B 883 " distance=2.00 Simple disulfide: pdb=" SG CYS A 883 " - pdb=" SG CYS C 707 " distance=1.99 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.15 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 707 " - pdb=" SG CYS C 883 " distance=2.00 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.16 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.15 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 801 " " NAG A1302 " - " ASN A1134 " " NAG A1303 " - " ASN A1098 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A1074 " " NAG A1306 " - " ASN A 717 " " NAG B1301 " - " ASN B 801 " " NAG B1302 " - " ASN B1134 " " NAG B1303 " - " ASN B1098 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B1074 " " NAG B1306 " - " ASN B 717 " " NAG C1301 " - " ASN C 801 " " NAG C1302 " - " ASN C1134 " " NAG C1303 " - " ASN C1098 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C 717 " Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 1.1 seconds 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2196 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 12 sheets defined 48.2% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 752 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 898 through 908 removed outlier: 3.777A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 919 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.622A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 965 removed outlier: 3.603A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 982 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.801A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1141 through 1149 Processing helix chain 'B' and resid 752 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 898 through 908 removed outlier: 3.776A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 919 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.622A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 965 removed outlier: 3.603A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 982 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.801A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1141 through 1149 Processing helix chain 'C' and resid 752 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 898 through 908 removed outlier: 3.777A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 919 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.621A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 965 removed outlier: 3.602A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 982 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.800A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1141 through 1149 Processing sheet with id=AA1, first strand: chain 'A' and resid 711 through 715 removed outlier: 4.524A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.395A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AA4, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.419A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 711 through 715 removed outlier: 4.524A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.395A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AA8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.419A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 711 through 715 removed outlier: 4.524A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.394A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AB3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.419A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 516 hydrogen bonds defined for protein. 1512 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: 2.07 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1828 1.33 - 1.45: 1965 1.45 - 1.58: 4202 1.58 - 1.71: 6 1.71 - 1.83: 54 Bond restraints: 8055 Sorted by residual: bond pdb=" CA GLN A 804 " pdb=" C GLN A 804 " ideal model delta sigma weight residual 1.523 1.600 -0.077 1.34e-02 5.57e+03 3.29e+01 bond pdb=" CA GLN B 804 " pdb=" C GLN B 804 " ideal model delta sigma weight residual 1.523 1.600 -0.077 1.34e-02 5.57e+03 3.26e+01 bond pdb=" CA GLN C 804 " pdb=" C GLN C 804 " ideal model delta sigma weight residual 1.523 1.600 -0.077 1.34e-02 5.57e+03 3.26e+01 bond pdb=" CA PHE C 817 " pdb=" C PHE C 817 " ideal model delta sigma weight residual 1.523 1.588 -0.065 1.30e-02 5.92e+03 2.50e+01 bond pdb=" CA PHE B 817 " pdb=" C PHE B 817 " ideal model delta