Starting phenix.real_space_refine on Tue Feb 11 14:27:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ste_40759/02_2025/8ste_40759.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ste_40759/02_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_40759/02_2025/8ste_40759.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ste_40759/02_2025/8ste_40759.map" model { file = "/net/cci-nas-00/data/ceres_data/8ste_40759/02_2025/8ste_40759.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ste_40759/02_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-5592/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: 5.47, per 1000 atoms: 0.94 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: 1.80 Conformation dependent library (CDL) restraints added in 868.5 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: 0.59 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: 1.48 Time building geometry restraints manager: 1.77 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: 3.410 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: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.560 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.320 ------------------------------------------------------------------------------- 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= 0.346 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 *********************** 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 : 0.770 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: 0.2018 time to fit residues: 29.3036 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 : 0.669 ------------------------------------------------------------------------------- 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 = 0.3755 r_free = 0.3755 target = 0.146908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.113224 restraints weight = 6975.082| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.49 r_work: 0.3147 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 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= 0.279 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 *********************** 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 : 0.697 Fit side-chains REVERT: A 863 LEU cc_start: 0.7727 (tp) cc_final: 0.7367 (mm) REVERT: B 835 MET cc_start: 0.8468 (ttm) cc_final: 0.8226 (mtm) REVERT: B 912 ASP cc_start: 0.8205 (m-30) cc_final: 0.7927 (m-30) REVERT: B 1047 LYS cc_start: 0.7097 (mttt) cc_final: 0.6801 (pttt) outliers start: 13 outliers final: 10 residues processed: 108 average time/residue: 0.1886 time to fit residues: 26.4256 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 : 0.677 ------------------------------------------------------------------------------- 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: 0.0040 chunk 63 optimal weight: 0.9980 chunk 35 optimal weight: 0.0020 chunk 27 optimal weight: 1.9990 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: 4.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.4600 ------------------------------------------------------------------------------- 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 = 0.3780 r_free = 0.3780 target = 0.149138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.114986 restraints weight = 7029.176| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.51 r_work: 0.3119 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1668 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= 0.198 Angle : 0.595 8.140 8012 Z= 0.293 Chirality : 0.044 0.134 883 Planarity : 0.004 0.043 1009 Dihedral : 7.955 88.710 780 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.87 % Allowed : 9.08 % Favored : 88.06 % 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: -0.33 (0.31), residues: 704 helix: 1.31 (0.28), residues: 333 sheet: -1.21 (0.46), residues: 138 loop : -1.80 (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 0.023 0.001 PHE A1030 TYR 0.014 0.001 TYR A 903 ARG 0.008 0.001 ARG A 898 *********************** 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 103 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.733 Fit side-chains REVERT: A 863 LEU cc_start: 0.7747 (tp) cc_final: 0.7336 (mm) REVERT: A 870 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8411 (mt) REVERT: A 1053 LYS cc_start: 0.8380 (ttpp) cc_final: 0.8164 (ttpt) REVERT: B 835 MET cc_start: 0.8467 (ttm) cc_final: 0.8235 (mtm) REVERT: B 912 ASP cc_start: 0.8170 (m-30) cc_final: 0.7939 (m-30) REVERT: B 1047 LYS cc_start: 0.7135 (mttt) cc_final: 0.6785 (pttt) outliers start: 18 outliers final: 12 residues processed: 96 average time/residue: 0.1836 time to fit residues: 23.3178 Evaluate side-chains 90 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.676 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 16 optimal weight: 0.4980 chunk 66 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 26 optimal weight: 0.0060 chunk 36 optimal weight: 3.