Starting phenix.real_space_refine on Fri Aug 22 19:31:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t04_40934/08_2025/8t04_40934.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t04_40934/08_2025/8t04_40934.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8t04_40934/08_2025/8t04_40934.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t04_40934/08_2025/8t04_40934.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t04_40934/08_2025/8t04_40934.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t04_40934/08_2025/8t04_40934.map" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.088 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 2 5.49 5 S 44 5.16 5 C 4492 2.51 5 N 1092 2.21 5 O 1242 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6874 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1593 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 190} Chain: "B" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1593 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: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 76 Unusual residues: {' ZN': 1, 'CLR': 1, 'LBN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "B" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 76 Unusual residues: {' ZN': 1, 'CLR': 1, 'LBN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Time building chain proxies: 1.87, per 1000 atoms: 0.27 Number of scatterers: 6874 At special positions: 0 Unit cell: (72.21, 108.73, 103.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 44 16.00 P 2 15.00 O 1242 8.00 N 1092 7.00 C 4492 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=2.04 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 59 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 97 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 97 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.59 Conformation dependent library (CDL) restraints added in 362.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 180 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 184 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 48 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 184 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 180 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 48 " 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: 28 helices and 12 sheets defined 43.1% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 5 through 14 removed outlier: 3.745A 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 17 through 28 removed outlier: 4.144A pdb=" N THR A 21 " --> pdb=" O ALA A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 52 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 62 through 87 Processing helix chain 'A' and resid 91 through 111 Processing helix chain 'A' and resid 118 through 141 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 175 through 195 removed outlier: 3.898A pdb=" N SER A 181 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS A 185 " --> pdb=" O SER A 181 " (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 17 through 28 removed outlier: 4.142A pdb=" N THR B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 52 Processing helix chain 'B' and resid 55 through 59 Processing helix chain 'B' and resid 62 through 87 Processing helix chain 'B' and resid 91 through 111 removed outlier: 3.501A pdb=" N THR B 95 " --> pdb=" O PRO B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 141 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 175 through 195 removed outlier: 3.899A pdb=" N SER B 181 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N CYS B 185 " --> pdb=" O SER B 181 " (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 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 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: 7.054A pdb=" N VAL C 36 " --> pdb=" O HIS C 52 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N HIS C 52 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.623A 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: 3.816A 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: 6.426A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE D 33 " --> pdb=" O HIS D 49 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N HIS D 49 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 6.751A 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: 6.426A 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: 7.050A pdb=" N VAL E 36 " --> pdb=" O HIS E 52 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N HIS E 52 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 6.621A 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: 3.813A 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: 6.423A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE F 33 " --> pdb=" O HIS F 49 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N HIS F 49 " --> pdb=" O ILE F 33 " (cutoff:3.500A) removed outlier: 6.747A 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: 6.423A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) 393 hydrogen bonds defined for protein. 