Starting phenix.real_space_refine on Sun Apr 27 23:54:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t07_40937/04_2025/8t07_40937.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t07_40937/04_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_40937/04_2025/8t07_40937.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t07_40937/04_2025/8t07_40937.map" model { file = "/net/cci-nas-00/data/ceres_data/8t07_40937/04_2025/8t07_40937.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t07_40937/04_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-5669/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: 5.12, per 1000 atoms: 0.76 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: 1.43 Conformation dependent library (CDL) restraints added in 935.8 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: 1.01 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: 2.64 Time building geometry restraints manager: 1.76 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: 0.04 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: 3.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 23.680 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.190 ------------------------------------------------------------------------------- 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 : 0.716 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: 0.2356 time to fit residues: 46.1893 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 : 0.724 ------------------------------------------------------------------------------- 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 = 0.158912 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 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 : 0.741 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: 0.2075 time to fit residues: 32.0716 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 : 0.718 ------------------------------------------------------------------------------- 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 6898 Z= 0.113 Angle : 0.523 5.799 9346 Z= 0.275 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 Details of bonding type rmsd hydrogen bonds : bond 0.03910 ( 368) hydrogen bonds : angle 4.54423 ( 1014) metal coordination : bond 0.00094 ( 6) SS BOND : bond 0.00076 ( 4) SS BOND : angle 1.52962 ( 8) covalent geometry : bond 0.00246 ( 6888) covalent geometry : angle 0.52117 ( 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 125 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.703 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: 0.1888 time to fit residues: 28.9158 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 : 0.776 ------------------------------------------------------------------------------- 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: 0.8980 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: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.4158 r_free = 0.4158 target = 0.182069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.150381 restraints weight = 7565.489| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 1.63 r_work: 0.3637 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6898 Z= 0.182 Angle : 0.570 8.046 9346 Z= 0.298 Chirality : 0.043 0.163 1036 Planarity : 0.004 0.030 1148 Dihedral : 4.925 46.706 932 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.50 % Allowed : 12.84 % 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: 0.96 (0.30), residues: 840 helix: 1.80 (0.29), residues: 300 sheet: 0.30 (0.35), residues: 230 loop : -0.15 (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 0.021 0.002 TYR D 91 ARG 0.004 0.000 ARG E 68 Details of bonding type rmsd hydrogen bonds : bond 0.04340 ( 368) hydrogen bonds : angle 4.66998 ( 1014) metal coordination : bond 0.00224 ( 6) SS BOND : bond 0.00183 ( 4) SS BOND : angle 1.46776 ( 8) covalent geometry : bond 0.00434 ( 6888) covalent geometry : angle 0.56911 ( 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 120 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8123 (mptt) cc_final: 0.7747 (mtpp) REVERT: B 138 LYS cc_start: 0.8109 (mptt) cc_final: 0.7746 (mtpp) REVERT: E 107 MET cc_start: 0.8574 (ptp) cc_final: 0.8108 (ptp) outliers start: 11 outliers final: 7 residues processed: 116 average time/residue: 0.2146 time to fit residues: 32.7328 Evaluate side-chains 114 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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 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 94 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 44 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 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: 0.0570 chunk 64 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 19 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 GLN F 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.194272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.162597 restraints weight = 7234.999| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 1.62 r_work: 0.3703 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3570 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6898 Z= 0.114 Angle : 0.512 6.943 9346 Z= 0.265 Chirality : 0.041 0.140 1036 Planarity : 0.004 0.029 1148 Dihedral : 4.104 22.916 924 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.46 % Allowed : 13.25 % Favored : 84.29 % 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: 1.21 (0.30), residues: 840 helix: 2.08 (0.29), residues: 300 sheet: 0.66 (0.35), residues: 232 loop : -0.31 (0.37), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 110 HIS 0.002 0.001 HIS E 52 PHE 0.012 0.001 PHE A 39 TYR 0.008 0.001 TYR B 72 ARG 0.006 0.000 ARG E 68 Details of bonding type rmsd hydrogen bonds : bond 0.03773 ( 368) hydrogen bonds : angle 4.30742 ( 1014) metal coordination : bond 0.00093 ( 6) SS BOND : bond 0.00025 ( 4) SS BOND : angle 1.30407 ( 8) covalent geometry : bond 0.00253 ( 6888) covalent geometry : angle 0.51033 ( 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 133 