Starting phenix.real_space_refine on Sat May 10 18:04:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t07_40937/05_2025/8t07_40937.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t07_40937/05_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_40937/05_2025/8t07_40937.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t07_40937/05_2025/8t07_40937.map" model { file = "/net/cci-nas-00/data/ceres_data/8t07_40937/05_2025/8t07_40937.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t07_40937/05_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-5687/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: 4.33, per 1000 atoms: 0.65 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: 1.41 Conformation dependent library (CDL) restraints added in 893.1 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: 0.86 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: 1.93 Time building geometry restraints manager: 1.69 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: 1.170 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: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.430 Find NCS groups from input model: 0.300 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.930 ------------------------------------------------------------------------------- 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 0.175 6898 Z= 1.050 Angle : 1.712 7.637 9346 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 Details of bonding type rmsd hydrogen bonds : bond 0.20411 ( 368) hydrogen bonds : angle 8.90982 ( 1014) metal coordination : bond 0.14203 ( 6) SS BOND : bond 0.00548 ( 4) SS BOND : angle 3.10718 ( 8) covalent geometry : bond 0.01364 ( 6888) covalent geometry : angle 1.70998 ( 9338) *********************** 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 : 0.736 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: 0.2020 time to fit residues: 39.4832 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 : 0.653 ------------------------------------------------------------------------------- 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: 0.9990 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 = 0.158913 restraints weight = 7411.736| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 1.66 r_work: 0.3692 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3558 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3558 ------------------------------------------------------------------------------- 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 6898 Z= 0.140 Angle : 0.596 6.296 9346 Z= 0.312 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 Details of bonding type rmsd hydrogen bonds : bond 0.04400 ( 368) hydrogen bonds : angle 5.13697 ( 1014) metal coordination : bond 0.01104 ( 6) SS BOND : bond 0.00104 ( 4) SS BOND : angle 1.81332 ( 8) covalent geometry : bond 0.00313 ( 6888) covalent geometry : angle 0.59394 ( 9338) *********************** 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 : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8183 (mptt) cc_final: 0.7842 (mtpp) REVERT: B 138 LYS cc_start: 0.8186 (mptt) cc_final: 0.7850 (mtpp) REVERT: C 107 MET cc_start: 0.8455 (ptp) cc_final: 0.8061 (ptp) REVERT: E 107 MET cc_start: 0.8462 (ptp) cc_final: 0.8134 (ptp) outliers start: 9 outliers final: 9 residues processed: 118 average time/residue: 0.1949 time to fit residues: 30.0828 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 : 0.659 ------------------------------------------------------------------------------- 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: 2.9990 chunk 42 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 80 optimal weight: 0.0870 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- 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 = 0.4081 r_free = 0.4081 target = 0.185000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.146062 restraints weight = 7426.140| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 1.95 r_work: 0.3620 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6898 Z= 0.146 Angle : 0.554 5.897 9346 Z= 0.293 Chirality : 0.043 0.198 1036 Planarity : 0.004 0.032 1148 Dihedral : 5.148 52.459 932 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.32 % Allowed : 11.34 % Favored : 86.34 % 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: 0.84 (0.30), residues: 840 helix: 1.66 (0.29), residues: 304 sheet: -0.09 (0.35), residues: 216 loop : 0.10 (0.37), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 110 HIS 0.003 0.001 HIS E 52 PHE 0.015 0.002 PHE A 39 TYR 0.017 0.002 TYR D 91 ARG 0.003 0.000 ARG E 68 Details of bonding type rmsd hydrogen bonds : bond 0.04255 ( 368) hydrogen bonds : angle 4.74719 ( 1014) metal coordination : bond 0.00163 ( 6) SS BOND : bond 0.00072 ( 4) SS BOND : angle 1.60823 ( 8) covalent geometry : bond 0.00339 ( 6888) covalent geometry : angle 0.55241 ( 9338) *********************** 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 127 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8125 (mptt) cc_final: 0.7705 (mtpp) REVERT: B 138 LYS cc_start: 0.8115 (mptt) cc_final: 0.7693 (mtpp) outliers start: 17 outliers final: 12 residues processed: 115 average time/residue: 0.1923 time to fit residues: 29.5373 Evaluate side-chains 114 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 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 84 ILE Chi-restraints excluded: chain F residue 19 VAL 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: 2.9990 chunk 58 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4158 r_free = 0.4158 target = 0.192050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.159978 restraints weight = 7406.669| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 1.71 r_work: 0.3672 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6898 Z= 0.134 Angle : 0.540 7.573 9346 Z= 0.281 Chirality : 0.042 0.177 1036 Planarity : 0.004 0.030 1148 Dihedral : 4.882 47.545 932 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.78 % Allowed : 12.43 % Favored : 85.79 % 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: 1.08 (0.30), residues: 840 helix: 1.86 (0.29), residues: 304 sheet: 0.32 (0.35), residues: 230 loop : -0.02 (0.38), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 110 HIS 0.003 0.001 HIS E 52 PHE 0.014 0.001 PHE A 39 TYR 0.013 0.001 TYR B 72 ARG 0.004 0.000 ARG E 68 Details of bonding type rmsd hydrogen bonds : bond 0.04025 ( 368) hydrogen bonds : angle 4.52367 ( 1014) metal coordination : bond 0.00140 ( 6) SS BOND : bond 0.00052 ( 4) SS BOND : angle 1.41029 ( 8) covalent geometry : bond 0.00310 ( 6888) covalent geometry : angle 0.53832 ( 9338) *********************** 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 124 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8128 (mptt) cc_final: 0.7724 (mtpp) REVERT: B 138 LYS cc_start: 0.8145 (mptt) cc_final: 0.7737 (mtpp) REVERT: E 107 MET cc_start: 0.8583 (ptp) cc_final: 0.8109 (ptp) outliers start: 13 outliers final: 6 residues processed: 117 average time/residue: 0.1963 time to fit residues: 30.3867 Evaluate side-chains 116 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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: 0.0000 chunk 4 optimal weight: 0.5980 chunk 63 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 chunk 77 optimal weight: 0.1980 chunk 64 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 GLN F 30 ASN F 90 GLN 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 = 0.197361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.165797 restraints weight = 7220.717| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 1.62 r_work: 0.3735 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3596 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6898 Z= 0.101 Angle : 0.500 6.961 9346 Z= 0.260 Chirality : 0.040 0.139 1036 Planarity : 0.004 0.028 1148 Dihedral : 3.997 22.212 924 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.91 % Allowed : 13.52 % Favored : 84.56 % 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: 1.37 (0.30), residues: 840 helix: 2.14 (0.29), residues: 304 sheet: 0.66 (0.36), residues: 218 loop : -0.04 (0.37), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 110 HIS 0.004 0.001 HIS E 52 PHE 0.012 0.001 PHE B 39 TYR 0.007 0.001 TYR B 72 ARG 0.006 0.000 ARG C 68 Details of bonding type rmsd hydrogen bonds : bond 0.03661 ( 368) hydrogen bonds : angle 4.21342 ( 1014) metal coordination : bond 0.00066 ( 6) SS BOND : bond 0.00046 ( 4) SS BOND : angle 1.23358 ( 8) covalent geometry : bond 0.00219 ( 6888) covalent geometry : angle 0.49908 ( 9338) *********************** 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: 14 poor density : 117 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8036 (mptt) cc_final: 0.7734 (mtpp) REVERT: B 138 LYS cc_start: 0.8080 (mptt) cc_final: 0.7762 (mtpp) REVERT: C 107 MET cc_start: 0.8141 (ptp) cc_final: 0.7723 (ptp) REVERT: E 107 MET cc_start: 0.8344 (ptp) cc_final: 0.7827 (ptp) outliers start: 14 outliers final: 8 residues processed: 122 average time/residue: 0.1857 time to fit residues: 30.0416 Evaluate side-chains 116 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 C residue 84 ILE 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: 4.9990 chunk 46 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 75 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 6 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN F 30 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.180772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.142299 restraints weight = 7486.648| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 1.93 r_work: 0.3555 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 6898 Z= 0.259 Angle : 0.630 6.628 9346 Z= 0.332 Chirality : 0.046 0.143 1036 Planarity : 0.004 0.028 1148 Dihedral : 4.516 27.303 924 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.60 % Allowed : 14.07 % Favored : 83.33 % 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: 0.65 (0.29), residues: 840 helix: 1.57 (0.29), residues: 288 sheet: 0.34 (0.35), residues: 230 loop : -0.45 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 110 HIS 0.003 0.001 HIS D 