Starting phenix.real_space_refine on Fri Jun 6 17:56:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dya_27779/06_2025/8dya_27779.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dya_27779/06_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_27779/06_2025/8dya_27779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dya_27779/06_2025/8dya_27779.map" model { file = "/net/cci-nas-00/data/ceres_data/8dya_27779/06_2025/8dya_27779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dya_27779/06_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-5710/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: 5.49, per 1000 atoms: 0.70 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: 2.15 Conformation dependent library (CDL) restraints added in 1.3 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: 1.00 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: 2.44 Time building geometry restraints manager: 2.55 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: 1.570 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.470 Find NCS groups from input model: 0.180 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.650 ------------------------------------------------------------------------------- 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 : 0.011 0.167 8082 Z= 0.637 Angle : 1.527 21.149 11148 Z= 1.010 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 Details of bonding type rmsd link_NAG-ASN : bond 0.08613 ( 18) link_NAG-ASN : angle 3.67174 ( 54) hydrogen bonds : bond 0.18793 ( 516) hydrogen bonds : angle 6.29650 ( 1512) SS BOND : bond 0.07478 ( 9) SS BOND : angle 5.70683 ( 18) covalent geometry : bond 0.00993 ( 8055) covalent geometry : angle 1.49273 (11076) *********************** 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 : 0.893 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: 0.1845 time to fit residues: 40.1391 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 : 0.890 ------------------------------------------------------------------------------- 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 8082 Z= 0.141 Angle : 0.621 18.166 11148 Z= 0.309 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00661 ( 18) link_NAG-ASN : angle 3.84272 ( 54) hydrogen bonds : bond 0.04551 ( 516) hydrogen bonds : angle 4.38469 ( 1512) SS BOND : bond 0.00302 ( 9) SS BOND : angle 1.13768 ( 18) covalent geometry : bond 0.00293 ( 8055) covalent geometry : angle 0.56007 (11076) *********************** 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 : 0.889 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: 0.2114 time to fit residues: 25.8894 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 : 0.956 ------------------------------------------------------------------------------- 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: 0.0040 chunk 2 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.6072 ------------------------------------------------------------------------------- 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 = 0.4303 r_free = 0.4303 target = 0.198801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.187617 restraints weight = 9308.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.186206 restraints weight = 16910.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.185750 restraints weight = 17311.310| |-----------------------------------------------------------------------------| r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8082 Z= 0.143 Angle : 0.616 17.170 11148 Z= 0.300 Chirality : 0.044 0.234 1377 Planarity : 0.004 0.033 1464 Dihedral : 4.523 30.325 1569 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.09 % Favored : 96.65 % Rotamer: Outliers : 2.61 % Allowed : 10.06 % Favored : 87.34 % 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: 1.91 (0.24), residues: 1134 helix: 3.41 (0.21), residues: 522 sheet: 1.11 (0.43), residues: 108 loop : -1.16 (0.23), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1102 HIS 0.005 0.001 HIS A1064 PHE 0.021 0.002 PHE C 906 TYR 0.017 0.002 TYR C1067 ARG 0.004 0.001 ARG B 815 Details of bonding type rmsd link_NAG-ASN : bond 0.00609 ( 18) link_NAG-ASN : angle 3.84730 ( 54) hydrogen bonds : bond 0.04086 ( 516) hydrogen bonds : angle 3.95365 ( 1512) SS BOND : bond 0.00361 ( 9) SS BOND : angle 0.82354 ( 18) covalent geometry : bond 0.00330 ( 8055) covalent geometry : angle 0.55596 (11076) *********************** 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 : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 805 ILE cc_start: 0.6313 (OUTLIER) cc_final: 0.6031 (pt) REVERT: C 1027 THR cc_start: 0.7650 (m) cc_final: 0.7433 (m) outliers start: 14 outliers final: 10 residues processed: 82 average time/residue: 0.2013 time to fit residues: 23.2191 Evaluate side-chains 73 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.898 ------------------------------------------------------------------------------- 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: 0.9980 chunk 53 optimal weight: 0.9980 chunk 105 optimal weight: 0.0050 chunk 58 optimal weight: 10.0000 chunk 32 optimal weight: 0.2980 chunk 15 optimal weight: 0.5980 chunk 16 optimal weight: 0.2980 chunk 11 optimal weight: 0.4980 chunk 20 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.3394 ------------------------------------------------------------------------------- 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 = 0.4316 r_free = 0.4316 target = 0.200522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.193000 restraints weight = 9205.