Starting phenix.real_space_refine on Thu Jun 5 10:36:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ste_40759/06_2025/8ste_40759.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ste_40759/06_2025/8ste_40759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ste_40759/06_2025/8ste_40759.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ste_40759/06_2025/8ste_40759.map" model { file = "/net/cci-nas-00/data/ceres_data/8ste_40759/06_2025/8ste_40759.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ste_40759/06_2025/8ste_40759.cif" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.063 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: 5 Type Number sf(0) Gaussians S 38 5.16 5 Cl 2 4.86 5 C 3719 2.51 5 N 1020 2.21 5 O 1037 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 5816 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2878 Classifications: {'peptide': 355} Link IDs: {'PTRANS': 13, 'TRANS': 341} Chain breaks: 1 Chain: "B" Number of atoms: 2896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2896 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 13, 'TRANS': 343} Chain breaks: 1 Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'FUN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'FUN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.02, per 1000 atoms: 0.86 Number of scatterers: 5816 At special positions: 0 Unit cell: (78.11, 82.39, 113.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 38 16.00 O 1037 8.00 N 1020 7.00 C 3719 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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 Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 808.9 milliseconds 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1352 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 5 sheets defined 49.2% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 763 through 780 removed outlier: 3.736A pdb=" N VAL A 780 " --> pdb=" O ARG A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 812 removed outlier: 3.797A pdb=" N PHE A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 849 Processing helix chain 'A' and resid 862 through 874 Processing helix chain 'A' and resid 896 through 913 Processing helix chain 'A' and resid 1034 through 1045 Proline residue: A1040 - end of helix removed outlier: 3.610A pdb=" N THR A1045 " --> pdb=" O TYR A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1080 Processing helix chain 'A' and resid 1097 through 1109 removed outlier: 3.863A pdb=" N ILE A1101 " --> pdb=" O LYS A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1110 through 1112 No H-bonds generated for 'chain 'A' and resid 1110 through 1112' Processing helix chain 'A' and resid 1119 through 1130 Processing helix chain 'A' and resid 1135 through 1142 Processing helix chain 'A' and resid 1142 through 1160 Processing helix chain 'A' and resid 1179 through 1191 Processing helix chain 'B' and resid 763 through 780 removed outlier: 3.588A pdb=" N VAL B 780 " --> pdb=" O ARG B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 811 removed outlier: 3.622A pdb=" N LEU B 805 " --> pdb=" O ARG B 801 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE B 811 " --> pdb=" O LEU B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 849 Processing helix chain 'B' and resid 862 through 874 Processing helix chain 'B' and resid 896 through 913 removed outlier: 3.582A pdb=" N VAL B 900 " --> pdb=" O ASP B 896 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE B 907 " --> pdb=" O TYR B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 1034 through 1045 Proline residue: B1040 - end of helix Processing helix chain 'B' and resid 1064 through 1080 removed outlier: 4.193A pdb=" N ASP B1068 " --> pdb=" O ARG B1064 " (cutoff:3.500A) Processing helix chain 'B' and resid 1097 through 1108 Processing helix chain 'B' and resid 1119 through 1130 Processing helix chain 'B' and resid 1136 through 1142 Processing helix chain 'B' and resid 1142 through 1160 Processing helix chain 'B' and resid 1179 through 1191 Processing sheet with id=AA1, first strand: chain 'A' and resid 853 through 859 removed outlier: 6.761A pdb=" N MET A 818 " --> pdb=" O PHE A 854 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ALA A 856 " --> pdb=" O MET A 818 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N CYS A 820 " --> pdb=" O ALA A 856 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N VAL A 858 " --> pdb=" O CYS A 820 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N HIS A 822 " --> pdb=" O VAL A 858 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N CYS A 791 " --> pdb=" O ILE A 819 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLY A 821 " --> pdb=" O