1047 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: 1.00 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1024 1.31 - 1.44: 2033 1.44 - 1.56: 3921 1.56 - 1.69: 8 1.69 - 1.82: 72 Bond restraints: 7058 Sorted by residual: bond pdb=" C ARG B 93 " pdb=" N SER B 94 " ideal model delta sigma weight residual 1.335 1.446 -0.111 1.31e-02 5.83e+03 7.19e+01 bond pdb=" C25 LBN B 303 " pdb=" O5 LBN B 303 " ideal model delta sigma weight residual 1.326 1.433 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" C25 LBN A 303 " pdb=" O5 LBN A 303 " ideal model delta sigma weight residual 1.326 1.432 -0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" C34 LBN A 303 " pdb=" O7 LBN A 303 " ideal model delta sigma weight residual 1.331 1.423 -0.092 2.00e-02 2.50e+03 2.12e+01 bond pdb=" C34 LBN B 303 " pdb=" O7 LBN B 303 " ideal model delta sigma weight residual 1.331 1.422 -0.091 2.00e-02 2.50e+03 2.08e+01 ... (remaining 7053 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 8955 3.36 - 6.73: 584 6.73 - 10.09: 22 10.09 - 13.45: 1 13.45 - 16.82: 2 Bond angle restraints: 9564 Sorted by residual: angle pdb=" O ARG A 93 " pdb=" C ARG A 93 " pdb=" N SER A 94 " ideal model delta sigma weight residual 122.09 129.02 -6.93 1.04e+00 9.25e-01 4.45e+01 angle pdb=" O1 LBN A 303 " pdb=" P1 LBN A 303 " pdb=" O2 LBN A 303 " ideal model delta sigma weight residual 93.45 110.27 -16.82 3.00e+00 1.11e-01 3.14e+01 angle pdb=" O1 LBN B 303 " pdb=" P1 LBN B 303 " pdb=" O2 LBN B 303 " ideal model delta sigma weight residual 93.45 110.19 -16.74 3.00e+00 1.11e-01 3.12e+01 angle pdb=" N GLU B 90 " pdb=" CA GLU B 90 " pdb=" C GLU B 90 " ideal model delta sigma weight residual 110.07 103.09 6.98 1.26e+00 6.30e-01 3.07e+01 angle pdb=" N GLU A 90 " pdb=" CA GLU A 90 " pdb=" C GLU A 90 " ideal model delta sigma weight residual 110.07 103.11 6.96 1.26e+00 6.30e-01 3.06e+01 ... (remaining 9559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.41: 4126 34.41 - 68.82: 103 68.82 - 103.23: 17 103.23 - 137.64: 2 137.64 - 172.05: 2 Dihedral angle restraints: 4250 sinusoidal: 1788 harmonic: 2462 Sorted by residual: dihedral pdb=" CA HIS F 49 " pdb=" C HIS F 49 " pdb=" N TYR F 50 " pdb=" CA TYR F 50 " ideal model delta harmonic sigma weight residual -180.00 -150.96 -29.04 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA HIS D 49 " pdb=" C HIS D 49 " pdb=" N TYR D 50 " pdb=" CA TYR D 50 " ideal model delta harmonic sigma weight residual -180.00 -151.08 -28.92 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA GLU A 90 " pdb=" C GLU A 90 " pdb=" N PRO A 91 " pdb=" CA PRO A 91 " ideal model delta harmonic sigma weight residual 0.00 26.21 -26.21 0 5.00e+00 4.00e-02 2.75e+01 ... (remaining 4247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.983: 1052 0.983 - 1.966: 0 1.966 - 2.949: 0 2.949 - 3.932: 0 3.932 - 4.915: 2 Chirality restraints: 1054 Sorted by residual: chirality pdb=" C2 LBN B 303 " pdb=" C1 LBN B 303 " pdb=" C3 LBN B 303 " pdb=" O7 LBN B 303 " both_signs ideal model delta sigma weight residual False -2.36 2.55 -4.91 2.00e-01 2.50e+01 6.04e+02 chirality pdb=" C2 LBN A 303 " pdb=" C1 LBN A 303 " pdb=" C3 LBN A 303 " pdb=" O7 LBN A 303 " both_signs ideal model delta sigma weight residual False -2.36 2.55 -4.91 2.00e-01 2.50e+01 6.03e+02 chirality pdb=" CA ILE D 21 " pdb=" N ILE D 21 " pdb=" C ILE D 21 " pdb=" CB ILE D 21 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 1051 not shown) Planarity restraints: 1156 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 110 " 0.021 2.00e-02 2.50e+03 1.19e-02 3.55e+00 pdb=" CG TRP C 110 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP C 110 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP C 110 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP C 110 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP C 110 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 110 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 110 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 110 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 110 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 110 " -0.021 2.00e-02 2.50e+03 1.18e-02 3.46e+00 pdb=" CG TRP E 110 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP E 110 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP E 110 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP E 110 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP E 110 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 