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.147853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.113088 restraints weight = 7271.050| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.59 r_work: 0.3088 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5937 Z= 0.263 Angle : 0.615 9.240 8012 Z= 0.299 Chirality : 0.044 0.130 883 Planarity : 0.004 0.044 1009 Dihedral : 7.895 87.550 780 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.55 % Allowed : 10.83 % Favored : 86.62 % 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: -0.38 (0.31), residues: 704 helix: 1.26 (0.28), residues: 332 sheet: -1.19 (0.46), residues: 138 loop : -1.82 (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 B 908 PHE 0.020 0.001 PHE A1030 TYR 0.014 0.001 TYR A 903 ARG 0.006 0.000 ARG B 878 *********************** 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 106 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.717 Fit side-chains REVERT: A 863 LEU cc_start: 0.7797 (tp) cc_final: 0.7360 (mm) REVERT: A 870 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8480 (mt) REVERT: A 1053 LYS cc_start: 0.8391 (ttpp) cc_final: 0.8162 (ttpt) REVERT: B 912 ASP cc_start: 0.8239 (m-30) cc_final: 0.8009 (m-30) REVERT: B 1047 LYS cc_start: 0.7160 (mttt) cc_final: 0.6783 (pttt) REVERT: B 1072 MET cc_start: 0.6987 (mmm) cc_final: 0.6661 (ttt) REVERT: B 1143 LYS cc_start: 0.8286 (tppp) cc_final: 0.8021 (tptt) outliers start: 16 outliers final: 13 residues processed: 99 average time/residue: 0.1868 time to fit residues: 24.0595 Evaluate side-chains 99 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.663 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 21 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 48 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3775 r_free = 0.3775 target = 0.148392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.114221 restraints weight = 7056.689| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.52 r_work: 0.3102 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1977 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= 0.225 Angle : 0.583 8.187 8012 Z= 0.289 Chirality : 0.043 0.136 883 Planarity : 0.004 0.044 1009 Dihedral : 7.752 86.304 780 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.18 % Allowed : 11.31 % Favored : 85.51 % 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: -0.29 (0.31), residues: 704 helix: 1.33 (0.28), residues: 333 sheet: -1.08 (0.46), residues: 138 loop : -1.85 (0.37), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 0.012 0.001 ARG A 898 *********************** 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 111 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.685 Fit side-chains REVERT: A 863 LEU cc_start: 0.7798 (tp) cc_final: 0.7381 (mm) REVERT: A 870 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8446 (mt) REVERT: A 1053 LYS cc_start: 0.8376 (ttpp) cc_final: 0.8158 (ttpt) REVERT: A 1188 GLU cc_start: 0.7729 (tp30) cc_final: 0.7480 (tp30) REVERT: B 768 LEU cc_start: 0.8199 (mp) cc_final: 0.7854 (mp) REVERT: B 1047 LYS cc_start: 0.7191 (mttt) cc_final: 0.6837 (pttt) REVERT: B 1072 MET cc_start: 0.6867 (mmm) cc_final: 0.6581 (ttt) REVERT: B 1143 LYS cc_start: 0.8287 (tppp) cc_final: 0.8019 (tptt) outliers start: 20 outliers final: 17 residues processed: 103 average time/residue: 0.1879 time to fit residues: 25.2247 Evaluate side-chains 101 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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 792 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 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: 0.6980 chunk 51 optimal weight: 0.0970 chunk 7 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 44 optimal weight: 0.0770 chunk 59 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.5336 ------------------------------------------------------------------------------- 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 = 0.3757 r_free = 0.3757 target = 0.146946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.113103 restraints weight = 7092.582| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.50 r_work: 0.3125 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2156 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= 0.203 Angle : 0.591 9.591 8012 Z= 0.290 Chirality : 0.043 0.141 883 Planarity : 0.004 0.046 1009 Dihedral : 7.631 85.543 780 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.71 % Allowed : 12.26 % Favored : 85.03 % 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: -0.17 (0.32), residues: 704 helix: 1.44 (0.28), residues: 332 sheet: -0.93 (0.47), residues: 138 loop : -1.84 (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 0.018 0.001 PHE A1030 TYR 0.013 0.001 TYR A 903 ARG 0.011 0.000 ARG A 898 *********************** 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 109 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.715 Fit side-chains REVERT: A 765 LEU cc_start: 0.8533 (mp) cc_final: 0.8287 (tp) REVERT: A 863 LEU cc_start: 0.7763 (tp) cc_final: 