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.190096 restraints weight = 13972.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.161528 restraints weight = 19009.323| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8082 Z= 0.105 Angle : 0.526 15.708 11148 Z= 0.256 Chirality : 0.042 0.199 1377 Planarity : 0.004 0.027 1464 Dihedral : 4.193 36.982 1569 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.47 % Favored : 97.27 % Rotamer: Outliers : 3.54 % Allowed : 11.55 % Favored : 84.92 % 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: 2.07 (0.24), residues: 1134 helix: 3.55 (0.21), residues: 522 sheet: 1.10 (0.45), residues: 108 loop : -1.06 (0.24), residues: 504 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 C1121 TYR 0.020 0.001 TYR C1067 ARG 0.001 0.000 ARG A 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00551 ( 18) link_NAG-ASN : angle 3.12850 ( 54) hydrogen bonds : bond 0.03529 ( 516) hydrogen bonds : angle 3.71456 ( 1512) SS BOND : bond 0.00365 ( 9) SS BOND : angle 0.69958 ( 18) covalent geometry : bond 0.00226 ( 8055) covalent geometry : angle 0.47970 (11076) *********************** 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 94 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 805 ILE cc_start: 0.5838 (OUTLIER) cc_final: 0.5620 (pt) REVERT: C 902 MET cc_start: 0.7383 (tpp) cc_final: 0.7037 (tpt) outliers start: 19 outliers final: 13 residues processed: 86 average time/residue: 0.1883 time to fit residues: 23.1564 Evaluate side-chains 86 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.821 ------------------------------------------------------------------------------- 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 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: 0.3980 chunk 92 optimal weight: 1.9990 chunk 86 optimal weight: 0.0370 chunk 70 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 11 optimal weight: 0.0270 chunk 84 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1023 ASN C1023 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.182796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.144160 restraints weight = 8480.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.147361 restraints weight = 6043.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.149489 restraints weight = 4808.627| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8082 Z= 0.108 Angle : 0.525 14.988 11148 Z= 0.254 Chirality : 0.042 0.202 1377 Planarity : 0.003 0.023 1464 Dihedral : 4.053 35.520 1569 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.26 % Favored : 96.47 % Rotamer: Outliers : 3.72 % Allowed : 12.48 % 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: 2.15 (0.24), residues: 1134 helix: 3.59 (0.21), residues: 525 sheet: 0.98 (0.46), residues: 108 loop : -0.96 (0.24), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B1102 HIS 0.003 0.001 HIS C1101 PHE 0.011 0.001 PHE A1121 TYR 0.020 0.001 TYR C1007 ARG 0.003 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00482 ( 18) link_NAG-ASN : angle 3.08892 ( 54) hydrogen bonds : bond 0.03471 ( 516) hydrogen bonds : angle 3.62999 ( 1512) SS BOND : bond 0.00261 ( 9) SS BOND : angle 0.72013 ( 18) covalent geometry : bond 0.00238 ( 8055) covalent geometry : angle 0.48005 (11076) *********************** 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 101 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 902 MET cc_start: 0.6983 (tpt) cc_final: 0.6540 (tpt) outliers start: 20 outliers final: 16 residues processed: 95 average time/residue: 0.2030 time to fit residues: 26.6436 Evaluate side-chains 88 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 729 VAL 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 707 CYS Chi-restraints excluded: chain C residue 729 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 63 optimal weight: 5.9990 chunk 75 optimal weight: 0.4980 chunk 105 optimal weight: 0.3980 chunk 7 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 86 optimal weight: 0.0020 chunk 56 optimal weight: 2.9990 chunk 35 optimal weight: 0.0020 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1023 ASN B 804 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.179614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.132023 restraints weight = 8886.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.135716 restraints weight = 6195.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.138393 restraints weight = 4941.788| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.4825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8082 Z= 0.122 Angle : 0.543 14.310 11148 Z= 0.265 Chirality : 0.043 0.205 1377 Planarity : 0.003 0.036 1464 Dihedral : 4.290 37.512 1569 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.00 % Favored : 96.74 % Rotamer: Outliers : 3.91 % Allowed : 12.10 % Favored : 83.99 % 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: 2.05 (0.24), residues: 1134 helix: 3.51 (0.21), residues: 525 sheet: 0.55 (0.45), residues: 114 loop : -0.93 (0.24), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B1102 HIS 0.003 0.001 HIS C1101 PHE 0.011 0.001 PHE C1121 TYR 0.022 0.002 TYR C1007 ARG 0.003 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00472 ( 18) link_NAG-ASN : angle 2.97743 ( 54) hydrogen bonds : bond 0.03534 ( 516) hydrogen bonds : angle 3.72219 ( 1512) SS BOND : bond 0.00314 ( 9) SS BOND : angle 0.83207 ( 18) covalent geometry : bond 0.00285 ( 8055) covalent geometry : angle 0.50241 (11076) *********************** 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 92 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 15 residues processed: 83 average time/residue: 0.2083 time to fit residues: 23.6346 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 : 0.825 ------------------------------------------------------------------------------- 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 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 729 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 6 optimal weight: 0.3980 chunk 70 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 59 optimal weight: 20.0000 chunk 99 optimal weight: 6.9990 chunk 106 optimal weight: 0.1980 chunk 26 optimal weight: 0.9980 chunk 60 optimal weight: 50.