Starting phenix.real_space_refine on Sat Dec 28 07:18:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dya_27779/12_2024/8dya_27779.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dya_27779/12_2024/8dya_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_27779/12_2024/8dya_27779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dya_27779/12_2024/8dya_27779.map" model { file = "/net/cci-nas-00/data/ceres_data/8dya_27779/12_2024/8dya_27779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dya_27779/12_2024/8dya_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-5532/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: 5.24, per 1000 atoms: 0.66 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=2, symmetry=0 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 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: 2.22 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: 0.89 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: 2.45 Time building geometry restraints manager: 2.43 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: 4743 17.80 - 35.59: 148 35.59 - 53.38: 23 53.38 - 71.18: 6 71.18 - 88.97: 6 Dihedral angle restraints: 4926 sinusoidal: 1554 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 4923 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: 1.99 - 2.58: 16 2.58 - 3.16: 6267 3.16 - 3.74: 11674 3.74 - 4.32: 15541 4.32 - 4.90: 25125 Nonbonded interactions: 58623 Sorted by model distance: nonbonded pdb=" SG CYS A 883 " pdb=" SG CYS C 707 " model vdw 1.995 3.760 nonbonded pdb=" SG CYS A 707 " pdb=" SG CYS B 883 " model vdw 1.995 3.760 nonbonded pdb=" SG CYS B 707 " pdb=" SG CYS C 883 " model vdw 1.996 3.760 nonbonded pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " model vdw 2.021 3.760 nonbonded pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " model vdw 2.021 3.760 ... (remaining 58618 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 2.200 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.770 Find NCS groups from input model: 0.260 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.550 ------------------------------------------------------------------------------- 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= 0.674 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 : 1.995 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 : 0.807 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: 0.1847 time to fit residues: 40.0652 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 : 0.857 ------------------------------------------------------------------------------- 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: 0.7980 chunk 34 optimal weight: 0.0980 chunk 54 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6611 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8055 Z= 0.221 Angle : 0.578 6.775 11076 Z= 0.305 Chirality : 0.045 0.283 1377 Planarity : 0.005 0.052 1464 Dihedral : 5.700 51.609 1569 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.56 % Favored : 97.18 % Rotamer: Outliers : 1.86 % Allowed : 7.64 % Favored : 90.50 % 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: 1.59 (0.24), residues: 1134 helix: 2.99 (0.21), residues: 522 sheet: 1.18 (0.42), residues: 114 loop : -1.22 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1102 HIS 0.005 0.001 HIS A1064 PHE 0.014 0.002 PHE B 906 TYR 0.016 0.002 TYR C1067 ARG 0.004 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 90 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 902 MET cc_start: 0.7047 (mmm) cc_final: 0.6322 (tpt) REVERT: B 1082 CYS cc_start: 0.7435 (t) cc_final: 0.7212 (t) REVERT: C 1027 THR cc_start: 0.7501 (m) cc_final: 0.7158 (p) outliers start: 10 outliers final: 6 residues processed: 85 average time/residue: 0.1908 time to fit residues: 23.0742 Evaluate side-chains 74 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.785 ------------------------------------------------------------------------------- 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 57 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 86 optimal weight: 0.0010 chunk 70 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8055 Z= 0.235 Angle : 0.553 6.768 11076 Z= 0.285 Chirality : 0.044 0.232 1377 Planarity : 0.004 0.034 1464 Dihedral : 4.800 33.520 1569 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.73 % Favored : 97.00 % Rotamer: Outliers : 2.61 % Allowed : 9.68 % Favored : 87.71 % 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: 1.89 (0.24), residues: 1134 helix: 3.41 (0.21), residues: 522 sheet: 1.23 (0.43), residues: 108 loop : -1.23 (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 A 906 TYR 0.017 0.002 TYR C1067 ARG 0.003 0.001 ARG A 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 82 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.830 Fit side-chains revert: symmetry clash REVERT: C 805 ILE cc_start: 0.6229 (OUTLIER) cc_final: 0.5975 (pt) REVERT: C 1027 THR cc_start: 0.7640 (m) cc_final: 0.7127 (p) outliers start: 14 outliers final: 11 residues processed: 78 average time/residue: 0.1840 time to fit residues: 20.4492 Evaluate side-chains 74 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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 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 102 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 11 optimal weight: 0.0980 chunk 49 optimal weight: 0.0050 chunk 69 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 98 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8055 Z= 0.166 Angle : 0.489 6.864 11076 Z= 0.251 Chirality : 0.042 0.207 1377 Planarity : 0.004 0.029 1464 Dihedral : 4.300 37.105 1569 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.09 % Favored : 96.65 % Rotamer: Outliers : 2.79 % Allowed : 10.80 % Favored : 86.41 % 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: 3.50 (0.21), residues: 522 sheet: 0.98 (0.45), residues: 108 loop : -1.12 (0.24), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B1102 HIS 0.003 0.001 HIS C1101 PHE 0.017 0.001 PHE B 823 TYR 0.020 0.001 TYR C1067 ARG 0.005 0.001 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 86 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 805 ILE cc_start: 0.6029 (OUTLIER) cc_final: 0.5798 (pt) outliers start: 15 outliers final: 11 residues processed: 80 average time/residue: 0.1731 time to fit residues: 20.0379 Evaluate side-chains 79 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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 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 91 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 98 optimal weight: 50.0000 chunk 27 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1088 HIS C1023 ASN C1088 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8055 Z= 0.259 Angle : 0.542 5.954 11076 Z= 0.278 Chirality : 0.044 0.226 1377 Planarity : 0.004 0.027 1464 Dihedral : 4.696 39.490 1569 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.62 % Favored : 96.12 % Rotamer: Outliers : 3.72 % Allowed : 11.36 % 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: 1.76 (0.24), residues: 1134 helix: 3.34 (0.21), residues: 528 sheet: -0.06 (0.38), residues: 144 loop : -1.14 (0.25), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B1102 HIS 0.004 0.001 HIS A1064 PHE 0.018 0.002 PHE B 906 TYR 0.021 0.002 TYR C1067 ARG 0.003 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 92 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 794 ILE cc_start: 0.7013 (mt) cc_final: 0.6803 (mt) outliers start: 20 outliers final: 14 residues processed: 83 average time/residue: 0.2152 time to fit residues: 24.6039 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 : 0.877 ------------------------------------------------------------------------------- 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 865 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 21 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN B 804 GLN B1088 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.5353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 8055 Z= 0.424 Angle : 0.646 6.565 11076 Z= 0.332 Chirality : 0.049 0.255 1377 Planarity : 0.004 0.035 1464 Dihedral : 5.826 43.788 1569 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.23 % Favored : 95.50 % Rotamer: Outliers : 4.28 % Allowed : 10.99 % Favored : 84.73 % 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: 1.26 (0.24), residues: 1134 helix: 3.05 (0.21), residues: 528 sheet: -0.74 (0.36), residues: 150 loop : -1.40 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP B1102 HIS 0.005 0.002 HIS C1088 PHE 0.022 0.002 PHE A 906 TYR 0.024 0.002 TYR C1067 ARG 0.004 0.001 ARG B 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 96 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.6015 (mmm) cc_final: 0.5696 (mtp) REVERT: B 823 PHE cc_start: 0.7357 (OUTLIER) cc_final: 0.6412 (t80) REVERT: B 869 MET cc_start: 0.6260 (mmm) cc_final: 0.5890 (mmm) outliers start: 23 outliers final: 17 residues processed: 87 average time/residue: 0.1891 time to fit residues: 23.0095 Evaluate side-chains 84 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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 821 LEU Chi-restraints excluded: chain B residue 823 PHE 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 791 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 109 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 0.0970 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.5450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8055 Z= 0.217 Angle : 0.534 6.380 11076 Z= 0.272 Chirality : 0.044 0.224 1377 Planarity : 0.004 0.032 1464 Dihedral : 5.194 42.062 1569 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.91 % Favored : 96.83 % Rotamer: Outliers : 3.35 % Allowed : 13.59 % 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: 1.36 (0.25), residues: 1134 helix: 3.19 (0.21), residues: 528 sheet: -0.70 (0.36), residues: 144 loop : -1.41 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B1102 HIS 0.003 0.001 HIS A1088 PHE 0.012 0.001 PHE B1121 TYR 0.022 0.001 TYR C1067 ARG 0.003 0.000 ARG B 815 *********************** 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 80 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.929 Fit side-chains REVERT: A 869 MET cc_start: 0.5770 (mmm) cc_final: 0.5508 (mtp) REVERT: B 823 PHE cc_start: 0.7312 (OUTLIER) cc_final: 0.6935 (m-80) outliers start: 18 outliers final: 15 residues processed: 76 average time/residue: 0.1873 time to fit residues: 20.3094 Evaluate side-chains 74 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.809 ------------------------------------------------------------------------------- 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 823 PHE Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 791 THR 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 43 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 21 optimal weight: 20.0000 chunk 69 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 86 optimal weight: 0.0970 chunk 99 optimal weight: 6.9990 chunk 105 optimal weight: 0.1980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.5532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8055 Z= 0.170 Angle : 0.514 10.386 11076 Z= 0.257 Chirality : 0.043 0.215 1377 Planarity : 0.004 0.032 1464 Dihedral : 4.756 40.125 1569 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.09 % Favored : 96.65 % Rotamer: Outliers : 2.79 % Allowed : 13.97 % 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: 1.57 (0.24), residues: 1134 helix: 3.26 (0.21), residues: 528 sheet: -0.10 (0.42), residues: 114 loop : -1.30 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 886 HIS 0.003 0.001 HIS C1101 PHE 0.011 0.001 PHE A1121 TYR 0.020 0.001 TYR C1067 ARG 0.003 0.000 ARG C 815 *********************** 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 78 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 822 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7104 (mp) REVERT: A 869 MET cc_start: 0.5754 (mmm) cc_final: 0.5490 (mtp) REVERT: B 815 ARG cc_start: 0.6819 (ttp-170) cc_final: 0.6611 (ttm170) outliers start: 15 outliers final: 14 residues processed: 75 average time/residue: 0.2030 time to fit residues: 21.3220 Evaluate side-chains 76 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 822 LEU 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 896 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 791 THR 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 96 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 61 optimal weight: 8.9990 chunk 44 optimal weight: 0.0370 chunk 80 optimal weight: 6.9990 chunk 31 optimal weight: 0.4980 chunk 92 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.0862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 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 : 0.005 0.059 8055 Z= 0.306 Angle : 0.580 11.084 11076 Z= 0.293 Chirality : 0.046 0.233 1377 Planarity : 0.004 0.035 1464 Dihedral : 5.236 42.009 1569 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.06 % Favored : 95.68 % Rotamer: Outliers : 3.17 % Allowed : 13.59 % 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: 1.20 (0.24), residues: 1134 helix: 3.15 (0.22), residues: 510 sheet: -0.83 (0.35), residues: 144 loop : -1.40 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 886 HIS 0.004 0.001 HIS C1088 PHE 0.014 0.002 PHE B 906 TYR 0.023 0.002 TYR C1067 ARG 0.003 0.001 ARG C 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: 17 poor density : 67 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.5909 (mmm) cc_final: 0.5601 (mtp) REVERT: B 815 ARG cc_start: 0.6996 (ttp-170) cc_final: 0.6722 (ttm170) outliers start: 17 outliers final: 16 residues processed: 80 average time/residue: 0.1839 time to fit residues: 21.1226 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 : 0.760 ------------------------------------------------------------------------------- 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 791 THR 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 51 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 90 optimal weight: 0.0060 chunk 9 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 96 optimal weight: 20.0000 chunk 27 optimal weight: 0.9980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.5799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8055 Z= 0.207 Angle : 0.527 10.766 11076 Z= 0.264 Chirality : 0.044 0.217 1377 Planarity : 0.004 0.038 1464 Dihedral : 4.877 40.503 1569 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.53 % Favored : 96.21 % Rotamer: Outliers : 3.17 % Allowed : 13.59 % 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: 1.36 (0.24), residues: 1134 helix: 3.24 (0.21), residues: 510 sheet: -0.60 (0.40), residues: 120 loop : -1.30 (0.24), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 886 HIS 0.002 0.001 HIS A1088 PHE 0.011 0.001 PHE B1121 TYR 0.020 0.001 TYR C1067 ARG 0.004 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 77 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 822 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7198 (mp) REVERT: A 869 MET cc_start: 0.5797 (mmm) cc_final: 0.5499 (mtp) outliers start: 17 outliers final: 16 residues processed: 74 average time/residue: 0.1855 time to fit residues: 19.5231 Evaluate side-chains 76 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 822 LEU 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 729 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 791 THR 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 83 optimal weight: 0.0170 chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 79 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 overall best weight: 0.7422 ------------------------------------------------------------------------------- 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 = 0.4125 r_free = 0.4125 target = 0.188364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 105)---------------| | r_work = 0.3761 r_free = 0.3761 target = 0.154906 restraints weight = 8205.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.154762 restraints weight = 8142.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.154575 restraints weight = 8264.536| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.5896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8055 Z= 0.228 Angle : 0.535 10.497 11076 Z= 0.269 Chirality : 0.044 0.222 1377 Planarity : 0.004 0.035 1464 Dihedral : 4.891 40.474 1569 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.06 % Favored : 95.68 % Rotamer: Outliers : 3.17 % Allowed : 14.15 % Favored : 82.68 % 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: 1.25 (0.24), residues: 1134 helix: 3.22 (0.21), residues: 510 sheet: -1.04 (0.34), residues: 150 loop : -1.32 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 886 HIS 0.003 0.001 HIS C1088 PHE 0.012 0.001 PHE C1121 TYR 0.021 0.001 TYR C1067 ARG 0.006 0.001 ARG B 815 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1674.76 seconds wall clock time: 31 minutes 13.45 seconds (1873.45 seconds total)