Starting phenix.real_space_refine on Fri Oct 10 13:23:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ste_40759/10_2025/8ste_40759.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ste_40759/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ste_40759/10_2025/8ste_40759.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ste_40759/10_2025/8ste_40759.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ste_40759/10_2025/8ste_40759.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ste_40759/10_2025/8ste_40759.map" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 1.53, per 1000 atoms: 0.26 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: 0.52 Conformation dependent library (CDL) restraints added in 413.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.21 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: 0.98 Time building geometry restraints manager: 0.71 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: 5.820 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.870 Find NCS groups from input model: 0.100 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:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.510 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.001 ARG B 878 TYR 0.016 0.001 TYR A 903 PHE 0.013 0.002 PHE A 811 TRP 0.008 0.001 TRP A1028 HIS 0.006 0.001 HIS B 908 Details of bonding type rmsd covalent geometry : bond 0.00545 ( 5937) covalent geometry : angle 0.69486 ( 8012) hydrogen bonds : bond 0.14517 ( 259) hydrogen bonds : angle 6.05245 ( 774) *********************** 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 : 0.163 Fit side-chains revert: symmetry clash REVERT: A 829 ARG cc_start: 0.8454 (mmp-170) cc_final: 0.8252 (mtt90) 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) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.0854 time to fit residues: 12.4889 Evaluate side-chains 86 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.3980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.0980 chunk 27 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1067 HIS A1164 ASN B1100 ASN B1114 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.149951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.114887 restraints weight = 7161.924| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.64 r_work: 0.3224 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5937 Z= 0.142 Angle : 0.627 9.277 8012 Z= 0.304 Chirality : 0.045 0.179 883 Planarity : 0.004 0.039 1009 Dihedral : 7.993 89.803 780 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.75 % Allowed : 7.32 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.32), residues: 704 helix: 1.39 (0.28), residues: 333 sheet: -1.29 (0.46), residues: 137 loop : -1.85 (0.36), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 878 TYR 0.015 0.001 TYR A 767 PHE 0.027 0.002 PHE A1030 TRP 0.012 0.001 TRP A1028 HIS 0.005 0.001 HIS A 773 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 5937) covalent geometry : angle 0.62654 ( 8012) hydrogen bonds : bond 0.04660 ( 259) hydrogen bonds : angle 5.05482 ( 774) *********************** 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 109 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.169 Fit side-chains REVERT: A 829 ARG cc_start: 0.8858 (mmp-170) cc_final: 0.8178 (mtt90) REVERT: B 851 MET cc_start: 0.8810 (mtt) cc_final: 0.8539 (mtt) REVERT: B 912 ASP cc_start: 0.8242 (m-30) cc_final: 0.7996 (m-30) REVERT: B 1047 LYS cc_start: 0.7081 (mttt) cc_final: 0.6790 (pttt) outliers start: 11 outliers final: 9 residues processed: 104 average time/residue: 0.0900 time to fit residues: 12.0798 Evaluate side-chains 90 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.186 ------------------------------------------------------------------------------- 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 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 43 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 50 optimal weight: 0.0370 chunk 0 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.7260 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.148541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.114356 restraints weight = 7037.537| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.49 r_work: 0.3125 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5937 Z= 0.154 Angle : 0.611 9.126 8012 Z= 0.298 Chirality : 0.044 0.138 883 Planarity : 0.004 0.042 1009 Dihedral : 7.979 89.107 780 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.31), residues: 