Starting phenix.real_space_refine on Tue Mar 11 21:10:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t07_40937/03_2025/8t07_40937.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t07_40937/03_2025/8t07_40937.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t07_40937/03_2025/8t07_40937.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t07_40937/03_2025/8t07_40937.map" model { file = "/net/cci-nas-00/data/ceres_data/8t07_40937/03_2025/8t07_40937.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t07_40937/03_2025/8t07_40937.cif" } resolution = 3.38 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= 0.003 sd= 0.066 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 Zn 2 6.06 5 S 44 5.16 5 C 4352 2.51 5 N 1090 2.21 5 O 1222 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6710 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1586 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 190} Chain: "B" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1586 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 190} Chain: "C" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 936 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "D" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "E" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 936 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "F" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.65, per 1000 atoms: 0.69 Number of scatterers: 6710 At special positions: 0 Unit cell: (87.15, 110.39, 104.58, 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) Zn 2 29.99 S 44 16.00 O 1222 8.00 N 1090 7.00 C 4352 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 59 " distance=2.03 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 59 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 97 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 97 " distance=2.04 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: 1.53 Conformation dependent library (CDL) restraints added in 931.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 184 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 48 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 180 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 184 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 48 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 180 " 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1572 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 12 sheets defined 44.0% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 5 through 14 removed outlier: 3.586A pdb=" N LEU A 9 " --> pdb=" O VAL A 5 " (cutoff:3.500A) Proline residue: A 11 - end of helix Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 18 through 28 Processing helix chain 'A' and resid 30 through 50 Processing helix chain 'A' and resid 55 through 59 removed outlier: 3.701A pdb=" N CYS A 59 " --> pdb=" O SER A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 87 removed outlier: 3.620A pdb=" N LEU A 66 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 85 " --> pdb=" O SER A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 111 Processing helix chain 'A' and resid 115 through 141 Proline residue: A 121 - end of helix Processing helix chain 'A' and resid 146 through 153 Processing helix chain 'A' and resid 153 through 170 Processing helix chain 'A' and resid 171 through 174 Processing helix chain 'A' and resid 177 through 195 removed outlier: 3.513A pdb=" N SER A 181 " --> pdb=" O THR A 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 14 Proline residue: B 11 - end of helix Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 18 through 28 Processing helix chain 'B' and resid 30 through 50 Processing helix chain 'B' and resid 55 through 59 removed outlier: 3.702A pdb=" N CYS B 59 " --> pdb=" O SER B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 87 removed outlier: 3.620A pdb=" N LEU B 66 " --> pdb=" O ARG B 62 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 111 Processing helix chain 'B' and resid 115 through 141 Proline residue: B 121 - end of helix Processing helix chain 'B' and resid 146 through 153 Processing helix chain 'B' and resid 153 through 170 Processing helix chain 'B' and resid 171 through 174 Processing helix chain 'B' and resid 177 through 195 removed outlier: 3.513A pdb=" N SER B 181 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 67 No H-bonds generated for 'chain 'C' and resid 65 through 67' Processing helix chain 'C' and resid 75 through 77 No H-bonds generated for 'chain 'C' and resid 75 through 77' Processing helix