CYS A 791 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL A 793 " --> pdb=" O GLY A 821 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N VAL A 823 " --> pdb=" O VAL A 793 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLY A 887 " --> pdb=" O MET A 794 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU A 884 " --> pdb=" O VAL A 918 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ILE A 920 " --> pdb=" O LEU A 884 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU A 886 " --> pdb=" O ILE A 920 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE A1166 " --> pdb=" O LEU A1198 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL A1200 " --> pdb=" O ILE A1166 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N MET A1168 " --> pdb=" O VAL A1200 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER A1169 " --> pdb=" O TRP A1027 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE A1024 " --> pdb=" O ARG A1055 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N PHE A1057 " --> pdb=" O ILE A1024 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL A1026 " --> pdb=" O PHE A1057 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N GLY A1059 " --> pdb=" O VAL A1026 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N MET A1087 " --> pdb=" O ILE A1054 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N VAL A1056 " --> pdb=" O MET A1087 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N LEU A1089 " --> pdb=" O VAL A1056 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE A1058 " --> pdb=" O LEU A1089 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 791 through 793 removed outlier: 6.451A pdb=" N ILE B1166 " --> pdb=" O LEU B1198 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL B1200 " --> pdb=" O ILE B1166 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N MET B1168 " --> pdb=" O VAL B1200 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASP B1025 " --> pdb=" O VAL B1167 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N SER B1169 " --> pdb=" O ASP B1025 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N TRP B1027 " --> pdb=" O SER B1169 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ILE B1024 " --> pdb=" O ARG B1055 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N PHE B1057 " --> pdb=" O ILE B1024 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL B1026 " --> pdb=" O PHE B1057 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N GLY B1059 " --> pdb=" O VAL B1026 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ILE B1054 " --> pdb=" O ASP B1085 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N MET B1087 " --> pdb=" O ILE B1054 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL B1056 " --> pdb=" O MET B1087 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N LEU B1089 " --> pdb=" O VAL B1056 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE B1058 " --> pdb=" O LEU B1089 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 818 through 819 removed outlier: 6.511A pdb=" N MET B 818 " --> pdb=" O PHE B 854 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 822 through 824 Processing sheet with id=AA5, first strand: chain 'B' and resid 1112 through 1113 259 hydrogen bonds defined for protein. 774 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: 1.56 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1886 1.34 - 1.46: 1166 1.46 - 1.58: 2813 1.58 - 1.70: 0 1.70 - 1.82: 72 Bond restraints: 5937 Sorted by residual: bond pdb=" C4 FUN B1301 " pdb=" N2 FUN B1301 " ideal model delta sigma weight residual 1.340 1.462 -0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C4 FUN A1301 " pdb=" N2 FUN A1301 " ideal model delta sigma weight residual 1.340 1.450 -0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" C7 FUN B1301 " pdb=" C8 FUN B1301 " ideal model delta sigma weight residual 1.429 1.359 0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C7 FUN A1301 " pdb=" C8 FUN A1301 " ideal model delta sigma weight residual 1.429 1.359 0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" N1 FUN A1301 " pdb=" S1 FUN A1301 " ideal model delta sigma weight residual 1.647 1.707 -0.060 2.00e-02 2.50e+03 8.94e+00 ... (remaining 5932 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.55: 7977 3.55 - 7.10: 30 7.10 - 10.65: 3 10.65 - 14.20: 0 14.20 - 17.75: 2 Bond angle restraints: 8012 Sorted by residual: angle pdb=" O1 FUN B1301 " pdb=" S1 FUN B1301 " pdb=" O2 FUN B1301 " ideal model delta sigma weight residual 119.17 101.42 17.75 3.00e+00 1.11e-01 3.50e+01 angle pdb=" O1 FUN A1301 " pdb=" S1 FUN A1301 " pdb=" O2 FUN A1301 " ideal model delta sigma weight residual 119.17 101.65 17.52 3.00e+00 1.11e-01 3.41e+01 