49 PHE 0.017 0.002 PHE B 39 TYR 0.022 0.002 TYR B 72 ARG 0.003 0.000 ARG E 68 Details of bonding type rmsd hydrogen bonds : bond 0.04884 ( 368) hydrogen bonds : angle 4.87493 ( 1014) metal coordination : bond 0.00377 ( 6) SS BOND : bond 0.00320 ( 4) SS BOND : angle 1.41969 ( 8) covalent geometry : bond 0.00626 ( 6888) covalent geometry : angle 0.62914 ( 9338) *********************** 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 129 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8178 (mptt) cc_final: 0.7726 (mtpp) REVERT: B 138 LYS cc_start: 0.8155 (mptt) cc_final: 0.7693 (mtpp) REVERT: C 107 MET cc_start: 0.8697 (ptp) cc_final: 0.8397 (ptp) outliers start: 19 outliers final: 12 residues processed: 120 average time/residue: 0.2034 time to fit residues: 32.2263 Evaluate side-chains 119 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 70 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain D residue 67 SER 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 33 ILE Chi-restraints excluded: chain F residue 94 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 27 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 30 optimal weight: 0.0770 chunk 11 optimal weight: 0.0980 chunk 29 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 30 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.191538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.156653 restraints weight = 7289.246| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 1.77 r_work: 0.3663 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6898 Z= 0.111 Angle : 0.528 6.366 9346 Z= 0.272 Chirality : 0.041 0.138 1036 Planarity : 0.004 0.029 1148 Dihedral : 4.150 25.621 924 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.78 % Allowed : 14.62 % Favored : 83.61 % 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: 1.03 (0.29), residues: 840 helix: 1.95 (0.29), residues: 292 sheet: 0.65 (0.36), residues: 232 loop : -0.46 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 49 HIS 0.003 0.001 HIS C 52 PHE 0.012 0.001 PHE A 39 TYR 0.008 0.001 TYR B 72 ARG 0.006 0.000 ARG C 68 Details of bonding type rmsd hydrogen bonds : bond 0.03838 ( 368) hydrogen bonds : angle 4.34375 ( 1014) metal coordination : bond 0.00066 ( 6) SS BOND : bond 0.00082 ( 4) SS BOND : angle 1.22623 ( 8) covalent geometry : bond 0.00247 ( 6888) covalent geometry : angle 0.52699 ( 9338) *********************** 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 129 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8095 (mptt) cc_final: 0.7722 (mtpp) REVERT: B 138 LYS cc_start: 0.8057 (mptt) cc_final: 0.7699 (mtpp) REVERT: F 11 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7437 (tt) outliers start: 13 outliers final: 5 residues processed: 122 average time/residue: 0.1820 time to fit residues: 30.1206 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 : 0.732 ------------------------------------------------------------------------------- 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 11 LEU Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 94 LEU 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: 0.3980 chunk 36 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 51 optimal weight: 0.0060 chunk 29 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.186113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.149958 restraints weight = 7440.753| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 1.83 r_work: 0.3683 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3538 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6898 Z= 0.111 Angle : 0.516 6.072 9346 Z= 0.265 Chirality : 0.041 0.135 1036 Planarity : 0.004 0.028 1148 Dihedral : 3.984 23.561 924 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.46 % Allowed : 14.75 % Favored : 82.79 % 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: 1.16 (0.29), residues: 840 helix: 2.15 (0.29), residues: 300 sheet: 0.55 (0.37), residues: 220 loop : -0.35 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 49 HIS 0.002 0.001 HIS C 52 PHE 0.012 0.001 PHE B 39 TYR 0.009 0.001 TYR B 72 ARG 0.006 0.000 ARG E 68 Details of bonding type rmsd hydrogen bonds : bond 0.03754 ( 368) hydrogen bonds : angle 4.20621 ( 1014) metal coordination : bond 0.00097 ( 6) SS BOND : bond 0.00036 ( 4) SS BOND : angle 1.18288 ( 8) covalent geometry : bond 0.00248 ( 6888) covalent geometry : angle 0.51527 ( 9338) *********************** 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 132 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8098 (mptt) cc_final: 0.7726 (mtpp) REVERT: B 138 LYS cc_start: 0.8110 (mptt) cc_final: 0.7732 (mtpp) REVERT: D 11 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7464 (tt) REVERT: F 11 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7438 (tt) outliers start: 18 outliers final: 5 residues processed: 124 average time/residue: 0.1758 time to fit residues: 29.5898 Evaluate side-chains 116 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 109 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain F residue 11 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4152 