sigma weight residual 1.523 1.588 -0.065 1.30e-02 5.92e+03 2.50e+01 ... (remaining 8050 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.23: 10829 4.23 - 8.46: 220 8.46 - 12.69: 18 12.69 - 16.92: 3 16.92 - 21.15: 6 Bond angle restraints: 11076 Sorted by residual: angle pdb=" N ALA C 956 " pdb=" CA ALA C 956 " pdb=" C ALA C 956 " ideal model delta sigma weight residual 111.28 100.80 10.48 1.09e+00 8.42e-01 9.25e+01 angle pdb=" CD1 LEU B 922 " pdb=" CG LEU B 922 " pdb=" CD2 LEU B 922 " ideal model delta sigma weight residual 110.80 131.95 -21.15 2.20e+00 2.07e-01 9.24e+01 angle pdb=" CD1 LEU A 922 " pdb=" CG LEU A 922 " pdb=" CD2 LEU A 922 " ideal model delta sigma weight residual 110.80 131.92 -21.12 2.20e+00 2.07e-01 9.21e+01 angle pdb=" N ALA A 956 " pdb=" CA ALA A 956 " pdb=" C ALA A 956 " ideal model delta sigma weight residual 111.28 100.82 10.46 1.09e+00 8.42e-01 9.20e+01 angle pdb=" CD1 LEU C 922 " pdb=" CG LEU C 922 " pdb=" CD2 LEU C 922 " ideal model delta sigma weight residual 110.80 131.85 -21.05 2.20e+00 2.07e-01 9.16e+01 ... (remaining 11071 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 4755 17.80 - 35.59: 157 35.59 - 53.38: 23 53.38 - 71.18: 6 71.18 - 88.97: 6 Dihedral angle restraints: 4947 sinusoidal: 1575 harmonic: 3372 Sorted by residual: dihedral pdb=" N ILE B 805 " pdb=" C ILE B 805 " pdb=" CA ILE B 805 " pdb=" CB ILE B 805 " ideal model delta harmonic sigma weight residual 123.40 137.30 -13.90 0 2.50e+00 1.60e-01 3.09e+01 dihedral pdb=" N ILE A 805 " pdb=" C ILE A 805 " pdb=" CA ILE A 805 " pdb=" CB ILE A 805 " ideal model delta harmonic sigma weight residual 123.40 137.27 -13.87 0 2.50e+00 1.60e-01 3.08e+01 dihedral pdb=" N ILE C 805 " pdb=" C ILE C 805 " pdb=" CA ILE C 805 " pdb=" CB ILE C 805 " ideal model delta harmonic sigma weight residual 123.40 137.21 -13.81 0 2.50e+00 1.60e-01 3.05e+01 ... (remaining 4944 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 1233 0.147 - 0.294: 114 0.294 - 0.440: 26 0.440 - 0.587: 1 0.587 - 0.734: 3 Chirality restraints: 1377 Sorted by residual: chirality pdb=" C1 NAG A1306 " pdb=" ND2 ASN A 717 " pdb=" C2 NAG A1306 " pdb=" O5 NAG A1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.67 -0.73 2.00e-01 2.50e+01 1.35e+01 chirality pdb=" C1 NAG C1306 " pdb=" ND2 ASN C 717 " pdb=" C2 NAG C1306 " pdb=" O5 NAG C1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.67 -0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" C1 NAG B1306 " pdb=" ND2 ASN B 717 " pdb=" C2 NAG B1306 " pdb=" O5 NAG B1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.67 -0.73 2.00e-01 2.50e+01 1.34e+01 ... (remaining 1374 not shown) Planarity restraints: 1482 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 817 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.03e+00 pdb=" C PHE B 817 " 0.042 2.00e-02 2.50e+03 pdb=" O PHE B 817 " -0.017 2.00e-02 2.50e+03 pdb=" N ILE B 818 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 817 " 0.012 2.00e-02 2.50e+03 2.45e-02 6.01e+00 pdb=" C PHE C 817 " -0.042 2.00e-02 2.50e+03 pdb=" O PHE C 817 " 0.017 2.00e-02 2.50e+03 pdb=" N ILE C 818 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 817 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.96e+00 pdb=" C PHE A 817 " -0.042 2.00e-02 2.50e+03 pdb=" O PHE A 817 " 0.017 2.00e-02 2.50e+03 pdb=" N ILE A 818 " 0.014 2.00e-02 2.50e+03 ... (remaining 1479 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.01: 4257 3.01 - 3.48: 7691 3.48 - 3.95: 12087 3.95 - 4.43: 13300 4.43 - 4.90: 21267 Nonbonded interactions: 58602 Sorted by model distance: nonbonded pdb=" NZ LYS C 733 " pdb=" OD2 ASP C 775 " model vdw 2.532 3.120 nonbonded pdb=" NZ LYS B 733 " pdb=" OD2 ASP B 775 " model vdw 2.533 3.120 nonbonded pdb=" NZ LYS A 733 " pdb=" OD2 ASP A 775 " model vdw 2.533 3.120 nonbonded pdb=" N ASP C 775 " pdb=" N LYS C 776 " model vdw 2.537 2.560 nonbonded pdb=" N ASP A 775 " pdb=" N LYS A 776 " model vdw 2.537 2.560 ... (remaining 58597 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.830 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6254 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 : 0.010 0.077 8055 Z= 0.677 Angle : 1.493 21.149 11076 Z= 1.004 Chirality : 0.095 0.734 1377 Planarity : 0.005 0.025 1464 Dihedral : 9.995 88.972 2724 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.53 % Allowed : 3.88 % Favored : 95.59 % Rotamer: Outliers : 0.56 % Allowed : 0.56 % Favored : 98.88 % Cbeta Deviations : 0.27 % 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: 0.63 (0.22), residues: 1134 helix: 1.64 (0.20), residues: 501 sheet: 1.32 (0.36), residues: 129 loop : -1.13 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.004 TRP C 886 HIS 0.004 0.001 HIS B1083 PHE 0.013 0.003 PHE C 906 TYR 0.013 0.003 TYR B1067 ARG 0.003 0.001 ARG B 905 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 157 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 801 ASN cc_start: 0.7346 (t0) cc_final: 0.6963 (t0) REVERT: C 1027 THR cc_start: 0.7695 (m) cc_final: 0.7475 (m) outliers start: 3 outliers final: 0 residues processed: 158 average time/residue: 0.1801 time to fit residues: 39.2736 Evaluate side-chains 76 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 0.2980 chunk 58 optimal weight: 9.9990 chunk 46 optimal weight: 0.5980 chunk 89 optimal weight: 0.5980 chunk 34 optimal weight: 0.0980 chunk 54 optimal weight: 0.5980 chunk 66 optimal weight: 0.0870 chunk 103 optimal weight: 0.7980 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1011 GLN B1106 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.210834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.199464 restraints weight = 8980.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.173915 restraints weight = 13868.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.174628 restraints weight = 12646.585| |-----------------------------------------------------------------------------| r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8055 Z= 0.194 Angle : 0.560 6.514 11076 Z= 0.296 Chirality : 0.045 0.359 1377 Planarity : 0.005 0.053 1464 Dihedral : 5.649 51.572 1569 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.03 % Favored : 97.71 % Rotamer: Outliers : 1.86 % Allowed : 8.01 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.24), residues: 1134 helix: 2.99 (0.21), residues: 522 sheet: 0.85 (0.38), residues: 144 loop : -1.24 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1102 HIS 0.005 0.001 HIS A1064 PHE 0.013 0.001 PHE C 782 TYR 0.016 0.002 TYR C1067 ARG 0.003 0.001 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 902 MET cc_start: 0.6971 (mmm) cc_final: 0.6307 (tpt) REVERT: C 1027 THR cc_start: 0.7482 (m) cc_final: 0.7162 (p) outliers start: 10 outliers final: 6 residues processed: 86 average time/residue: 0.1800 time to fit residues: 22.1680 Evaluate side-chains 76 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 85 optimal weight: 0.0370 chunk 43 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 112 optimal weight: 5.9990 chunk 8 optimal weight: 0.0020 chunk 2 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 overall best weight: 0.5266 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 928 ASN B1119 ASN C1119 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.200618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.189776 restraints weight = 9277.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.188534 restraints weight = 15427.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.187346 restraints weight = 15994.874| |-----------------------------------------------------------------------------| r_work (final): 0.4204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8055 Z= 0.204 Angle : 0.532 6.866 11076 Z= 0.274 Chirality : 0.044 0.227 1377 Planarity : 0.004 0.033 1464 Dihedral : 4.408 29.782 1569 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.00 % Favored : 96.74 % Rotamer: Outliers : 2.61 % Allowed : 10.24 % Favored : 87.15 % 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: 1.98 (0.24), residues: 1134 helix: 3.46 (0.21), residues: 522 sheet: 1.24 (0.45), residues: 108 loop : -1.13 (0.24), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1102 HIS 0.004 0.001 HIS A1064 PHE 0.018 0.002 PHE C 906 TYR 0.018 0.002 TYR C1067 ARG 0.006 0.001 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 822 LEU cc_start: 0.6583 (mt) cc_final: 0.6336 (tp) REVERT: B 902 MET cc_start: 0.7271 (mmm) cc_final: 0.6438 (tpt) REVERT: C 805 ILE cc_start: 0.6225 (OUTLIER) cc_final: 0.5971 (pt) outliers start: 14 outliers final: 10 residues processed: 81 average time/residue: 0.1796 time to fit residues: 20.7689 Evaluate side-chains 76 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 74 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 105 optimal weight: 0.0170 chunk 58 optimal weight: 9.9990 chunk 32 optimal weight: 0.4980 chunk 15 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 11 optimal weight: 0.0000 chunk 20 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.3822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.200675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.190074 restraints weight = 9210.