chain 'C' and resid 88 through 91 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'E' and resid 65 through 67 No H-bonds generated for 'chain 'E' and resid 65 through 67' Processing helix chain 'E' and resid 75 through 77 No H-bonds generated for 'chain 'E' and resid 75 through 77' Processing helix chain 'E' and resid 88 through 91 Processing helix chain 'F' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.952A pdb=" N VAL C 36 " --> pdb=" O HIS C 52 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N HIS C 52 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TRP C 38 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.710A pdb=" N TYR C 109 " --> pdb=" O ARG C 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AA5, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.060A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE D 33 " --> pdb=" O HIS D 49 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N HIS D 49 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.060A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.952A pdb=" N VAL E 36 " --> pdb=" O HIS E 52 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N HIS E 52 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TRP E 38 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.709A pdb=" N TYR E 109 " --> pdb=" O ARG E 99 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AB2, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.060A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE F 33 " --> pdb=" O HIS F 49 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N HIS F 49 " --> pdb=" O ILE F 33 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.060A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) 382 hydrogen bonds defined for protein. 1014 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: 1.83 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1243 1.33 - 1.46: 1814 1.46 - 1.58: 3759 1.58 - 1.70: 0 1.70 - 1.82: 72 Bond restraints: 6888 Sorted by residual: bond pdb=" C ARG B 93 " pdb=" N SER B 94 " ideal model delta sigma weight residual 1.335 1.423 -0.088 1.30e-02 5.92e+03 4.61e+01 bond pdb=" N ARG C 68 " pdb=" CA ARG C 68 " ideal model delta sigma weight residual 1.458 1.502 -0.044 1.00e-02 1.00e+04 1.97e+01 bond pdb=" N ARG E 68 " pdb=" CA ARG E 68 " ideal model delta sigma weight residual 1.458 1.502 -0.044 1.00e-02 1.00e+04 1.96e+01 bond pdb=" C ALA B 86 " pdb=" N ASP B 87 " ideal model delta sigma weight residual 1.330 1.277 0.053 1.30e-02 5.92e+03 1.69e+01 bond pdb=" N SER D 7 " pdb=" CA SER D 7 " ideal model delta sigma weight residual 1.463 1.488 -0.025 6.90e-03 2.10e+04 1.34e+01 ... (remaining 6883 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 5911 1.53 - 3.06: 2675 3.06 - 4.58: 679 4.58 - 6.11: 66 6.11 - 7.64: 7 Bond angle restraints: 9338 Sorted by residual: angle pdb=" CA GLY D 66 " pdb=" C GLY D 66 " pdb=" O GLY D 66 " ideal model delta sigma weight residual 122.23 118.61 3.62 6.90e-01 2.10e+00 2.76e+01 angle pdb=" CA GLY F 66 " pdb=" C GLY F 66 " pdb=" O GLY F 66 " ideal model delta sigma weight residual 122.23 118.65 3.58 6.90e-01 2.10e+00 2.69e+01 angle pdb=" CA GLY E 113 " pdb=" C GLY E 113 " pdb=" O GLY E 113 " ideal model delta sigma weight residual 122.29 118.11 4.18 8.10e-01 1.52e+00 2.67e+01 angle pdb=" CA GLY C 113 " pdb=" C GLY C 113 " pdb=" O GLY C 113 " ideal model delta sigma weight residual 122.29 118.11 4.18 8.10e-01 1.52e+00 2.66e+01 angle pdb=" C PHE E 54 " pdb=" N TRP E 55 " pdb=" CA TRP E 55 " ideal model delta sigma weight residual 120.38 127.28 -6.90 1.37e+00 5.33e-01 2.54e+01 ... (remaining 9333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.92: 3542 13.92 - 27.85: 371 27.85 - 41.77: 87 41.77 - 55.70: 20 55.70 - 69.62: 14 Dihedral angle restraints: 4034 sinusoidal: 1574 harmonic: 2460 Sorted by residual: dihedral pdb=" CB CYS B 50 " pdb=" SG CYS B 50 " pdb=" SG CYS B 59 " pdb=" CB CYS B 59 " ideal model delta sinusoidal sigma weight residual 93.00 151.19 -58.19 1 1.00e+01 1.00e-02 4.54e+01 dihedral pdb=" CB CYS A 50 " pdb=" SG CYS A 50 " pdb=" SG CYS A 59 " pdb=" CB CYS A 59 " ideal model delta sinusoidal sigma weight residual 93.00 151.16 -58.16 1 1.00e+01 1.00e-02 4.54e+01 dihedral pdb=" CA LEU B 58 " pdb=" C LEU B 58 " pdb=" N CYS B 59 " pdb=" CA CYS B 59 " ideal model delta harmonic sigma weight residual -180.00 -153.40 -26.60 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 4031 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 395 0.043 - 0.086: 310 0.086 - 0.129: 221 0.129 - 0.172: 90 0.172 - 0.215: 20 Chirality restraints: 