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A1088 HIS C1088 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.180256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.143711 restraints weight = 8620.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.146441 restraints weight = 6313.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.148258 restraints weight = 5130.226| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.5108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8082 Z= 0.127 Angle : 0.542 13.630 11148 Z= 0.264 Chirality : 0.043 0.209 1377 Planarity : 0.003 0.026 1464 Dihedral : 4.395 37.871 1569 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.62 % Favored : 96.12 % Rotamer: Outliers : 3.72 % Allowed : 12.66 % 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: 1.87 (0.24), residues: 1134 helix: 3.49 (0.21), residues: 507 sheet: 0.44 (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 B1102 HIS 0.003 0.001 HIS C1101 PHE 0.012 0.001 PHE C1121 TYR 0.020 0.001 TYR C1067 ARG 0.003 0.001 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00455 ( 18) link_NAG-ASN : angle 2.90199 ( 54) hydrogen bonds : bond 0.03540 ( 516) hydrogen bonds : angle 3.71490 ( 1512) SS BOND : bond 0.00341 ( 9) SS BOND : angle 0.82289 ( 18) covalent geometry : bond 0.00299 ( 8055) covalent geometry : angle 0.50396 (11076) *********************** 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: 20 poor density : 65 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.6345 (mmm) cc_final: 0.5947 (mtp) REVERT: C 794 ILE cc_start: 0.6133 (mt) cc_final: 0.5351 (tt) outliers start: 20 outliers final: 17 residues processed: 80 average time/residue: 0.2005 time to fit residues: 22.1780 Evaluate side-chains 81 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.777 ------------------------------------------------------------------------------- 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 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 729 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 1 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 76 optimal weight: 0.1980 chunk 37 optimal weight: 0.3980 chunk 14 optimal weight: 0.6980 chunk 98 optimal weight: 0.0030 chunk 4 optimal weight: 40.0000 chunk 28 optimal weight: 0.4980 chunk 23 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 113 optimal weight: 0.0980 overall best weight: 0.2390 ------------------------------------------------------------------------------- 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 = 0.4072 r_free = 0.4072 target = 0.184386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.147174 restraints weight = 8488.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.150188 restraints weight = 6095.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.151999 restraints weight = 4923.062| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8082 Z= 0.094 Angle : 0.498 12.732 11148 Z= 0.241 Chirality : 0.041 0.194 1377 Planarity : 0.003 0.025 1464 Dihedral : 4.026 35.175 1569 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.73 % Favored : 97.00 % Rotamer: Outliers : 2.79 % Allowed : 13.22 % Favored : 83.99 % 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: 2.06 (0.24), residues: 1134 helix: 3.61 (0.21), residues: 507 sheet: 0.57 (0.45), residues: 114 loop : -0.87 (0.24), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 886 HIS 0.002 0.000 HIS C1101 PHE 0.009 0.001 PHE C1121 TYR 0.018 0.001 TYR C1067 ARG 0.004 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00432 ( 18) link_NAG-ASN : angle 2.65171 ( 54) hydrogen bonds : bond 0.03275 ( 516) hydrogen bonds : angle 3.53587 ( 1512) SS BOND : bond 0.00198 ( 9) SS BOND : angle 0.54546 ( 18) covalent geometry : bond 0.00193 ( 8055) covalent geometry : angle 0.46318 (11076) *********************** 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 84 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.6287 (mmm) cc_final: 0.5857 (mtp) REVERT: C 794 ILE cc_start: 0.6081 (mt) cc_final: 0.5324 (tt) outliers start: 15 outliers final: 14 residues processed: 81 average time/residue: 0.1876 time to fit residues: 21.5506 Evaluate side-chains 81 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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 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 729 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=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: 0.0970 chunk 68 optimal weight: 0.6980 chunk 97 optimal weight: 20.0000 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 = 0.4119 r_free = 0.4119 target = 0.186957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.154865 restraints weight = 8414.