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.188760 restraints weight = 15896.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.187502 restraints weight = 16863.449| |-----------------------------------------------------------------------------| r_work (final): 0.4204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8055 Z= 0.153 Angle : 0.480 6.673 11076 Z= 0.246 Chirality : 0.042 0.199 1377 Planarity : 0.004 0.026 1464 Dihedral : 4.159 36.758 1569 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.00 % Favored : 96.74 % Rotamer: Outliers : 3.54 % Allowed : 12.29 % Favored : 84.17 % 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: 2.09 (0.24), residues: 1134 helix: 3.62 (0.21), residues: 519 sheet: 1.09 (0.45), residues: 108 loop : -1.08 (0.24), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B1102 HIS 0.003 0.001 HIS C1101 PHE 0.011 0.001 PHE B 823 TYR 0.020 0.001 TYR C1067 ARG 0.002 0.000 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.7601 (mtm) REVERT: B 822 LEU cc_start: 0.6656 (mt) cc_final: 0.6393 (tp) REVERT: C 805 ILE cc_start: 0.5810 (OUTLIER) cc_final: 0.5594 (pt) REVERT: C 902 MET cc_start: 0.7252 (tpp) cc_final: 0.6909 (tpt) outliers start: 19 outliers final: 13 residues processed: 82 average time/residue: 0.1662 time to fit residues: 19.9214 Evaluate side-chains 83 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 100 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 11 optimal weight: 0.0070 chunk 84 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1023 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.177279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.140660 restraints weight = 8620.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.143205 restraints weight = 6434.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.145068 restraints weight = 5294.291| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8055 Z= 0.273 Angle : 0.558 6.285 11076 Z= 0.285 Chirality : 0.045 0.230 1377 Planarity : 0.004 0.027 1464 Dihedral : 4.765 39.444 1569 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.70 % Favored : 96.03 % Rotamer: Outliers : 3.91 % Allowed : 12.29 % Favored : 83.80 % 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: 1.80 (0.24), residues: 1134 helix: 3.42 (0.21), residues: 525 sheet: -0.04 (0.38), residues: 144 loop : -1.14 (0.25), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B1102 HIS 0.005 0.001 HIS C1064 PHE 0.018 0.002 PHE A 906 TYR 0.022 0.002 TYR C1067 ARG 0.004 0.001 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 779 GLN cc_start: 0.8021 (tt0) cc_final: 0.7779 (mm-40) REVERT: C 794 ILE cc_start: 0.5938 (mt) cc_final: 0.5727 (mt) outliers start: 21 outliers final: 15 residues processed: 91 average time/residue: 0.1979 time to fit residues: 24.9757 Evaluate side-chains 84 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 707 CYS Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 63 optimal weight: 6.9990 chunk 75 optimal weight: 0.4980 chunk 105 optimal weight: 0.0870 chunk 7 optimal weight: 0.0030 chunk 76 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 9 optimal weight: 0.3980 chunk 28 optimal weight: 2.9990 overall best weight: 0.3568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.181195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.143624 restraints weight = 8530.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.146514 restraints weight = 6176.