704 helix: 1.35 (0.28), residues: 332 sheet: -1.25 (0.46), residues: 138 loop : -1.79 (0.36), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 898 TYR 0.014 0.001 TYR A 903 PHE 0.022 0.001 PHE A1030 TRP 0.010 0.001 TRP A1028 HIS 0.005 0.001 HIS B 908 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 5937) covalent geometry : angle 0.61147 ( 8012) hydrogen bonds : bond 0.04364 ( 259) hydrogen bonds : angle 4.90825 ( 774) *********************** 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 106 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.281 Fit side-chains REVERT: A 829 ARG cc_start: 0.8862 (mmp-170) cc_final: 0.8264 (mtt90) REVERT: A 863 LEU cc_start: 0.7724 (tp) cc_final: 0.7306 (mm) REVERT: A 870 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8435 (mt) REVERT: A 1053 LYS cc_start: 0.8384 (ttpp) cc_final: 0.8163 (ttpt) REVERT: B 835 MET cc_start: 0.8514 (ttm) cc_final: 0.8242 (mtm) REVERT: B 912 ASP cc_start: 0.8178 (m-30) cc_final: 0.7932 (m-30) REVERT: B 1047 LYS cc_start: 0.7143 (mttt) cc_final: 0.6797 (pttt) outliers start: 17 outliers final: 8 residues processed: 102 average time/residue: 0.0847 time to fit residues: 11.4213 Evaluate side-chains 94 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.234 ------------------------------------------------------------------------------- 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 1091 ASP 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 0 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 0.0020 chunk 23 optimal weight: 1.9990 chunk 48 optimal weight: 0.2980 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 54 optimal weight: 0.0980 chunk 67 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.3588 ------------------------------------------------------------------------------- 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 = 0.3808 r_free = 0.3808 target = 0.151390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.116766 restraints weight = 7085.672| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.56 r_work: 0.3227 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5937 Z= 0.121 Angle : 0.574 7.383 8012 Z= 0.283 Chirality : 0.042 0.131 883 Planarity : 0.004 0.043 1009 Dihedral : 7.800 88.004 780 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.91 % Allowed : 10.67 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.31), residues: 704 helix: 1.34 (0.28), residues: 335 sheet: -1.17 (0.46), residues: 139 loop : -1.82 (0.36), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 878 TYR 0.013 0.001 TYR A 903 PHE 0.020 0.001 PHE A1030 TRP 0.010 0.001 TRP A1028 HIS 0.003 0.001 HIS B 908 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 5937) covalent geometry : angle 0.57415 ( 8012) hydrogen bonds : bond 0.03991 ( 259) hydrogen bonds : angle 4.75729 ( 774) *********************** 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 105 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.239 Fit side-chains REVERT: A 765 LEU cc_start: 0.8550 (mp) cc_final: 0.8319 (tp) REVERT: A 829 ARG cc_start: 0.8802 (mmp-170) cc_final: 0.8258 (mtt90) REVERT: B 771 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8005 (tp) REVERT: B 1047 LYS cc_start: 0.7120 (mttt) cc_final: 0.6756 (pttt) REVERT: B 1072 MET cc_start: 0.7010 (mmm) cc_final: 0.6667 (ttt) REVERT: B 1143 LYS cc_start: 0.8315 (tppp) cc_final: 0.8009 (tptt) outliers start: 12 outliers final: 8 residues processed: 99 average time/residue: 0.0813 time to fit residues: 10.6061 Evaluate side-chains 93 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.230 ------------------------------------------------------------------------------- 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 771 LEU 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 1165 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 64 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.146196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.111595 restraints weight = 7364.046| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.68 r_work: 0.3207 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1995 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= 0.156 Angle : 0.594 7.892 8012 Z= 0.291 Chirality : 0.044 0.132 883 Planarity : 0.004 0.044 1009 Dihedral : 7.725 86.667 780 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.39 % Allowed : 11.62 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.31), residues: 704 helix: 1.37 (0.28), residues: 334 sheet: -1.02 (0.46), residues: 137 loop : -1.78 (0.37), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 878 TYR 0.013 0.001 TYR A 903 PHE 0.018 0.001 PHE A1030 TRP 0.009 0.001 TRP A1028 HIS 0.005 0.001 HIS B 908 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 5937) covalent geometry : angle 0.59380 ( 8012) hydrogen bonds : bond 0.04070 ( 259) hydrogen bonds : angle 4.71661 ( 774) *********************** 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 106 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.231 Fit side-chains REVERT: A 765 LEU cc_start: 0.8546 (mp) cc_final: 0.8329 (tp) REVERT: A 829 ARG cc_start: 0.8868 (mmp-170) cc_final: 0.8276 (mtt90) REVERT: A 863 LEU cc_start: 0.7847 (tp) cc_final: 0.7402 (mm) REVERT: A 870 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8488 (mt) REVERT: B 768 LEU cc_start: 0.8311 (mp) cc_final: 0.7925 (mp) REVERT: B 771 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8101 (tp) REVERT: B 1047 LYS cc_start: 0.7192 (mttt) cc_final: 0.6810 (pttt) REVERT: B 1072 MET cc_start: 0.6944 (mmm) cc_final: 0.6643 (ttt) REVERT: B 1143 LYS cc_start: 0.8403 (tppp) cc_final: 0.8131 (tptt) outliers start: 15 outliers final: 11 residues processed: 98 average time/residue: 0.0892 time to fit residues: 11.3687 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 : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 763 GLN 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 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 59 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 53 optimal weight: 0.0570 chunk 14 optimal weight: 0.6980 chunk 24 optimal weight: 0.4980 chunk 12 optimal weight: 0.1980 chunk 13 optimal weight: 0.2980 chunk 67 optimal weight: 0.0970 chunk 2 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 overall best weight: 0.2296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1067 HIS B1164 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.152078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.118099 restraints weight = 7043.979| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.51 r_work: 0.3248 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5937 Z= 0.114 Angle : 0.569 7.302 8012 Z= 0.283 Chirality : 0.042 0.129 883 Planarity : 0.004 0.044 1009 Dihedral : 7.552 85.687 780 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.75 % Allowed : 13.38 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.32), residues: 704 helix: 1.47 (0.28), residues: 334 sheet: -0.84 (0.47), residues: 137 loop : -1.80 (0.36), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 898 TYR 0.013 0.001 TYR A 903 PHE 0.018 0.001 PHE A1030 TRP 0.010 0.001 TRP A1028 HIS 0.003 0.001 HIS A1067 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 5937) covalent geometry : angle 0.56919 ( 8012) hydrogen bonds : bond 0.03748 ( 259) hydrogen bonds : angle 4.63522 ( 774) *********************** 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 103 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.247 Fit side-chains REVERT: A 765 LEU cc_start: 0.8525 (mp) cc_final: 0.8279 (tp) REVERT: A 829 ARG cc_start: 0.8799 (mmp-170) cc_final: 0.8277 (mtt90) REVERT: A 870 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8400 (mt) REVERT: A 1067 HIS cc_start: 0.8168 (OUTLIER) cc_final: 0.7341 (p-80) REVERT: B 771 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.7974 (tp) REVERT: B 1047 LYS cc_start: 0.7090 (mttt) cc_final: 0.6719 (pttt) REVERT: B 1072 MET cc_start: 0.6884 (mmm) cc_final: 0.6618 (ttt) REVERT: B 1143 LYS cc_start: 0.8358 (tppp) cc_final: 0.8043 (tptt) outliers start: 11 outliers final: 4 residues processed: 97 average time/residue: 0.0849 time to fit residues: 10.9294 Evaluate side-chains 92 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 763 GLN 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 1114 HIS Chi-restraints excluded: chain B residue 1126 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 34 optimal weight: 0.0470 chunk 11 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 57 optimal weight: 0.0870 chunk 56 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 0.3980 chunk 19 optimal weight: 0.9990 overall best weight: 0.3656 ------------------------------------------------------------------------------- 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 = 0.3810 r_free = 0.3810 target = 0.149480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.115047 restraints weight = 7194.889| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.66 