angle pdb=" C5 FUN B1301 " pdb=" C6 FUN B1301 " pdb=" O3 FUN B1301 " ideal model delta sigma weight residual 117.64 126.47 -8.83 3.00e+00 1.11e-01 8.67e+00 angle pdb=" C5 FUN A1301 " pdb=" C6 FUN A1301 " pdb=" O3 FUN A1301 " ideal model delta sigma weight residual 117.64 125.56 -7.92 3.00e+00 1.11e-01 6.97e+00 angle pdb=" N ILE B 913 " pdb=" CA ILE B 913 " pdb=" C ILE B 913 " ideal model delta sigma weight residual 111.91 109.70 2.21 8.90e-01 1.26e+00 6.18e+00 ... (remaining 8007 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 3233 17.61 - 35.23: 293 35.23 - 52.84: 56 52.84 - 70.46: 13 70.46 - 88.07: 6 Dihedral angle restraints: 3601 sinusoidal: 1519 harmonic: 2082 Sorted by residual: dihedral pdb=" CA PHE A1030 " pdb=" C PHE A1030 " pdb=" N ASP A1031 " pdb=" CA ASP A1031 " ideal model delta harmonic sigma weight residual -180.00 -154.80 -25.20 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA ASN A 849 " pdb=" C ASN A 849 " pdb=" N LYS A 850 " pdb=" CA LYS A 850 " ideal model delta harmonic sigma weight residual -180.00 -161.88 -18.12 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CG ARG B1055 " pdb=" CD ARG B1055 " pdb=" NE ARG B1055 " pdb=" CZ ARG B1055 " ideal model delta sinusoidal sigma weight residual -90.00 -133.56 43.56 2 1.50e+01 4.44e-03 1.01e+01 ... (remaining 3598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 504 0.027 - 0.055: 241 0.055 - 0.082: 74 0.082 - 0.109: 45 0.109 - 0.136: 19 Chirality restraints: 883 Sorted by residual: chirality pdb=" CA ILE A1024 " pdb=" N ILE A1024 " pdb=" C ILE A1024 " pdb=" CB ILE A1024 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.65e-01 chirality pdb=" CA ILE B1165 " pdb=" N ILE B1165 " pdb=" C ILE B1165 " pdb=" CB ILE B1165 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA ILE A1086 " pdb=" N ILE A1086 " pdb=" C ILE A1086 " pdb=" CB ILE A1086 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 ... (remaining 880 not shown) Planarity restraints: 1009 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 880 " -0.024 5.00e-02 4.00e+02 3.55e-02 2.02e+00 pdb=" N PRO B 881 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 881 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 881 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B1195 " 0.018 5.00e-02 4.00e+02 2.79e-02 1.25e+00 pdb=" N PRO B1196 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO B1196 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B1196 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO A1096 " 0.005 2.00e-02 2.50e+03 1.01e-02 1.02e+00 pdb=" C PRO A1096 " -0.017 2.00e-02 2.50e+03 pdb=" O PRO A1096 " 0.007 2.00e-02 2.50e+03 pdb=" N LYS A1097 " 0.006 2.00e-02 2.50e+03 ... (remaining 1006 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 44 2.56 - 3.15: 4936 3.15 - 3.73: 9000 3.73 - 4.32: 12126 4.32 - 4.90: 20873 Nonbonded interactions: 46979 Sorted by model distance: nonbonded pdb=" OD2 ASP B1025 " pdb=" OG SER B1160 " model vdw 1.979 3.040 nonbonded pdb=" O ASP B 810 " pdb=" NZ LYS B1046 " model vdw 2.055 3.120 nonbonded pdb=" OD1 ASP A 901 " pdb=" OG SER A1180 " model vdw 2.124 3.040 nonbonded pdb=" OD2 ASP A1025 " pdb=" OG SER A1160 " model vdw 2.145 3.040 nonbonded pdb=" ND2 ASN B1100 " pdb=" OE2 GLU B1154 " model vdw 2.146 3.120 ... (remaining 46974 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' and (resid 760 through 1208 or resid 1301)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.710 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 18.520 Find NCS groups from input model: 0.220 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 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 : 0.005 0.122 5937 Z= 0.256 Angle : 0.695 17.754 8012 Z= 0.331 Chirality : 0.041 0.136 883 Planarity : 0.003 0.036 1009 Dihedral : 14.376 88.070 2249 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: -0.32 (0.32), residues: 704 helix: 1.48 (0.29), residues: 325 sheet: -1.30 (0.47), residues: 129 loop : -1.88 (0.35), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1028 HIS 0.006 0.001 HIS B 908 PHE 0.013 0.002 PHE A 811 TYR 0.016 0.001 TYR A 903 ARG 0.006 0.001 ARG B 878 Details of bonding type rmsd hydrogen bonds : bond 0.14517 ( 259) hydrogen bonds : angle 6.05245 ( 774) covalent geometry : bond 0.00545 ( 5937) covalent geometry : angle 0.69486 ( 8012) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.665 Fit side-chains REVERT: A 863 LEU cc_start: 0.7996 (tp) cc_final: 0.7512 (mm) REVERT: A 868 GLN cc_start: 0.8707 (tp40) cc_final: 0.8474 (tp40) REVERT: A 903 TYR cc_start: 0.8747 (t80) cc_final: 0.8528 (t80) REVERT: B 912 ASP cc_start: 0.7657 (m-30) cc_final: 0.7302 (m-30) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.2014 