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.148560 restraints weight = 4987.092| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8055 Z= 0.154 Angle : 0.491 6.481 11076 Z= 0.250 Chirality : 0.042 0.206 1377 Planarity : 0.003 0.026 1464 Dihedral : 4.390 38.013 1569 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.65 % Favored : 97.09 % Rotamer: Outliers : 3.54 % Allowed : 12.85 % Favored : 83.61 % 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: 1.98 (0.24), residues: 1134 helix: 3.49 (0.21), residues: 525 sheet: 0.47 (0.45), residues: 114 loop : -1.01 (0.24), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B1102 HIS 0.003 0.000 HIS C1101 PHE 0.010 0.001 PHE B1121 TYR 0.020 0.001 TYR C1067 ARG 0.001 0.000 ARG C 815 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1011 GLN cc_start: 0.8878 (mm-40) cc_final: 0.8563 (mm-40) outliers start: 19 outliers final: 14 residues processed: 81 average time/residue: 0.2650 time to fit residues: 29.8764 Evaluate side-chains 82 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 707 CYS Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 707 CYS Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 6 optimal weight: 0.4980 chunk 70 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 59 optimal weight: 30.0000 chunk 99 optimal weight: 6.9990 chunk 106 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 60 optimal weight: 50.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1088 HIS C1088 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.177872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.130876 restraints weight = 8971.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.134303 restraints weight = 6455.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.136388 restraints weight = 5237.495| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8055 Z= 0.227 Angle : 0.538 13.085 11076 Z= 0.269 Chirality : 0.044 0.216 1377 Planarity : 0.003 0.028 1464 Dihedral : 4.568 38.716 1569 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.26 % Favored : 96.47 % Rotamer: Outliers : 2.61 % Allowed : 13.22 % Favored : 84.17 % 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: 1.68 (0.24), residues: 1134 helix: 3.42 (0.21), residues: 507 sheet: -0.13 (0.38), residues: 144 loop : -1.12 (0.25), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B1102 HIS 0.003 0.001 HIS C1064 PHE 0.013 0.001 PHE C1121 TYR 0.020 0.001 TYR C1067 ARG 0.003 0.001 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.6248 (mmm) cc_final: 0.5978 (mtp) outliers start: 14 outliers final: 14 residues processed: 81 average time/residue: 0.2106 time to fit residues: 23.6812 Evaluate side-chains 83 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 1 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 76 optimal weight: 0.3980 chunk 37 optimal weight: 0.0170 chunk 14 optimal weight: 0.6980 chunk 98 optimal weight: 50.0000 chunk 4 optimal weight: 40.0000 chunk 28 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 104 optimal weight: 0.3980 chunk 113 optimal weight: 0.1980 overall best weight: 0.3418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 804 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.180776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.133230 restraints weight = 8927.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.138051 restraints weight = 6105.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.139241 restraints weight = 4549.834| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.5261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8055 Z= 0.151 Angle : 0.518 14.024 11076 Z= 0.254 Chirality : 0.042 0.202 1377 Planarity : 0.003 0.027 1464 Dihedral : 4.267 36.845 1569 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.56 % Favored : 97.18 % Rotamer: Outliers : 2.42 % Allowed : 13.97 % Favored : 83.61 % 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: 1.85 (0.24), residues: 1134 helix: 3.48 (0.21), residues: 507 sheet: 0.41 (0.44), residues: 114 loop : -1.02 (0.24), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 886 HIS 0.003 0.001 HIS C1101 PHE 0.010 0.001 PHE C1121 TYR 0.020 0.001 TYR C1067 ARG 0.002 0.000 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.6266 (mmm) cc_final: 0.5898 (mtp) outliers start: 13 outliers final: 11 residues processed: 80 average time/residue: 0.2012 time to fit residues: 22.2643 Evaluate side-chains 76 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 111 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 0.0980 chunk 68 optimal weight: 0.0870 chunk 97 optimal weight: 20.0000 overall best weight: 1.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN B1088 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.189297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.180128 restraints weight = 8342.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.178202 restraints weight = 15332.