1036 Sorted by residual: chirality pdb=" CA ILE F 33 " pdb=" N ILE F 33 " pdb=" C ILE F 33 " pdb=" CB ILE F 33 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA ILE D 33 " pdb=" N ILE D 33 " pdb=" C ILE D 33 " pdb=" CB ILE D 33 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA ILE C 84 " pdb=" N ILE C 84 " pdb=" C ILE C 84 " pdb=" CB ILE C 84 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1033 not shown) Planarity restraints: 1148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 86 " -0.019 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" C ALA A 86 " 0.067 2.00e-02 2.50e+03 pdb=" O ALA A 86 " -0.024 2.00e-02 2.50e+03 pdb=" N ASP A 87 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 86 " 0.018 2.00e-02 2.50e+03 3.64e-02 1.32e+01 pdb=" C ALA B 86 " -0.063 2.00e-02 2.50e+03 pdb=" O ALA B 86 " 0.023 2.00e-02 2.50e+03 pdb=" N ASP B 87 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 93 " 0.010 2.00e-02 2.50e+03 2.15e-02 4.62e+00 pdb=" C ARG B 93 " -0.037 2.00e-02 2.50e+03 pdb=" O ARG B 93 " 0.015 2.00e-02 2.50e+03 pdb=" N SER B 94 " 0.012 2.00e-02 2.50e+03 ... (remaining 1145 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 1664 2.87 - 3.38: 6811 3.38 - 3.89: 11017 3.89 - 4.39: 13006 4.39 - 4.90: 22414 Nonbonded interactions: 54912 Sorted by model distance: nonbonded pdb=" O PRO B 91 " pdb=" OG1 THR B 95 " model vdw 2.368 3.040 nonbonded pdb=" NH2 ARG E 99 " pdb=" OD2 ASP E 108 " model vdw 2.394 3.120 nonbonded pdb=" NH2 ARG C 99 " pdb=" OD2 ASP C 108 " model vdw 2.395 3.120 nonbonded pdb=" O ILE B 104 " pdb=" OG1 THR B 108 " model vdw 2.486 3.040 nonbonded pdb=" O ILE A 104 " pdb=" OG1 THR A 108 " model vdw 2.487 3.040 ... (remaining 54907 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: 0.03 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.070 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.430 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 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 : 0.014 0.088 6888 Z= 0.887 Angle : 1.710 7.637 9338 Z= 1.277 Chirality : 0.080 0.215 1036 Planarity : 0.004 0.039 1148 Dihedral : 12.725 69.621 2450 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 0.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.27 % Allowed : 5.74 % Favored : 93.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.27), residues: 840 helix: -1.20 (0.24), residues: 302 sheet: -0.35 (0.34), residues: 182 loop : -0.63 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP E 110 HIS 0.007 0.002 HIS A 180 PHE 0.029 0.003 PHE B 46 TYR 0.024 0.003 TYR A 144 ARG 0.003 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 151 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.7361 (mmm160) cc_final: 0.7048 (mtm-85) REVERT: A 138 LYS cc_start: 0.7683 (mptt) cc_final: 0.7028 (mtpp) REVERT: B 29 ARG cc_start: 0.7380 (mmm160) cc_final: 0.7130 (mtm-85) REVERT: B 138 LYS cc_start: 0.7669 (mptt) cc_final: 0.7017 (mtpp) REVERT: C 48 GLU cc_start: 0.7563 (tt0) cc_final: 0.7358 (tt0) REVERT: C 94 THR cc_start: 0.7716 (p) cc_final: 0.7253 (p) REVERT: D 14 SER cc_start: 0.7686 (p) cc_final: 0.7309 (m) REVERT: E 94 THR cc_start: 0.7710 (p) cc_final: 0.7262 (p) REVERT: F 45 ARG cc_start: 0.7436 (mtp85) cc_final: 0.7225 (mtp85) outliers start: 2 outliers final: 2 residues processed: 151 average time/residue: 0.1979 time to fit residues: 38.8841 Evaluate side-chains 118 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 116 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain F residue 61 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 41 optimal weight: 0.3980 chunk 33 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN B 92 GLN D 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.188178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.158912 restraints weight = 7411.736| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 1.66 r_work: 0.3693 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3557 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6888 Z= 0.203 Angle : 0.594 6.296 9338 Z= 0.311 Chirality : 0.042 0.147 1036 Planarity : 0.004 0.033 1148 Dihedral : 5.677 59.911 932 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.23 % Allowed : 11.07 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.46 (0.30), residues: 840 helix: 1.32 (0.29), residues: 302 sheet: -0.53 (0.33), residues: 226 loop : 0.14 (0.38), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 55 HIS 0.003 0.001 HIS E 105 PHE 0.014 0.002 PHE B 43 TYR 0.013 0.001 TYR A 72 ARG 0.003 0.000 ARG E 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8175 (mptt) cc_final: 0.7845 (mtpp) REVERT: B 138 LYS cc_start: 0.8173 (mptt) cc_final: 0.7847 (mtpp) REVERT: C 107 MET cc_start: 0.8469 (ptp) cc_final: 0.8074 (ptp) REVERT: E 107 MET cc_start: 0.8480 (ptp) cc_final: 0.8149 (ptp) outliers start: 9 outliers final: 9 residues processed: 118 average time/residue: 0.2009 time to fit residues: 31.1317 Evaluate side-chains 119 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain F residue 61 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 42 optimal weight: 0.0050 chunk 47 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 80 optimal weight: 0.0770 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 8.9990 overall best weight: 0.5152 ------------------------------------------------------------------------------- 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 = 0.4120 r_free = 0.4120 target = 0.189041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.150375 restraints weight = 7388.637| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 1.97 r_work: 0.3700 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3545 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6888 Z= 0.163 Angle : 0.521 5.799 9338 Z= 0.274 Chirality : 0.041 0.218 1036 Planarity : 0.004 0.031 1148 Dihedral : 5.045 54.168 932 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.91 % Allowed : 11.48 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.30), residues: 840 helix: 1.91 (0.29), residues: 302 sheet: -0.18 (0.34), residues: 224 loop : 0.23 (0.38), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 35 HIS 0.004 0.001 HIS E 52 PHE 0.013 0.001 PHE A 39 TYR 0.010 0.001 TYR D 91 ARG 0.002 0.000 ARG E 68 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8025 (mptt) cc_final: 0.7604 (mtpp) REVERT: B 138 LYS cc_start: 0.8034 (mptt) cc_final: 0.7609 (mtpp) outliers start: 14 outliers final: 9 residues processed: 115 average time/residue: 0.1927 time to fit residues: 29.5097 Evaluate side-chains 110 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain F residue 61 ARG Chi-restraints excluded: chain F residue 94 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 80 optimal weight: 0.4980 chunk 1 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN B 152 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.182185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.150426 restraints weight = 7561.801| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 1.63 r_work: 0.3658 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6888 Z= 0.275 Angle : 0.568 8.299 9338 Z= 0.297 Chirality : 0.043 0.166 1036 Planarity : 0.004 0.030 1148 Dihedral : 4.917 47.355 932 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.78 % Allowed : 12.57 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.99 (0.30), residues: 840 helix: 1.83 (0.29), residues: 300 sheet: 0.30 (0.35), residues: 230 loop : -0.13 (0.37), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 110 HIS 0.003 0.001 HIS D 49 PHE 0.016 0.002 PHE B 39 TYR 0.020 0.002 TYR D 91 ARG 0.004 0.000 ARG E 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8092 (mptt) cc_final: 0.7737 (mtpp) REVERT: B 138 LYS cc_start: 0.8101 (mptt) cc_final: 0.7750 (mtpp) REVERT: E 107 MET cc_start: 0.8555 (ptp) cc_final: 0.8091 (ptp) outliers start: 13 outliers final: 6 residues processed: 117 average time/residue: 0.2080 time to fit residues: 32.2494 Evaluate side-chains 112 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain F residue 94 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 44 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 59 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.189700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.156643 restraints weight = 7351.373| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 1.83 r_work: 0.3647 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6888 Z= 0.221 Angle : 0.534 7.044 9338 Z= 0.279 Chirality : 0.042 0.140 1036 Planarity : 0.004 0.029 1148 Dihedral : 4.222 23.833 924 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.19 % Allowed : 13.39 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.99 (0.29), residues: 840 helix: 1.89 (0.29), residues: 300 sheet: 0.41 (0.35), residues: 230 loop : -0.29 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 110 HIS 0.002 0.001 HIS C 52 PHE 0.013 0.001 PHE A 39 TYR 0.013 0.001 TYR D 91 ARG 0.005 0.000 ARG E 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8129 (mptt) cc_final: 0.7760 (mtpp) REVERT: B 138 LYS cc_start: 0.8108 (mptt) cc_final: 0.7749 (mtpp) REVERT: E 107 MET cc_start: 