time to fit residues: 29.2711 Evaluate side-chains 85 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1067 HIS A1164 ASN B 872 GLN B1100 ASN B1114 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.147030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.113144 restraints weight = 6979.122| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.50 r_work: 0.3146 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5937 Z= 0.180 Angle : 0.655 8.794 8012 Z= 0.318 Chirality : 0.047 0.192 883 Planarity : 0.004 0.040 1009 Dihedral : 8.081 89.002 780 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.07 % Allowed : 7.48 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.32), residues: 704 helix: 1.33 (0.28), residues: 333 sheet: -1.40 (0.45), residues: 138 loop : -1.83 (0.36), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1028 HIS 0.005 0.001 HIS B 908 PHE 0.027 0.002 PHE A1030 TYR 0.017 0.002 TYR A 767 ARG 0.006 0.001 ARG B 878 Details of bonding type rmsd hydrogen bonds : bond 0.04833 ( 259) hydrogen bonds : angle 5.09784 ( 774) covalent geometry : bond 0.00426 ( 5937) covalent geometry : angle 0.65462 ( 8012) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.690 Fit side-chains REVERT: A 863 LEU cc_start: 0.7729 (tp) cc_final: 0.7369 (mm) REVERT: B 835 MET cc_start: 0.8468 (ttm) cc_final: 0.8226 (mtm) REVERT: B 912 ASP cc_start: 0.8206 (m-30) cc_final: 0.7926 (m-30) REVERT: B 1047 LYS cc_start: 0.7099 (mttt) cc_final: 0.6802 (pttt) outliers start: 13 outliers final: 10 residues processed: 108 average time/residue: 0.1923 time to fit residues: 27.0992 Evaluate side-chains 91 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 763 GLN Chi-restraints excluded: chain A residue 1032 ASP Chi-restraints excluded: chain A residue 1067 HIS Chi-restraints excluded: chain B residue 920 ILE Chi-restraints excluded: chain B residue 1082 ASP Chi-restraints excluded: chain B residue 1091 ASP Chi-restraints excluded: chain B residue 1107 ILE Chi-restraints excluded: chain B residue 1126 MET Chi-restraints excluded: chain B residue 1158 GLU Chi-restraints excluded: chain B residue 1165 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 42 optimal weight: 0.6980 chunk 67 optimal weight: 0.0060 chunk 63 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1067 HIS A1164 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.146718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.112515 restraints weight = 7071.989| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.52 r_work: 0.3091 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5937 Z= 0.149 Angle : 0.608 8.424 8012 Z= 0.299 Chirality : 0.044 0.142 883 Planarity : 0.004 0.043 1009 Dihedral : 7.991 88.439 780 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.71 % Allowed : 8.92 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.31), residues: 704 helix: 1.28 (0.28), residues: 333 sheet: -1.24 (0.46), residues: 138 loop : -1.80 (0.36), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1028 HIS 0.004 0.001 HIS B 908 PHE 0.023 0.001 PHE A1030 TYR 0.014 0.001 TYR A 903 ARG 0.007 0.001 ARG A 898 Details of bonding type rmsd hydrogen bonds : bond 0.04384 ( 259) hydrogen bonds : angle 4.95900 ( 774) covalent geometry : bond 0.00348 ( 5937) covalent geometry : angle 0.60756 ( 8012) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.708 Fit side-chains REVERT: A 863 LEU cc_start: 0.7803 (tp) cc_final: 0.7390 (mm) REVERT: A 870 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8445 (mt) REVERT: A 1053 LYS cc_start: 0.8380 (ttpp) cc_final: 0.8149 (ttpt) REVERT: B 835 MET cc_start: 0.8472 (ttm) cc_final: 0.8257 (mtm) REVERT: B 870 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8556 (mt) REVERT: B 912 ASP cc_start: 0.8211 (m-30) cc_final: 0.7976 (m-30) REVERT: B 1047 LYS cc_start: 0.7144 (mttt) cc_final: 0.6795 (pttt) outliers start: 17 outliers final: 12 residues processed: 98 average time/residue: 0.1976 time to fit residues: 26.4466 Evaluate side-chains 93 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 763 GLN Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 1032 ASP Chi-restraints excluded: chain A residue 1067 HIS Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 920 ILE Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1091 ASP Chi-restraints excluded: chain B residue 1114 HIS Chi-restraints excluded: chain B residue 1126 MET Chi-restraints excluded: chain B residue 1158 GLU Chi-restraints excluded: chain B residue 1165 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 6 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 16 optimal weight: 0.0040 chunk 66 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 26 optimal weight: 0.4980 chunk 36 optimal weight: 0.