0.7342 (mm) REVERT: A 870 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8422 (mt) REVERT: A 1053 LYS cc_start: 0.8353 (ttpp) cc_final: 0.8151 (ttpt) REVERT: A 1188 GLU cc_start: 0.7634 (tp30) cc_final: 0.7321 (tp30) REVERT: B 1047 LYS cc_start: 0.7196 (mttt) cc_final: 0.6825 (pttt) REVERT: B 1072 MET cc_start: 0.6984 (mmm) cc_final: 0.6667 (ttt) REVERT: B 1143 LYS cc_start: 0.8280 (tppp) cc_final: 0.8016 (tptt) REVERT: B 1184 MET cc_start: 0.8557 (mmm) cc_final: 0.8054 (tmm) outliers start: 17 outliers final: 14 residues processed: 102 average time/residue: 0.1864 time to fit residues: 25.0094 Evaluate side-chains 103 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 37 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 = 0.3756 r_free = 0.3756 target = 0.147018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.113039 restraints weight = 7118.527| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.50 r_work: 0.3089 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2200 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= 0.262 Angle : 0.605 8.921 8012 Z= 0.300 Chirality : 0.044 0.156 883 Planarity : 0.004 0.051 1009 Dihedral : 7.573 84.195 780 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.71 % Allowed : 12.74 % 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 (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: -0.15 (0.32), residues: 704 helix: 1.35 (0.28), residues: 334 sheet: -0.84 (0.47), residues: 138 loop : -1.76 (0.38), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1028 HIS 0.009 0.001 HIS A1067 PHE 0.017 0.002 PHE A1030 TYR 0.014 0.001 TYR A 903 ARG 0.011 0.000 ARG A 898 *********************** 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: 17 poor density : 88 time to evaluate : 0.632 Fit side-chains REVERT: A 863 LEU cc_start: 0.7787 (tp) cc_final: 0.7352 (mm) REVERT: A 870 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8460 (mt) REVERT: A 1053 LYS cc_start: 0.8366 (ttpp) cc_final: 0.8155 (ttpt) REVERT: A 1120 GLN cc_start: 0.7302 (mm-40) cc_final: 0.7005 (mm-40) REVERT: B 1047 LYS cc_start: 0.7151 (mttt) cc_final: 0.6784 (pttt) REVERT: B 1072 MET cc_start: 0.6950 (mmm) cc_final: 0.6687 (ttt) REVERT: B 1143 LYS cc_start: 0.8283 (tppp) cc_final: 0.8015 (tptt) outliers start: 17 outliers final: 16 residues processed: 100 average time/residue: 0.1847 time to fit residues: 24.2650 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 : 0.732 ------------------------------------------------------------------------------- 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 825 MET 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 792 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: 0.8980 chunk 61 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 53 optimal weight: 0.0020 chunk 68 optimal weight: 0.4980 overall best weight: 0.6588 ------------------------------------------------------------------------------- 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 = 0.3769 r_free = 0.3769 target = 0.148130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.114575 restraints weight = 6977.194| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.46 r_work: 0.3113 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2334 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= 0.214 Angle : 0.603 11.141 8012 Z= 0.294 Chirality : 0.043 0.191 883 Planarity : 0.004 0.050 1009 Dihedral : 7.424 83.825 780 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.55 % Allowed : 14.17 % Favored : 83.28 % 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: 1.36 (0.28), residues: 335 sheet: -0.70 (0.47), residues: 138 loop : -1.77 (0.38), residues: 231 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 0.014 0.001 ARG A 898 *********************** 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 103 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.695 Fit side-chains REVERT: A 776 ARG cc_start: 0.8184 (mmm160) cc_final: 0.7881 (tpp80) REVERT: A 863 LEU cc_start: 0.7775 (tp) cc_final: 0.7371 (mm) REVERT: A 870 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8442 (mt) REVERT: A 1053 LYS cc_start: 0.8353 (ttpp) cc_final: 0.8129 (ttpt) REVERT: B 1047 LYS cc_start: 0.7198 (mttt) cc_final: 0.6855 (pttt) REVERT: B 1072 MET cc_start: 0.6870 (mmm) cc_final: 0.6639 (ttt) REVERT: B 1143 LYS cc_start: 0.8283 (tppp) cc_final: 0.8023 (tptt) outliers start: 16 outliers final: 15 residues processed: 98 average time/residue: 0.1904 time to fit residues: 24.4384 Evaluate side-chains 101 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.662 ------------------------------------------------------------------------------- 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 825 MET 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 44 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3753 r_free = 0.3753 target = 0.146924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.113205 restraints weight = 7086.009| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.49 