0.8465 (ptp) cc_final: 0.7934 (ptp) outliers start: 16 outliers final: 7 residues processed: 125 average time/residue: 0.1921 time to fit residues: 31.8058 Evaluate side-chains 115 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 108 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 94 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 61 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN B 152 GLN F 30 ASN F 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.184041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.145853 restraints weight = 7441.174| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.91 r_work: 0.3621 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 6888 Z= 0.298 Angle : 0.578 6.586 9338 Z= 0.299 Chirality : 0.043 0.136 1036 Planarity : 0.004 0.029 1148 Dihedral : 4.306 23.544 924 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.32 % Allowed : 13.66 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.82 (0.29), residues: 840 helix: 1.81 (0.29), residues: 288 sheet: 0.41 (0.35), residues: 230 loop : -0.46 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 110 HIS 0.003 0.001 HIS F 49 PHE 0.015 0.002 PHE A 39 TYR 0.016 0.002 TYR B 72 ARG 0.005 0.000 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8156 (mptt) cc_final: 0.7706 (mtpp) REVERT: B 138 LYS cc_start: 0.8106 (mptt) cc_final: 0.7664 (mtpp) REVERT: C 83 MET cc_start: 0.6981 (mpp) cc_final: 0.6760 (mmt) outliers start: 17 outliers final: 13 residues processed: 118 average time/residue: 0.2031 time to fit residues: 31.6262 Evaluate side-chains 121 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 95 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 27 optimal weight: 0.4980 chunk 46 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 30 optimal weight: 0.0770 chunk 11 optimal weight: 0.3980 chunk 29 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN F 30 ASN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.193820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.161944 restraints weight = 7207.868| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 1.62 r_work: 0.3689 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6888 Z= 0.158 Angle : 0.504 6.046 9338 Z= 0.261 Chirality : 0.040 0.137 1036 Planarity : 0.004 0.030 1148 Dihedral : 4.040 24.318 924 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.05 % Allowed : 13.93 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.30), residues: 840 helix: 2.08 (0.29), residues: 300 sheet: 0.66 (0.36), residues: 234 loop : -0.48 (0.36), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 110 HIS 0.002 0.001 HIS C 52 PHE 0.012 0.001 PHE A 39 TYR 0.008 0.001 TYR B 72 ARG 0.005 0.000 ARG E 68 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8074 (mptt) cc_final: 0.7745 (mtpp) REVERT: B 138 LYS cc_start: 0.8046 (mptt) cc_final: 0.7727 (mtpp) outliers start: 15 outliers final: 5 residues processed: 126 average time/residue: 0.1956 time to fit residues: 32.6077 Evaluate side-chains 120 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 115 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 33 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 62 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 44 optimal weight: 0.3980 chunk 51 optimal weight: 0.4980 chunk 29 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN B 152 GLN D 30 ASN F 30 ASN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.192427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.163866 restraints weight = 7281.756| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 1.58 r_work: 0.3728 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3600 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6888 Z= 0.187 Angle : 0.516 6.111 9338 Z= 0.267 Chirality : 0.041 0.133 1036 Planarity : 0.004 0.028 1148 Dihedral : 4.034 23.788 924 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.46 % Allowed : 14.48 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.30), residues: 840 helix: 2.22 (0.29), residues: 288 sheet: 0.51 (0.37), residues: 220 loop : -0.31 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 113 HIS 0.002 0.001 HIS C 52 PHE 0.013 0.001 PHE B 39 TYR 0.011 0.001 TYR B 72 ARG 0.006 0.000 ARG E 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8011 (mptt) cc_final: 0.7678 (mtpp) REVERT: B 138 LYS cc_start: 0.8012 (mptt) cc_final: 0.7694 (mtpp) REVERT: F 11 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7425 (tt) outliers start: 18 outliers final: 6 residues processed: 121 average time/residue: 0.1991 time to fit residues: 