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1067 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.148572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.113924 restraints weight = 7260.046| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.57 r_work: 0.3104 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5937 Z= 0.149 Angle : 0.609 9.318 8012 Z= 0.295 Chirality : 0.043 0.142 883 Planarity : 0.004 0.043 1009 Dihedral : 7.894 88.041 780 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.87 % Allowed : 10.19 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.31), residues: 704 helix: 1.29 (0.28), residues: 332 sheet: -1.18 (0.46), residues: 138 loop : -1.83 (0.37), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1028 HIS 0.005 0.001 HIS A1067 PHE 0.020 0.001 PHE A1030 TYR 0.014 0.001 TYR A 903 ARG 0.006 0.000 ARG B 878 Details of bonding type rmsd hydrogen bonds : bond 0.04227 ( 259) hydrogen bonds : angle 4.85684 ( 774) covalent geometry : bond 0.00351 ( 5937) covalent geometry : angle 0.60867 ( 8012) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.631 Fit side-chains REVERT: A 863 LEU cc_start: 0.7799 (tp) cc_final: 0.7365 (mm) REVERT: A 870 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8459 (mt) REVERT: A 1053 LYS cc_start: 0.8371 (ttpp) cc_final: 0.8151 (ttpt) REVERT: B 835 MET cc_start: 0.8485 (ttm) cc_final: 0.8274 (mtm) REVERT: B 870 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8544 (mt) REVERT: B 912 ASP cc_start: 0.8221 (m-30) cc_final: 0.7992 (m-30) REVERT: B 1047 LYS cc_start: 0.7143 (mttt) cc_final: 0.6778 (pttt) REVERT: B 1072 MET cc_start: 0.6994 (mmm) cc_final: 0.6647 (ttt) outliers start: 18 outliers final: 14 residues processed: 101 average time/residue: 0.1793 time to fit residues: 23.7388 Evaluate side-chains 100 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 763 GLN Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 1032 ASP Chi-restraints excluded: chain A residue 1067 HIS Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 920 ILE Chi-restraints excluded: chain B residue 1082 ASP Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1091 ASP Chi-restraints excluded: chain B residue 1107 ILE Chi-restraints excluded: chain B residue 1114 HIS Chi-restraints excluded: chain B residue 1126 MET Chi-restraints excluded: chain B residue 1165 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 48 optimal weight: 0.0970 chunk 37 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1067 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.147284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.113359 restraints weight = 7077.724| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.50 r_work: 0.3109 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5937 Z= 0.145 Angle : 0.583 8.071 8012 Z= 0.289 Chirality : 0.044 0.146 883 Planarity : 0.004 0.046 1009 Dihedral : 7.761 86.249 780 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.18 % Allowed : 11.62 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.31), residues: 704 helix: 1.36 (0.28), residues: 333 sheet: -1.08 (0.46), residues: 138 loop : -1.84 (0.37), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1028 HIS 0.006 0.001 HIS A1067 PHE 0.019 0.001 PHE A1030 TYR 0.014 0.001 TYR A 903 ARG 0.011 0.001 ARG A 898 Details of bonding type rmsd hydrogen bonds : bond 0.04097 ( 259) hydrogen bonds : angle 4.78624 ( 774) covalent geometry : bond 0.00338 ( 5937) covalent geometry : angle 0.58346 ( 8012) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.628 Fit side-chains REVERT: A 765 LEU cc_start: 0.8541 (mp) cc_final: 0.8294 (tp) REVERT: A 863 LEU cc_start: 0.7782 (tp) cc_final: 0.7352 (mm) REVERT: A 870 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8435 (mt) REVERT: A 1120 GLN cc_start: 0.7438 (mm-40) cc_final: 0.7022 (mm-40) REVERT: A 1188 GLU cc_start: 0.7679 (tp30) cc_final: 0.7441 (tp30) REVERT: B 768 LEU cc_start: 0.8215 (mp) cc_final: 0.7874 (mp) REVERT: B 870 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8474 (mt) REVERT: B 1047 LYS cc_start: 0.7133 (mttt) cc_final: 0.6783 (pttt) REVERT: B 1072 MET cc_start: 0.6908 (mmm) cc_final: 0.6607 (ttt) REVERT: B 1143 LYS cc_start: 0.8267 (tppp) cc_final: 0.7994 (tptt) outliers start: 20 outliers final: 15 residues processed: 106 average time/residue: 0.1841 time to fit residues: 25.5293 Evaluate side-chains 99 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 763 GLN Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 1032 ASP Chi-restraints excluded: chain A residue 1067 HIS Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 920 ILE Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1091 