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8079 (mptt) cc_final: 0.7753 (mtpp) REVERT: B 138 LYS cc_start: 0.8078 (mptt) cc_final: 0.7748 (mtpp) REVERT: E 107 MET cc_start: 0.8361 (ptp) cc_final: 0.7831 (ptp) outliers start: 18 outliers final: 8 residues processed: 125 average time/residue: 0.1907 time to fit residues: 31.6792 Evaluate side-chains 118 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.699 ------------------------------------------------------------------------------- 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 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 54 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: 2.9990 chunk 68 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 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 = 0.4138 r_free = 0.4138 target = 0.178314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.148767 restraints weight = 7578.901| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 1.54 r_work: 0.3604 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 6898 Z= 0.263 Angle : 0.627 6.742 9346 Z= 0.329 Chirality : 0.046 0.140 1036 Planarity : 0.004 0.030 1148 Dihedral : 4.536 26.288 924 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.73 % Allowed : 13.66 % 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: 0.60 (0.29), residues: 840 helix: 1.56 (0.29), residues: 288 sheet: 0.33 (0.35), residues: 230 loop : -0.55 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 110 HIS 0.004 0.001 HIS F 49 PHE 0.018 0.002 PHE D 98 TYR 0.024 0.002 TYR D 91 ARG 0.005 0.000 ARG C 68 Details of bonding type rmsd hydrogen bonds : bond 0.04868 ( 368) hydrogen bonds : angle 4.87533 ( 1014) metal coordination : bond 0.00355 ( 6) SS BOND : bond 0.00307 ( 4) SS BOND : angle 1.40370 ( 8) covalent geometry : bond 0.00638 ( 6888) covalent geometry : angle 0.62559 ( 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 132 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8114 (mptt) cc_final: 0.7735 (mtpp) REVERT: B 138 LYS cc_start: 0.8105 (mptt) cc_final: 0.7709 (mtpp) outliers start: 20 outliers final: 12 residues processed: 123 average time/residue: 0.2097 time to fit residues: 33.7556 Evaluate side-chains 122 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 C residue 84 ILE Chi-restraints excluded: chain D residue 33 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 E residue 89 THR Chi-restraints excluded: chain F residue 19 VAL 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: 0.0980 chunk 46 optimal weight: 20.0000 chunk 14 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 11 optimal weight: 0.0370 chunk 29 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.5058 ------------------------------------------------------------------------------- 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 = 0.4181 r_free = 0.4181 target = 0.193982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.162601 restraints weight = 7208.752| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 1.59 r_work: 0.3739 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3599 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6898 Z= 0.110 Angle : 0.520 6.307 9346 Z= 0.268 Chirality : 0.040 0.139 1036 Planarity : 0.004 0.030 1148 Dihedral : 4.169 25.146 924 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.91 % Allowed : 14.89 % 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: 1.03 (0.30), residues: 840 helix: 2.07 (0.29), residues: 288 sheet: 0.67 (0.36), residues: 232 loop : -0.57 (0.35), residues: 320 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 0.012 0.001 PHE A 39 TYR 0.008 0.001 TYR D 91 ARG 0.005 0.000 ARG E 68 Details of bonding type rmsd hydrogen bonds : bond 0.03744 ( 368) hydrogen bonds : angle 4.30653 ( 1014) metal coordination : bond 0.00062 ( 6) SS BOND : bond 0.00093 ( 4) SS BOND : angle 1.28096 ( 8) covalent geometry : bond 0.00244 ( 6888) covalent geometry : angle 0.51852 ( 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 133 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8024 (mptt) cc_final: 0.7682 (mtpp) REVERT: B 138 LYS cc_start: 0.8028 (mptt) cc_final: 0.7688 (mtpp) outliers start: 14 outliers final: 6 residues processed: 126 average time/residue: 0.2014 time to fit residues: 33.3208 Evaluate side-chains 117 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 111 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 THR 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 62 optimal weight: 3.9990 chunk 74 optimal weight: 0.0970 chunk 36 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 79 optimal weight: 0.0970 chunk 23 optimal weight: 0.3980 overall best weight: 0.4176 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.194788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.163256 restraints weight = 7269.857| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 1.64 r_work: 0.3733 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3597 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6898 Z= 0.103 Angle : 0.517 9.057 9346 Z= 0.260 Chirality : 0.040 0.135 1036 Planarity : 0.004 0.028 1148 Dihedral : 3.961 23.140 924 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.23 % Allowed : 15.85 % 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: 1.17 (0.30), residues: 840 helix: 2.17 (0.29), residues: 300 sheet: 0.57 (0.37), residues: 220 loop : -0.37 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 113 HIS 0.002 0.001 HIS E 52 PHE 0.012 0.001 PHE A 39 TYR 0.013 0.001 TYR C 96 ARG 0.006 0.000 ARG C 68 Details of bonding type rmsd hydrogen bonds : bond 0.03648 ( 368) hydrogen bonds : angle 4.15995 ( 1014) metal coordination : bond 0.00084 ( 6) SS BOND : bond 0.00038 ( 4) SS BOND : angle 1.17576 ( 8) covalent geometry : bond 0.00226 ( 6888) covalent geometry : angle 0.51561 ( 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 127 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8026 (mptt) cc_final: 0.7683 (mtpp) REVERT: B 138 LYS cc_start: 0.8023 (mptt) cc_final: 0.7678 (mtpp) REVERT: F 11 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7427 (tt) outliers start: 9 outliers final: 2 residues processed: 120 average time/residue: 0.2209 time to fit residues: 35.3974 Evaluate side-chains 114 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 111 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 19 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 0.0000 chunk 21 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- 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 = 0.4173 r_free = 0.4173 target = 0.193330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.165151 restraints weight = 7299.470| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 1.54 r_work: 0.3726 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3598 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6898 Z= 0.127 Angle : 0.537 8.293 9346 Z= 0.271 Chirality : 0.041 0.138 1036 Planarity : 0.004 0.027 1148 Dihedral : 4.037 21.885 924 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.64 % Allowed : 15.85 % Favored : 82.51 % 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: 2.25 (0.29), residues: 288 sheet: 0.56 (0.36), residues: 220 loop : -0.38 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 49 HIS 0.002 0.001 HIS E 52 PHE 0.013 0.001 PHE A 39 TYR 0.011 0.001 TYR B 72 ARG 0.006 0.000 ARG C 68 Details of bonding type rmsd hydrogen bonds : bond 0.03867 ( 368) hydrogen bonds : angle 4.21882 ( 1014) metal coordination : bond 0.00133 ( 6) SS BOND : bond 0.00068 ( 4) SS BOND : angle 1.20209 ( 8) covalent geometry : bond 0.00296 ( 6888) covalent geometry : angle 0.53600 ( 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: 12 poor density : 115 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8008 (mptt) cc_final: 0.7693 (mtpp) REVERT: B 138 LYS cc_start: 0.7998 (mptt) cc_final: 0.7684 (mtpp) REVERT: D 11 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7485 (tt) REVERT: F 11 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7424 (tt) outliers start: 12 outliers final: 4 residues processed: 122 average time/residue: 0.2089 time to fit residues: 33.8085 Evaluate side-chains 117 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 111 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 33 ILE 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 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: 0.5980 chunk 51 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 39 optimal weight: 0.0020 chunk 72 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 overall best weight: 0.4988 ------------------------------------------------------------------------------- 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 = 0.4194 r_free = 0.4194 target = 0.195702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.164205 restraints weight = 7386.805| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 1.65 r_work: 0.3752 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3617 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6898 Z= 0.108 Angle : 0.517 8.300 9346 Z= 0.261 Chirality : 0.040 0.139 1036 Planarity : 0.004 0.028 1148 Dihedral : 3.945 25.173 924 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.37 % Allowed : 15.57 % 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: 1.28 (0.30), residues: 840 helix: 2.38 (0.29), residues: 288 sheet: 0.88 (0.36), residues: 214 loop : -0.52 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 49 HIS 0.003 0.001 HIS E 52 PHE 0.012 0.001 PHE A 39 TYR 0.010 0.001 TYR A 150 ARG 0.006 0.000 ARG E 68 Details of bonding type rmsd hydrogen bonds : bond 0.03650 ( 368) hydrogen bonds : angle 4.12002 ( 1014) metal coordination : bond 0.00094 ( 6) SS BOND : bond 0.00002 ( 4) SS BOND : angle 1.17965 ( 8) covalent geometry : bond 0.00243 ( 6888) covalent geometry : angle 0.51646 ( 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 127 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.8038 (mptt) cc_final: 0.7694 (mtpp) REVERT: B 138 LYS cc_start: 0.8046 (mptt) cc_final: 0.7702 (mtpp) REVERT: C 83 MET cc_start: 0.6813 (mpp) cc_final: 0.6580 (mmt) REVERT: D 11 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7420 (tt) REVERT: F 11 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7444 (tt) REVERT: F 31 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8124 (tt0) outliers start: 10 outliers final: 3 residues processed: 122 average time/residue: 0.1904 time to fit residues: 31.1789 Evaluate side-chains 115 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 110 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 33 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 76 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 61 optimal weight: 0.1980 chunk 21 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4190 r_free = 0.4190 target = 0.194999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.163514 restraints weight = 7369.745| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 1.64 r_work: 0.3776 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3643 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6898 Z= 0.117 Angle : 0.542 8.101 9346 Z= 0.271 Chirality : 0.041 0.195 1036 Planarity : 0.004 0.027 1148 Dihedral : 3.976 22.497 924 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.78 % Allowed : 15.57 % 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: 1.29 (0.30), residues: 840 helix: 2.39 (0.29), residues: 288 sheet: 0.90 (0.36), residues: 214 loop : -0.52 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 49 HIS 0.003 0.001 HIS E 52 PHE 0.012 0.001 PHE B 39 TYR 0.011 0.001 TYR B 150 ARG 0.007 0.000 ARG E 68 Details of bonding type rmsd hydrogen bonds : bond 0.03714 ( 368) hydrogen bonds : angle 4.13439 ( 1014) metal coordination : bond 0.00110 ( 6) SS BOND : bond 0.00037 ( 4) SS BOND : angle 1.15345 ( 8) covalent geometry : bond 0.00268 ( 6888) covalent geometry : angle 0.54083 ( 9338) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4114.48 seconds wall clock time: 71 minutes 24.73 seconds (4284.73 seconds total)