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.156494 restraints weight = 17652.864| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.5507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 8055 Z= 0.310 Angle : 0.591 11.527 11076 Z= 0.294 Chirality : 0.045 0.229 1377 Planarity : 0.004 0.029 1464 Dihedral : 4.959 39.584 1569 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.62 % Favored : 96.12 % Rotamer: Outliers : 2.98 % Allowed : 13.41 % Favored : 83.61 % 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: 1.62 (0.24), residues: 1134 helix: 3.34 (0.21), residues: 507 sheet: -0.15 (0.37), residues: 144 loop : -1.13 (0.25), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP B1102 HIS 0.005 0.001 HIS C1064 PHE 0.017 0.002 PHE A 906 TYR 0.022 0.002 TYR C1067 ARG 0.003 0.001 ARG A 815 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.764 Fit side-chains revert: symmetry clash REVERT: A 869 MET cc_start: 0.6262 (mmm) cc_final: 0.5953 (mtp) REVERT: B 823 PHE cc_start: 0.7543 (m-80) cc_final: 0.7199 (m-80) outliers start: 16 outliers final: 15 residues processed: 79 average time/residue: 0.1852 time to fit residues: 20.9387 Evaluate side-chains 81 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 63 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 32 optimal weight: 0.3980 chunk 92 optimal weight: 0.4980 chunk 3 optimal weight: 0.0170 chunk 15 optimal weight: 0.1980 chunk 9 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 overall best weight: 0.3618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.194062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.184868 restraints weight = 8134.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.182872 restraints weight = 15085.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.161888 restraints weight = 17388.709| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.5573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8055 Z= 0.151 Angle : 0.531 13.170 11076 Z= 0.257 Chirality : 0.043 0.209 1377 Planarity : 0.003 0.027 1464 Dihedral : 4.483 37.425 1569 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.47 % Favored : 97.27 % Rotamer: Outliers : 2.42 % Allowed : 14.34 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.82 (0.24), residues: 1134 helix: 3.46 (0.21), residues: 507 sheet: 0.34 (0.43), residues: 114 loop : -1.03 (0.24), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 886 HIS 0.002 0.001 HIS C1101 PHE 0.010 0.001 PHE B1121 TYR 0.020 0.001 TYR C1067 ARG 0.005 0.001 ARG C 815 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 822 LEU cc_start: 0.7294 (mp) cc_final: 0.6993 (mp) REVERT: A 869 MET cc_start: 0.6094 (mmm) cc_final: 0.5719 (mtp) REVERT: B 823 PHE cc_start: 0.7514 (m-80) cc_final: 0.7256 (m-80) outliers start: 13 outliers final: 13 residues processed: 76 average time/residue: 0.1535 time to fit residues: 17.2615 Evaluate side-chains 76 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 68 optimal weight: 0.2980 chunk 24 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 41 optimal weight: 30.0000 chunk 38 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 4 optimal weight: 40.0000 chunk 1 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.189462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.181029 restraints weight = 8301.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.179371 restraints weight = 12506.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.178843 restraints weight = 16734.901| |-----------------------------------------------------------------------------| r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.5713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8055 Z= 0.276 Angle : 0.578 12.424 11076 Z= 0.284 Chirality : 0.045 0.223 1377 Planarity : 0.004 0.031 1464 Dihedral : 4.856 38.732 1569 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.44 % Favored : 96.30 % Rotamer: Outliers : 2.98 % Allowed : 13.97 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.65 (0.24), residues: 1134 helix: 3.38 (0.21), residues: 507 sheet: -0.19 (0.37), residues: 144 loop : -1.10 (0.25), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP B1102 HIS 0.004 0.001 HIS A1088 PHE 0.015 0.002 PHE A 906 TYR 0.020 0.002 TYR C1067 ARG 0.005 0.001 ARG C 815 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2717.00 seconds wall clock time: 48 minutes 14.16 seconds (2894.16 seconds total)