r_work: 0.3115 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2441 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= 0.217 Angle : 0.590 8.490 8012 Z= 0.291 Chirality : 0.044 0.214 883 Planarity : 0.004 0.044 1009 Dihedral : 7.331 83.176 780 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.55 % Allowed : 14.49 % Favored : 82.96 % 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: -0.01 (0.32), residues: 704 helix: 1.44 (0.28), residues: 335 sheet: -0.62 (0.47), residues: 138 loop : -1.76 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 892 HIS 0.004 0.001 HIS B 908 PHE 0.017 0.001 PHE A1030 TYR 0.013 0.001 TYR A 903 ARG 0.012 0.000 ARG A 898 *********************** 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 104 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.619 Fit side-chains REVERT: A 765 LEU cc_start: 0.8474 (mp) cc_final: 0.8211 (tp) REVERT: A 776 ARG cc_start: 0.8212 (mmm160) cc_final: 0.7897 (tpp80) REVERT: A 863 LEU cc_start: 0.7761 (tp) cc_final: 0.7346 (mm) REVERT: A 870 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8439 (mt) REVERT: A 1053 LYS cc_start: 0.8349 (ttpp) cc_final: 0.8123 (ttpt) REVERT: A 1143 LYS cc_start: 0.7988 (tptt) cc_final: 0.7666 (tppt) REVERT: B 1047 LYS cc_start: 0.7158 (mttt) cc_final: 0.6751 (pttt) REVERT: B 1050 LYS cc_start: 0.8826 (mmmt) cc_final: 0.8199 (mtmm) REVERT: B 1143 LYS cc_start: 0.8275 (tppp) cc_final: 0.8008 (tptt) outliers start: 16 outliers final: 15 residues processed: 100 average time/residue: 0.1999 time to fit residues: 25.8763 Evaluate side-chains 104 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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 825 MET 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 5 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3759 r_free = 0.3759 target = 0.147310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.113580 restraints weight = 7163.418| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.50 r_work: 0.3098 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5937 Z= 0.250 Angle : 0.623 10.309 8012 Z= 0.303 Chirality : 0.044 0.204 883 Planarity : 0.004 0.044 1009 Dihedral : 7.341 84.204 780 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.71 % Allowed : 14.01 % Favored : 83.28 % 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: -0.04 (0.32), residues: 704 helix: 1.37 (0.28), residues: 335 sheet: -0.58 (0.48), residues: 138 loop : -1.73 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 892 HIS 0.005 0.001 HIS B 908 PHE 0.017 0.002 PHE A1030 TYR 0.013 0.001 TYR A 903 ARG 0.012 0.000 ARG A 898 ********************** 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 104 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.692 Fit side-chains REVERT: A 776 ARG cc_start: 0.8202 (mmm160) cc_final: 0.7911 (tpp80) REVERT: A 863 LEU cc_start: 0.7792 (tp) cc_final: 0.7369 (mm) REVERT: A 870 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8458 (mt) REVERT: A 1053 LYS cc_start: 0.8361 (ttpp) cc_final: 0.8137 (ttpt) REVERT: A 1143 LYS cc_start: 0.7998 (tptt) cc_final: 0.7667 (tppt) REVERT: B 863 LEU cc_start: 0.8609 (tt) cc_final: 0.8399 (tp) REVERT: B 1047 LYS cc_start: 0.7181 (mttt) cc_final: 0.6776 (pttt) REVERT: B 1050 LYS cc_start: 0.8828 (mmmt) cc_final: 0.8208 (mtmm) REVERT: B 1143 LYS cc_start: 0.8292 (tppp) cc_final: 0.8031 (tptt) outliers start: 17 outliers final: 14 residues processed: 99 average time/residue: 0.1997 time to fit residues: 25.5556 Evaluate side-chains 99 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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 825 MET Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 1032 ASP 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 30 optimal weight: 0.0040 chunk 5 optimal weight: 0.8980 chunk 48 optimal weight: 0.0670 chunk 53 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 overall best weight: 0.3930 ------------------------------------------------------------------------------- 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 = 0.3788 r_free = 0.3788 target = 0.149892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.115770 restraints weight = 7141.634| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.53 r_work: 0.3202 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2630 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= 0.177 Angle : 0.588 9.987 8012 Z= 0.286 Chirality : 0.043 0.200 883 Planarity : 0.004 0.043 1009 Dihedral : 7.188 86.254 780 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % 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: 0.11 (0.32), residues: 704 helix: 1.53 (0.28), residues: 334 sheet: -0.47 (0.48), residues: 137 loop : -1.74 (0.38), 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 0.017 0.001 TYR B1142 ARG 0.011 0.000 ARG A 898 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2894.25 seconds wall clock time: 52 minutes 19.33 seconds (3139.33 seconds total)