110 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 110 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 110 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP E 110 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 93 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.74e+00 pdb=" C ARG B 93 " 0.029 2.00e-02 2.50e+03 pdb=" O ARG B 93 " -0.011 2.00e-02 2.50e+03 pdb=" N SER B 94 " -0.009 2.00e-02 2.50e+03 ... (remaining 1153 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 1240 2.84 - 3.35: 6694 3.35 - 3.87: 10820 3.87 - 4.38: 14301 4.38 - 4.90: 23575 Nonbonded interactions: 56630 Sorted by model distance: nonbonded pdb=" NH1 ARG D 61 " pdb=" OD2 ASP D 82 " model vdw 2.320 3.120 nonbonded pdb=" NH1 ARG F 61 " pdb=" OD2 ASP F 82 " model vdw 2.320 3.120 nonbonded pdb=" NH2 ARG D 61 " pdb=" OE2 GLU D 81 " model vdw 2.479 3.120 nonbonded pdb=" NH2 ARG F 61 " pdb=" OE2 GLU F 81 " model vdw 2.479 3.120 nonbonded pdb=" N GLY B 116 " pdb=" O4 LBN B 303 " model vdw 2.483 3.120 ... (remaining 56625 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.720 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 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 : 0.015 0.220 7068 Z= 1.078 Angle : 1.828 16.817 9572 Z= 1.300 Chirality : 0.230 4.915 1054 Planarity : 0.004 0.027 1156 Dihedral : 16.387 172.049 2666 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.27 % Allowed : 6.81 % Favored : 92.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.29), residues: 840 helix: -1.11 (0.26), residues: 278 sheet: 0.01 (0.40), residues: 166 loop : -0.57 (0.34), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 62 TYR 0.028 0.003 TYR D 91 PHE 0.021 0.002 PHE B 69 TRP 0.030 0.003 TRP C 110 HIS 0.007 0.002 HIS C 52 Details of bonding type rmsd covalent geometry : bond 0.01440 ( 7058) covalent geometry : angle 1.82850 ( 9564) SS BOND : bond 0.00684 ( 4) SS BOND : angle 1.17853 ( 8) hydrogen bonds : bond 0.18540 ( 379) hydrogen bonds : angle 8.76850 ( 1047) metal coordination : bond 0.11773 ( 6) *********************** 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 115 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 113 time to evaluate : 0.280 Fit side-chains REVERT: A 9 LEU cc_start: 0.6311 (mt) cc_final: 0.6099 (mp) REVERT: A 29 ARG cc_start: 0.6564 (mmm160) cc_final: 0.6358 (mtp180) REVERT: A 61 MET cc_start: 0.6262 (mtm) cc_final: 0.6026 (mtp) REVERT: A 87 ASP cc_start: 0.6284 (t70) cc_final: 0.6065 (t70) REVERT: A 94 SER cc_start: 0.6510 (m) cc_final: 0.6075 (p) REVERT: A 137 MET cc_start: 0.5787 (mtm) cc_final: 0.5572 (mtm) REVERT: A 170 PHE cc_start: 0.6461 (t80) cc_final: 0.6152 (t80) REVERT: B 9 LEU cc_start: 0.7564 (mt) cc_final: 0.7242 (mp) REVERT: B 83 MET cc_start: 0.8086 (mmp) cc_final: 0.7550 (mmp) REVERT: B 137 MET cc_start: 0.7561 (mtm) cc_final: 0.7157 (mtm) REVERT: B 170 PHE cc_start: 0.7342 (t80) cc_final: 0.7119 (t80) REVERT: B 189 MET cc_start: 0.7518 (tpt) cc_final: 0.7299 (mmm) REVERT: C 61 TYR cc_start: 0.7574 (m-80) cc_final: 0.7330 (m-80) REVERT: C 83 MET cc_start: 0.5581 (mmt) cc_final: 0.5237 (mmt) REVERT: C 112 GLN cc_start: 0.7255 (mt0) cc_final: 0.6928 (mm110) REVERT: D 63 SER cc_start: 0.6740 (m) cc_final: 0.6539 (p) REVERT: E 83 MET cc_start: 0.6846 (mmt) cc_final: 0.6255 (mmt) outliers start: 2 outliers final: 0 residues processed: 115 average time/residue: 0.4055 time to fit residues: 49.9836 Evaluate side-chains 84 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.4021 r_free = 0.4021 target = 0.173885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.122943 restraints weight = 7115.045| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.37 r_work: 0.3279 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7068 Z= 0.186 Angle : 0.626 6.428 9572 Z= 0.327 Chirality : 0.045 0.163 1054 Planarity : 0.005 0.035 1156 Dihedral : 12.504 137.388 1136 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.54 % Allowed : 10.49 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.30), residues: 840 helix: 1.11 (0.28), residues: 288 sheet: 0.01 (0.36), residues: 230 loop : -0.13 (0.40), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 93 TYR 0.011 0.002 TYR F 91 PHE 0.020 0.002 PHE A 42 TRP 0.020 0.001 TRP E 110 HIS 0.006 0.002 HIS C 52 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 7058) covalent geometry : angle 0.62571 ( 9564) SS BOND : bond 0.00077 ( 4) SS BOND : angle 0.59451 ( 8) hydrogen bonds : bond 0.04462 ( 379) hydrogen bonds : angle 5.36114 ( 1047) metal coordination : bond 0.00482 ( 6) *********************** 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 128 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.271 Fit side-chains REVERT: A 27 LYS cc_start: 0.7611 (ttmt) cc_final: 