ASP Chi-restraints excluded: chain B residue 1107 ILE Chi-restraints excluded: chain B residue 1114 HIS Chi-restraints excluded: chain B residue 1126 MET Chi-restraints excluded: chain B residue 1158 GLU Chi-restraints excluded: chain B residue 1165 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 14 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 44 optimal weight: 0.0870 chunk 59 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1067 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1164 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.147280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.113109 restraints weight = 7091.130| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.51 r_work: 0.3104 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5937 Z= 0.146 Angle : 0.610 9.565 8012 Z= 0.298 Chirality : 0.043 0.143 883 Planarity : 0.004 0.048 1009 Dihedral : 7.683 85.348 780 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.87 % Allowed : 13.22 % Favored : 83.92 % 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: -0.21 (0.32), residues: 704 helix: 1.38 (0.28), residues: 333 sheet: -0.93 (0.47), residues: 137 loop : -1.85 (0.37), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1028 HIS 0.005 0.001 HIS A1067 PHE 0.018 0.001 PHE A1030 TYR 0.014 0.001 TYR A 903 ARG 0.011 0.000 ARG A 898 Details of bonding type rmsd hydrogen bonds : bond 0.04027 ( 259) hydrogen bonds : angle 4.73355 ( 774) covalent geometry : bond 0.00341 ( 5937) covalent geometry : angle 0.61039 ( 8012) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.774 Fit side-chains REVERT: A 765 LEU cc_start: 0.8541 (mp) cc_final: 0.8297 (tp) REVERT: A 863 LEU cc_start: 0.7789 (tp) cc_final: 0.7357 (mm) REVERT: A 870 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8449 (mt) REVERT: A 1120 GLN cc_start: 0.7403 (mm-40) cc_final: 0.7107 (mm-40) REVERT: A 1188 GLU cc_start: 0.7695 (tp30) cc_final: 0.7394 (tp30) REVERT: B 870 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8488 (mt) REVERT: B 1047 LYS cc_start: 0.7163 (mttt) cc_final: 0.6799 (pttt) REVERT: B 1072 MET cc_start: 0.6880 (mmm) cc_final: 0.6610 (ttt) REVERT: B 1143 LYS cc_start: 0.8294 (tppp) cc_final: 0.8029 (tptt) REVERT: B 1184 MET cc_start: 0.8552 (mmm) cc_final: 0.8017 (tmm) outliers start: 18 outliers final: 15 residues processed: 98 average time/residue: 0.1800 time to fit residues: 23.3555 Evaluate side-chains 101 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 763 GLN Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 1032 ASP Chi-restraints excluded: chain A residue 1067 HIS Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 920 ILE Chi-restraints excluded: chain B residue 1082 ASP Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1107 ILE Chi-restraints excluded: chain B residue 1114 HIS Chi-restraints excluded: chain B residue 1126 MET Chi-restraints excluded: chain B residue 1158 GLU Chi-restraints excluded: chain B residue 1165 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 37 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.147448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.113632 restraints weight = 7115.525| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.49 r_work: 0.3208 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5937 Z= 0.153 Angle : 0.600 8.818 8012 Z= 0.295 Chirality : 0.044 0.148 883 Planarity : 0.004 0.048 1009 Dihedral : 7.530 83.719 780 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.87 % Allowed : 13.22 % Favored : 83.92 % 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: -0.10 (0.32), residues: 704 helix: 1.41 (0.28), residues: 335 sheet: -0.84 (0.47), residues: 137 loop : -1.76 (0.38), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1028 HIS 0.005 0.001 HIS B 908 PHE 0.017 0.001 PHE A1030 TYR 0.014 0.001 TYR A 903 ARG 0.012 0.001 ARG A 898 Details of bonding type rmsd hydrogen bonds : bond 0.04053 ( 259) hydrogen bonds : angle 4.64578 ( 774) covalent geometry : bond 0.00362 ( 5937) covalent geometry : angle 0.60032 ( 8012) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.665 Fit side-chains REVERT: A 863 LEU cc_start: 0.7784 (tp) cc_final: 0.7341 (mm) REVERT: A 870 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8447 (mt) REVERT: A 1120 GLN cc_start: 0.7406 (mm-40) cc_final: 0.7014 (mm-40) REVERT: B 870 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8515 (mt) REVERT: B 1047 LYS cc_start: 0.7156 (mttt) cc_final: 0.6807 (pttt) REVERT: B 1072 MET cc_start: 0.7012 (mmm) cc_final: 0.6721 (ttt) REVERT: B 1143 LYS cc_start: 0.8309 (tppp) cc_final: 0.8041 (tptt) outliers start: 18 outliers final: 15 residues processed: 100 average time/residue: 