r_work: 0.3235 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5937 Z= 0.117 Angle : 0.560 7.222 8012 Z= 0.279 Chirality : 0.042 0.141 883 Planarity : 0.004 0.042 1009 Dihedral : 7.415 84.234 780 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.55 % Allowed : 12.90 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.32), residues: 704 helix: 1.51 (0.28), residues: 334 sheet: -0.76 (0.47), residues: 137 loop : -1.78 (0.36), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 898 TYR 0.013 0.001 TYR A 903 PHE 0.017 0.001 PHE A1030 TRP 0.010 0.001 TRP A1028 HIS 0.006 0.001 HIS A1067 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 5937) covalent geometry : angle 0.56027 ( 8012) hydrogen bonds : bond 0.03684 ( 259) hydrogen bonds : angle 4.58908 ( 774) *********************** 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: 16 poor density : 89 time to evaluate : 0.227 Fit side-chains REVERT: A 765 LEU cc_start: 0.8517 (mp) cc_final: 0.8310 (tp) REVERT: A 829 ARG cc_start: 0.8882 (mmp-170) cc_final: 0.8340 (mtt90) REVERT: A 870 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8447 (mt) REVERT: B 771 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8050 (tp) REVERT: B 1047 LYS cc_start: 0.7113 (mttt) cc_final: 0.6728 (pttt) REVERT: B 1143 LYS cc_start: 0.8402 (tppp) cc_final: 0.8117 (tptt) outliers start: 16 outliers final: 9 residues processed: 97 average time/residue: 0.0862 time to fit residues: 11.0168 Evaluate side-chains 96 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 763 GLN 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 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 1158 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 0.2980 chunk 69 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.150983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.117173 restraints weight = 7005.395| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.49 r_work: 0.3156 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5937 Z= 0.129 Angle : 0.575 7.976 8012 Z= 0.284 Chirality : 0.044 0.240 883 Planarity : 0.004 0.055 1009 Dihedral : 7.331 82.829 780 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.91 % Allowed : 13.69 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.32), residues: 704 helix: 1.44 (0.28), residues: 336 sheet: -0.68 (0.47), residues: 137 loop : -1.70 (0.36), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 898 TYR 0.012 0.001 TYR A 903 PHE 0.017 0.001 PHE A1030 TRP 0.010 0.001 TRP A1028 HIS 0.007 0.001 HIS A1067 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 5937) covalent geometry : angle 0.57531 ( 8012) hydrogen bonds : bond 0.03729 ( 259) hydrogen bonds : angle 4.59689 ( 774) *********************** 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 99 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.245 Fit side-chains REVERT: A 765 LEU cc_start: 0.8501 (mp) cc_final: 0.8276 (tp) REVERT: A 829 ARG cc_start: 0.8818 (mmp-170) cc_final: 0.8311 (mtt90) REVERT: A 870 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8404 (mt) REVERT: B 771 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.7971 (tp) REVERT: B 1047 LYS cc_start: 0.7057 (mttt) cc_final: 0.6604 (pttt) REVERT: B 1050 LYS cc_start: 0.8793 (mmmt) cc_final: 0.8109 (mtmm) REVERT: B 1143 LYS cc_start: 0.8342 (tppp) cc_final: 0.8019 (tptt) outliers start: 12 outliers final: 8 residues processed: 94 average time/residue: 0.0889 time to fit residues: 10.7688 Evaluate side-chains 95 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 763 GLN 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 66 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3784 r_free = 0.3784 target = 0.146989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.112813 restraints weight = 7261.942| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.66 r_work: 0.3196 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2360 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= 0.144 Angle : 0.585 8.333 8012 Z= 0.288 Chirality : 0.044 0.227 883 Planarity : 0.004 0.052 1009 Dihedral : 7.243 82.361 780 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.23 % Allowed : 13.22 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.32), residues: 704 helix: 1.49 (0.28), residues: 335 sheet: -0.57 (0.48), residues: 136 loop : -1.62 (0.37), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 898 TYR 0.013 0.001 TYR A 903 PHE 0.016 0.001 PHE A1030 TRP 0.010 0.001 TRP A1028 HIS 0.004 0.001 HIS B 908 