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.153975 restraints weight = 7992.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.153978 restraints weight = 7599.718| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.5482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 8082 Z= 0.196 Angle : 0.613 12.596 11148 Z= 0.303 Chirality : 0.046 0.229 1377 Planarity : 0.004 0.037 1464 Dihedral : 4.997 39.261 1569 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.53 % Favored : 96.21 % Rotamer: Outliers : 3.17 % Allowed : 13.04 % 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: 1.65 (0.24), residues: 1134 helix: 3.33 (0.21), residues: 510 sheet: -0.21 (0.37), residues: 144 loop : -1.07 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B1102 HIS 0.005 0.002 HIS C1088 PHE 0.019 0.002 PHE A 906 TYR 0.022 0.002 TYR C1067 ARG 0.004 0.001 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00444 ( 18) link_NAG-ASN : angle 2.92208 ( 54) hydrogen bonds : bond 0.03810 ( 516) hydrogen bonds : angle 3.91441 ( 1512) SS BOND : bond 0.00532 ( 9) SS BOND : angle 1.20699 ( 18) covalent geometry : bond 0.00492 ( 8055) covalent geometry : angle 0.57826 (11076) *********************** 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 87 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.6261 (mmm) cc_final: 0.5889 (mtp) REVERT: C 794 ILE cc_start: 0.6765 (mt) cc_final: 0.6044 (tt) outliers start: 17 outliers final: 16 residues processed: 84 average time/residue: 0.2055 time to fit residues: 24.3444 Evaluate side-chains 81 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 79 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 68 optimal weight: 0.2980 chunk 32 optimal weight: 0.3980 chunk 92 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4163 r_free = 0.4163 target = 0.191590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.183168 restraints weight = 8163.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 103)---------------| | r_work = 0.3793 r_free = 0.3793 target = 0.159952 restraints weight = 12950.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.160703 restraints weight = 12066.553| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.5562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8082 Z= 0.130 Angle : 0.556 12.085 11148 Z= 0.271 Chirality : 0.044 0.214 1377 Planarity : 0.003 0.029 1464 Dihedral : 4.704 37.977 1569 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.00 % Favored : 96.74 % Rotamer: Outliers : 2.61 % Allowed : 13.41 % Favored : 83.99 % 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: 1.76 (0.24), residues: 1134 helix: 3.42 (0.21), residues: 507 sheet: 0.30 (0.42), residues: 114 loop : -1.07 (0.24), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B1102 HIS 0.003 0.001 HIS C1088 PHE 0.021 0.001 PHE B 823 TYR 0.021 0.001 TYR C1067 ARG 0.004 0.001 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00425 ( 18) link_NAG-ASN : angle 2.75409 ( 54) hydrogen bonds : bond 0.03510 ( 516) hydrogen bonds : angle 3.80627 ( 1512) SS BOND : bond 0.00347 ( 9) SS BOND : angle 0.81285 ( 18) covalent geometry : bond 0.00309 ( 8055) covalent geometry : angle 0.52207 (11076) ********************** 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 79 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.765 Fit side-chains REVERT: A 869 MET cc_start: 0.6222 (mmm) cc_final: 0.5859 (mtp) REVERT: C 794 ILE cc_start: 0.6722 (mt) cc_final: 0.6004 (tt) outliers start: 14 outliers final: 14 residues processed: 76 average time/residue: 0.1801 time to fit residues: 19.3455 Evaluate side-chains 79 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 68 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 41 optimal weight: 20.0000 chunk 38 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 4 optimal weight: 40.0000 chunk 1 optimal weight: 0.5980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1088 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.190475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.182066 restraints weight = 8276.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.178543 restraints weight = 13171.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.178068 restraints weight = 18980.076| |-----------------------------------------------------------------------------| r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.5673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8082 Z= 0.146 Angle : 0.569 11.879 11148 Z= 0.278 Chirality : 0.044 0.217 1377 Planarity : 0.004 0.030 1464 Dihedral : 4.762 38.375 1569 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.53 % Favored : 96.21 % Rotamer: Outliers : 2.79 % Allowed : 13.41 % 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: 1.63 (0.24), residues: 1134 helix: 3.38 (0.21), residues: 507 sheet: -0.29 (0.36), residues: 144 loop : -1.09 (0.25), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B1102 HIS 0.003 0.001 HIS C1088 PHE 0.013 0.001 PHE A 906 TYR 0.021 0.001 TYR C1067 ARG 0.012 0.001 ARG B 815 Details of bonding type rmsd link_NAG-ASN : bond 0.00413 ( 18) link_NAG-ASN : angle 2.74781 ( 54) hydrogen bonds : bond 0.03567 ( 516) hydrogen bonds : angle 3.84126 ( 1512) SS BOND : bond 0.00405 ( 9) SS BOND : angle 0.96765 ( 18) covalent geometry : bond 0.00357 ( 8055) covalent geometry : angle 0.53620 (11076) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3111.49 seconds wall clock time: 55 minutes 42.34 seconds (3342.34 seconds total)