0.1912 time to fit residues: 25.3651 Evaluate side-chains 98 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 763 GLN Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 1032 ASP Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 920 ILE Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1107 ILE Chi-restraints excluded: chain B residue 1114 HIS Chi-restraints excluded: chain B residue 1126 MET Chi-restraints excluded: chain B residue 1158 GLU Chi-restraints excluded: chain B residue 1165 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 65 optimal weight: 0.5980 chunk 61 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 2 optimal weight: 0.3980 chunk 35 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 53 optimal weight: 0.0970 chunk 68 optimal weight: 0.8980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 = 0.3778 r_free = 0.3778 target = 0.149135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.115406 restraints weight = 6975.100| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.47 r_work: 0.3187 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5937 Z= 0.130 Angle : 0.603 10.610 8012 Z= 0.292 Chirality : 0.044 0.207 883 Planarity : 0.004 0.046 1009 Dihedral : 7.399 83.579 780 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.55 % Allowed : 14.65 % Favored : 82.80 % 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: -0.05 (0.32), residues: 704 helix: 1.44 (0.28), residues: 335 sheet: -0.71 (0.47), residues: 137 loop : -1.77 (0.38), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1028 HIS 0.004 0.001 HIS B 908 PHE 0.018 0.001 PHE A1030 TYR 0.014 0.001 TYR A 903 ARG 0.013 0.000 ARG A 898 Details of bonding type rmsd hydrogen bonds : bond 0.03859 ( 259) hydrogen bonds : angle 4.60654 ( 774) covalent geometry : bond 0.00299 ( 5937) covalent geometry : angle 0.60317 ( 8012) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 1.179 Fit side-chains REVERT: A 765 LEU cc_start: 0.8523 (mp) cc_final: 0.8268 (tp) REVERT: A 776 ARG cc_start: 0.8193 (mmm160) cc_final: 0.7881 (tpp80) REVERT: A 870 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8428 (mt) REVERT: A 1120 GLN cc_start: 0.7517 (mm-40) cc_final: 0.7180 (mm-40) REVERT: A 1188 GLU cc_start: 0.7739 (tp30) cc_final: 0.7317 (tp30) REVERT: B 870 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8484 (mt) REVERT: B 1047 LYS cc_start: 0.7169 (mttt) cc_final: 0.6785 (pttt) REVERT: B 1050 LYS cc_start: 0.8843 (mmmt) cc_final: 0.8222 (mtmm) REVERT: B 1143 LYS cc_start: 0.8310 (tppp) cc_final: 0.8047 (tptt) outliers start: 16 outliers final: 13 residues processed: 98 average time/residue: 0.2006 time to fit residues: 26.1306 Evaluate side-chains 97 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 763 GLN Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 1032 ASP Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 920 ILE Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1107 ILE Chi-restraints excluded: chain B residue 1114 HIS Chi-restraints excluded: chain B residue 1126 MET Chi-restraints excluded: chain B residue 1165 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 0.0050 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 16 optimal weight: 0.0870 chunk 41 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 1 optimal weight: 0.4980 overall best weight: 0.3972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1164 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.149640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.115588 restraints weight = 7092.480| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.53 r_work: 0.3147 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 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 0.027 5937 Z= 0.118 Angle : 0.576 7.716 8012 Z= 0.282 Chirality : 0.043 0.198 883 Planarity : 0.004 0.043 1009 Dihedral : 7.240 83.162 780 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.23 % Allowed : 15.29 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.32), residues: 704 helix: 1.57 (0.28), residues: 334 sheet: -0.63 (0.47), residues: 137 loop : -1.84 (0.36), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1028 HIS 0.003 0.001 HIS B 908 PHE 0.017 0.001 PHE A1030 TYR 0.014 0.001 TYR A 903 ARG 0.012 0.000 ARG A 898 Details of bonding type rmsd hydrogen bonds : bond 0.03701 ( 259) hydrogen bonds : angle 4.51845 ( 774) covalent geometry : bond 0.00266 ( 5937) covalent geometry : angle 0.57644 ( 8012) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.937 Fit side-chains REVERT: A 765 LEU cc_start: 0.8442 (mp) cc_final: 0.8207 (tp) REVERT: A 776 ARG cc_start: 0.8210 (mmm160) cc_final: 0.7885 (tpp80) REVERT: A 870 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8401 (mt) REVERT: B 870 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8432 (mt) REVERT: B 1047 LYS cc_start: 0.7118 (mttt) cc_final: 0.6742 (pttt) REVERT: B 1050 LYS cc_start: 0.8741 (mmmt) cc_final: 0.8156 (mtmm) REVERT: B 1143 LYS cc_start: 0.8291 (tppp) cc_final: 0.8030 (tptt) outliers start: 14 outliers final: 11 residues processed: 97 average time/residue: 0.1969 time to fit residues: 25.3783 Evaluate side-chains 96 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 763 GLN Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 1032 ASP Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 920 ILE Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1114 HIS Chi-restraints excluded: chain B residue 1126 MET Chi-restraints excluded: chain B residue 1165 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 5 optimal weight: 0.0970 chunk 63 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 16 optimal weight: 0.0970 overall best weight: 0.5976 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.149540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.115914 restraints weight = 7132.346| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.49 r_work: 0.3129 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5937 Z= 0.136 Angle : 0.610 11.023 8012 Z= 0.293 Chirality : 0.044 0.209 883 Planarity : 0.004 0.043 1009 Dihedral : 7.188 82.827 780 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.71 % Allowed : 15.29 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.32), residues: 704 helix: 1.52 (0.28), residues: 334 sheet: -0.53 (0.48), residues: 136 loop : -1.68 (0.37), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 892 HIS 0.005 0.001 HIS B 908 PHE 0.017 0.001 PHE A1030 TYR 0.014 0.001 TYR B1183 ARG 0.011 0.000 ARG A 898 Details of bonding type rmsd hydrogen bonds : bond 0.03791 ( 259) hydrogen bonds : angle 4.56745 ( 774) covalent geometry : bond 0.00317 ( 5937) covalent geometry : angle 0.61009 ( 8012) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.682 Fit side-chains REVERT: A 765 LEU cc_start: 0.8444 (mp) cc_final: 0.8185 (tp) REVERT: A 776 ARG cc_start: 0.8240 (mmm160) cc_final: 0.7898 (ttm170) REVERT: A 870 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8428 (mt) REVERT: B 863 LEU cc_start: 0.8619 (tt) cc_final: 0.8400 (tp) REVERT: B 870 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8451 (mt) REVERT: B 1047 LYS cc_start: 0.7148 (mttt) cc_final: 0.6758 (pttt) REVERT: B 1050 LYS cc_start: 0.8744 (mmmt) cc_final: 0.8108 (mtmm) REVERT: B 1143 LYS cc_start: 0.8269 (tppp) cc_final: 0.8015 (tptt) outliers start: 17 outliers final: 10 residues processed: 95 average time/residue: 0.2095 time to fit residues: 25.8635 Evaluate side-chains 95 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 763 GLN Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 1032 ASP Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 920 ILE Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1107 ILE Chi-restraints excluded: chain B residue 1114 HIS Chi-restraints excluded: chain B residue 1126 MET Chi-restraints excluded: chain B residue 1165 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 30 optimal weight: 0.0970 chunk 5 optimal weight: 0.8980 chunk 48 optimal weight: 0.0970 chunk 53 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 26 optimal weight: 0.0270 chunk 19 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 overall best weight: 0.2834 ------------------------------------------------------------------------------- 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 = 0.3828 r_free = 0.3828 target = 0.153469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.119564 restraints weight = 7105.778| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.53 r_work: 0.3223 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5937 Z= 0.111 Angle : 0.585 9.916 8012 Z= 0.282 Chirality : 0.043 0.197 883 Planarity : 0.004 0.049 1009 Dihedral : 7.029 83.004 780 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.91 % Allowed : 16.56 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.32), residues: 704 helix: 1.60 (0.28), residues: 334 sheet: -0.38 (0.48), residues: 137 loop : -1.72 (0.37), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1028 HIS 0.002 0.001 HIS B 908 PHE 0.017 0.001 PHE A1030 TYR 0.015 0.001 TYR B1142 ARG 0.014 0.000 ARG A 898 Details of bonding type rmsd hydrogen bonds : bond 0.03593 ( 259) hydrogen bonds : angle 4.51782 ( 774) covalent geometry : bond 0.00246 ( 5937) covalent geometry : angle 0.58451 ( 8012) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3348.52 seconds wall clock time: 59 minutes 25.86 seconds (3565.86 seconds total)