r_free = 0.4152 target = 0.182634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.153560 restraints weight = 7510.883| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 1.59 r_work: 0.3705 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6898 Z= 0.142 Angle : 0.557 8.571 9346 Z= 0.281 Chirality : 0.042 0.136 1036 Planarity : 0.004 0.027 1148 Dihedral : 4.083 22.186 924 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.19 % Allowed : 15.44 % Favored : 82.38 % 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: 1.12 (0.29), residues: 840 helix: 2.21 (0.29), residues: 288 sheet: 0.51 (0.36), residues: 220 loop : -0.36 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 49 HIS 0.003 0.001 HIS C 52 PHE 0.013 0.001 PHE B 39 TYR 0.017 0.001 TYR D 32 ARG 0.007 0.000 ARG E 68 Details of bonding type rmsd hydrogen bonds : bond 0.03987 ( 368) hydrogen bonds : angle 4.31801 ( 1014) metal coordination : bond 0.00161 ( 6) SS BOND : bond 0.00090 ( 4) SS BOND : angle 1.22477 ( 8) covalent geometry : bond 0.00334 ( 6888) covalent geometry : angle 0.55645 ( 9338) *********************** 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 127 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8043 (mptt) cc_final: 0.7703 (mtpp) REVERT: B 138 LYS cc_start: 0.8037 (mptt) cc_final: 0.7700 (mtpp) REVERT: F 11 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7436 (tt) outliers start: 16 outliers final: 7 residues processed: 120 average time/residue: 0.1806 time to fit residues: 29.2936 Evaluate side-chains 114 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 115 TYR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain F residue 11 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 56 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 57 optimal weight: 0.4980 chunk 42 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4161 r_free = 0.4161 target = 0.192089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.163654 restraints weight = 7401.906| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 1.59 r_work: 0.3743 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3609 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 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 : 0.003 0.029 6898 Z= 0.136 Angle : 0.560 8.483 9346 Z= 0.281 Chirality : 0.041 0.138 1036 Planarity : 0.004 0.027 1148 Dihedral : 4.132 25.398 924 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.91 % Allowed : 15.44 % Favored : 82.65 % 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: 1.12 (0.29), residues: 840 helix: 2.22 (0.29), residues: 288 sheet: 0.56 (0.36), residues: 218 loop : -0.41 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 49 HIS 0.003 0.001 HIS C 52 PHE 0.013 0.001 PHE B 39 TYR 0.014 0.001 TYR D 32 ARG 0.007 0.000 ARG C 68 Details of bonding type rmsd hydrogen bonds : bond 0.03945 ( 368) hydrogen bonds : angle 4.33621 ( 1014) metal coordination : bond 0.00151 ( 6) SS BOND : bond 0.00062 ( 4) SS BOND : angle 1.20818 ( 8) covalent geometry : bond 0.00318 ( 6888) covalent geometry : angle 0.55887 ( 9338) ********************** 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 126 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8012 (mptt) cc_final: 0.7695 (mtpp) REVERT: B 138 LYS cc_start: 0.8015 (mptt) cc_final: 0.7698 (mtpp) REVERT: F 11 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7422 (tt) outliers start: 14 outliers final: 7 residues processed: 118 average time/residue: 0.1793 time to fit residues: 28.3186 Evaluate side-chains 113 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 115 TYR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain F residue 11 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 76 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 61 optimal weight: 0.0670 chunk 21 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 = 0.4164 r_free = 0.4164 target = 0.192803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.157833 restraints weight = 7469.802| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 1.80 r_work: 0.3708 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6898 Z= 0.117 Angle : 0.549 8.459 9346 Z= 0.274 Chirality : 0.041 0.140 1036 Planarity : 0.004 0.027 1148 Dihedral : 4.049 21.595 924 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.50 % Allowed : 15.30 % 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: 1.23 (0.29), residues: 840 helix: 2.35 (0.29), residues: 288 sheet: 0.74 (0.36), residues: 214 loop : -0.48 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 49 HIS 0.004 0.001 HIS C 52 PHE 0.012 0.001 PHE B 39 TYR 0.014 0.001 TYR D 32 ARG 0.007 0.000 ARG E 68 Details of bonding type rmsd hydrogen bonds : bond 0.03788 ( 368) hydrogen bonds : angle 4.25347 ( 1014) metal coordination : bond 0.00116 ( 6) SS BOND : bond 0.00018 ( 4) SS BOND : angle 1.16579 ( 8) covalent geometry : bond 0.00268 ( 6888) covalent geometry : angle 0.54803 ( 9338) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3788.00 seconds wall clock time: 66 minutes 50.12 seconds (4010.12 seconds total)