31.8179 Evaluate side-chains 117 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 110 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 94 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 0.0030 chunk 21 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 28 optimal weight: 0.3980 chunk 70 optimal weight: 0.6980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN F 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.194503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.162852 restraints weight = 7300.821| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 1.61 r_work: 0.3750 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6888 Z= 0.160 Angle : 0.521 9.144 9338 Z= 0.263 Chirality : 0.040 0.138 1036 Planarity : 0.004 0.028 1148 Dihedral : 3.939 21.320 924 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.64 % Allowed : 15.44 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.29), residues: 840 helix: 2.34 (0.29), residues: 288 sheet: 0.54 (0.36), residues: 220 loop : -0.34 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 49 HIS 0.002 0.001 HIS E 105 PHE 0.012 0.001 PHE B 39 TYR 0.008 0.001 TYR B 72 ARG 0.006 0.000 ARG E 68 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8025 (mptt) cc_final: 0.7693 (mtpp) REVERT: B 138 LYS cc_start: 0.8037 (mptt) cc_final: 0.7672 (mtpp) REVERT: F 11 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7426 (tt) outliers start: 12 outliers final: 5 residues processed: 123 average time/residue: 0.2044 time to fit residues: 33.1801 Evaluate side-chains 114 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 94 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 56 optimal weight: 8.9990 chunk 29 optimal weight: 0.0370 chunk 51 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 75 optimal weight: 0.5980 overall best weight: 1.2662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN D 30 ASN F 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.188075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.154832 restraints weight = 7404.051| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 1.69 r_work: 0.3625 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6888 Z= 0.292 Angle : 0.592 8.624 9338 Z= 0.301 Chirality : 0.043 0.134 1036 Planarity : 0.004 0.027 1148 Dihedral : 4.300 26.507 924 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.64 % Allowed : 15.16 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.90 (0.29), residues: 840 helix: 2.00 (0.29), residues: 288 sheet: 0.42 (0.36), residues: 220 loop : -0.48 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 49 HIS 0.003 0.001 HIS E 52 PHE 0.015 0.002 PHE B 39 TYR 0.016 0.002 TYR D 91 ARG 0.007 0.001 ARG C 68 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8137 (mptt) cc_final: 0.7768 (mtpp) REVERT: B 138 LYS cc_start: 0.8115 (mptt) cc_final: 0.7728 (mtpp) REVERT: D 11 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7447 (tt) REVERT: F 4 MET cc_start: 0.7883 (mmm) cc_final: 0.7594 (tpt) REVERT: F 11 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7539 (tt) outliers start: 12 outliers final: 4 residues processed: 115 average time/residue: 0.1990 time to fit residues: 30.0224 Evaluate side-chains 113 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 107 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 94 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 76 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 17 optimal weight: 0.0980 chunk 46 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 21 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN F 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.194469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.162432 restraints weight = 7389.702| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 1.67 r_work: 0.3754 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3621 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6888 Z= 0.162 Angle : 0.534 8.815 9338 Z= 0.268 Chirality : 0.040 0.140 1036 Planarity : 0.004 0.028 1148 Dihedral : 4.011 21.688 924 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.23 % Allowed : 14.89 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.30), residues: 840 helix: 2.29 (0.29), residues: 288 sheet: 0.52 (0.36), residues: 218 loop : -0.47 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 49 HIS 0.002 0.001 HIS E 52 PHE 0.012 0.001 PHE B 39 TYR 0.010 0.001 TYR A 150 ARG 0.006 0.000 ARG C 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3957.05 seconds wall clock time: 68 minutes 39.23 seconds (4119.23 seconds total)