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 5937) covalent geometry : angle 0.58521 ( 8012) hydrogen bonds : bond 0.03887 ( 259) hydrogen bonds : angle 4.55357 ( 774) *********************** 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 102 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.166 Fit side-chains REVERT: A 765 LEU cc_start: 0.8502 (mp) cc_final: 0.8282 (tp) REVERT: A 829 ARG cc_start: 0.8902 (mmp-170) cc_final: 0.8366 (mtt90) REVERT: A 863 LEU cc_start: 0.7836 (tp) cc_final: 0.7407 (mm) REVERT: A 870 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8463 (mt) REVERT: B 771 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8230 (tp) REVERT: B 1047 LYS cc_start: 0.7153 (mttt) cc_final: 0.6682 (pttt) REVERT: B 1050 LYS cc_start: 0.8813 (mmmt) cc_final: 0.8114 (mtmm) REVERT: B 1143 LYS cc_start: 0.8334 (tppp) cc_final: 0.8094 (tptt) outliers start: 14 outliers final: 9 residues processed: 99 average time/residue: 0.0874 time to fit residues: 11.2476 Evaluate side-chains 97 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 763 GLN Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 920 ILE 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 37 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 53 optimal weight: 0.0470 chunk 46 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1067 HIS B1164 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.147555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.113235 restraints weight = 7276.319| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.66 r_work: 0.3224 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5937 Z= 0.131 Angle : 0.599 10.659 8012 Z= 0.290 Chirality : 0.043 0.215 883 Planarity : 0.004 0.043 1009 Dihedral : 7.174 82.405 780 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.75 % Allowed : 14.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.32), residues: 704 helix: 1.45 (0.28), residues: 336 sheet: -0.55 (0.48), residues: 137 loop : -1.62 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 898 TYR 0.016 0.001 TYR B1142 PHE 0.016 0.001 PHE A1030 TRP 0.010 0.001 TRP A1028 HIS 0.005 0.001 HIS B 908 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 5937) covalent geometry : angle 0.59869 ( 8012) hydrogen bonds : bond 0.03786 ( 259) hydrogen bonds : angle 4.54821 ( 774) ********************** 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: 11 poor density : 91 time to evaluate : 0.248 Fit side-chains REVERT: A 765 LEU cc_start: 0.8475 (mp) cc_final: 0.8260 (tp) REVERT: A 829 ARG cc_start: 0.8903 (mmp-170) cc_final: 0.8358 (mtt90) REVERT: A 870 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8459 (mt) REVERT: B 1047 LYS cc_start: 0.7144 (mttt) cc_final: 0.6700 (pttt) REVERT: B 1050 LYS cc_start: 0.8750 (mmmt) cc_final: 0.8077 (mtmm) REVERT: B 1143 LYS cc_start: 0.8353 (tppp) cc_final: 0.8111 (tptt) outliers start: 11 outliers final: 9 residues processed: 98 average time/residue: 0.0858 time to fit residues: 11.0741 Evaluate side-chains 100 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 763 GLN 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 48 optimal weight: 0.2980 chunk 8 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 1 optimal weight: 0.0370 overall best weight: 0.4658 ------------------------------------------------------------------------------- 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 = 0.3795 r_free = 0.3795 target = 0.148359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.114006 restraints weight = 7169.689| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.63 r_work: 0.3232 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5937 Z= 0.124 Angle : 0.581 8.831 8012 Z= 0.287 Chirality : 0.043 0.209 883 Planarity : 0.004 0.043 1009 Dihedral : 7.096 82.406 780 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.23 % Allowed : 13.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.32), residues: 704 helix: 1.47 (0.28), residues: 335 sheet: -0.51 (0.48), residues: 138 loop : -1.72 (0.36), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 898 TYR 0.012 0.001 TYR A 903 PHE 0.016 0.001 PHE A1030 TRP 0.010 0.001 TRP A1028 HIS 0.005 0.001 HIS A1067 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 5937) covalent geometry : angle 0.58147 ( 8012) hydrogen bonds : bond 0.03715 ( 259) hydrogen bonds : angle 4.56415 ( 774) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1536.50 seconds wall clock time: 27 minutes 11.27 seconds (1631.27 seconds total)