0.6700 (mptt) REVERT: A 138 LYS cc_start: 0.6674 (mttt) cc_final: 0.6227 (mppt) REVERT: B 27 LYS cc_start: 0.7616 (ttmt) cc_final: 0.6716 (mptt) REVERT: B 138 LYS cc_start: 0.6676 (mttt) cc_final: 0.6211 (mppt) REVERT: C 83 MET cc_start: 0.7278 (mmt) cc_final: 0.6754 (mmt) REVERT: C 107 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.8731 (pmm) REVERT: D 63 SER cc_start: 0.8451 (m) cc_final: 0.8156 (p) REVERT: D 65 SER cc_start: 0.8316 (m) cc_final: 0.8017 (p) REVERT: E 83 MET cc_start: 0.7318 (mmt) cc_final: 0.6778 (mmt) REVERT: F 65 SER cc_start: 0.8213 (m) cc_final: 0.7985 (p) outliers start: 26 outliers final: 11 residues processed: 117 average time/residue: 0.5633 time to fit residues: 69.5032 Evaluate side-chains 103 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 72 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 60 optimal weight: 6.9990 chunk 77 optimal weight: 0.3980 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4038 r_free = 0.4038 target = 0.175144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.124285 restraints weight = 7014.004| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.36 r_work: 0.3299 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7068 Z= 0.137 Angle : 0.536 6.182 9572 Z= 0.281 Chirality : 0.043 0.146 1054 Planarity : 0.004 0.035 1156 Dihedral : 11.253 136.237 1136 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.45 % Allowed : 14.44 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.31), residues: 840 helix: 1.69 (0.28), residues: 296 sheet: 0.24 (0.37), residues: 230 loop : -0.07 (0.40), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 168 TYR 0.009 0.001 TYR D 91 PHE 0.017 0.002 PHE A 39 TRP 0.014 0.001 TRP C 110 HIS 0.005 0.001 HIS E 52 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 7058) covalent geometry : angle 0.53607 ( 9564) SS BOND : bond 0.00055 ( 4) SS BOND : angle 0.35950 ( 8) hydrogen bonds : bond 0.03942 ( 379) hydrogen bonds : angle 4.91160 ( 1047) metal coordination : bond 0.00225 ( 6) *********************** 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 123 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.200 Fit side-chains REVERT: A 27 LYS cc_start: 0.7694 (ttmt) cc_final: 0.6803 (mptt) REVERT: A 138 LYS cc_start: 0.6703 (mttt) cc_final: 0.6272 (tppt) REVERT: B 27 LYS cc_start: 0.7720 (ttmt) cc_final: 0.6823 (mptt) REVERT: B 29 ARG cc_start: 0.8051 (mtp180) cc_final: 0.7795 (mtp85) REVERT: B 138 LYS cc_start: 0.6722 (mttt) cc_final: 0.6223 (mppt) REVERT: C 83 MET cc_start: 0.7353 (mmt) cc_final: 0.7067 (mmm) REVERT: D 61 ARG cc_start: 0.7179 (ptp-170) cc_final: 0.6974 (ptp-170) REVERT: D 63 SER cc_start: 0.8353 (m) cc_final: 0.8151 (p) REVERT: E 83 MET cc_start: 0.7337 (mmt) cc_final: 0.7064 (mmm) REVERT: F 61 ARG cc_start: 0.7232 (ptp-170) cc_final: 0.7017 (ptp-170) outliers start: 18 outliers final: 6 residues processed: 114 average time/residue: 0.5429 time to fit residues: 65.0887 Evaluate side-chains 102 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 72 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 2 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 60 optimal weight: 7.9990 chunk 23 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.4035 r_free = 0.4035 target = 0.174690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.124581 restraints weight = 7070.378| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.33 r_work: 0.3289 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7068 Z= 0.148 Angle : 0.536 6.184 9572 Z= 0.278 Chirality : 0.043 0.146 1054 Planarity : 0.004 0.033 1156 Dihedral : 11.039 137.354 1136 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.45 % Allowed : 14.71 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.30), residues: 840 helix: 1.85 (0.28), residues: 296 sheet: 0.26 (0.37), residues: 230 loop : -0.12 (0.39), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 168 TYR 0.010 0.001 TYR F 91 PHE 0.022 0.002 PHE B 42 TRP 0.014 0.001 TRP E 110 HIS 0.005 0.001 HIS C 52 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 7058) covalent geometry : angle 0.53626 ( 9564) SS BOND : bond 0.00021 ( 4) SS BOND : angle 0.34594 ( 8) hydrogen bonds : bond 0.03977 ( 379) hydrogen bonds : angle 4.85795 ( 1047) metal coordination : bond 0.00246 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.163 Fit side-chains REVERT: A 27 LYS cc_start: 0.7706 (ttmt) cc_final: 0.6776 (mptt) REVERT: A 29 ARG cc_start: 0.8149 (mtp180) cc_final: 0.7904 (mtp85) REVERT: A 138 LYS cc_start: 0.6755 (mttt) cc_final: 0.6256 (mppt) REVERT: B 27 LYS cc_start: 0.7693 (ttmt) cc_final: 0.6781 (mptt) REVERT: B 138 LYS cc_start: 0.6774 (mttt) cc_final: 0.6268 (mppt) REVERT: C 83 MET cc_start: 0.7349 (mmt) cc_final: 0.7113 (mmm) REVERT: C 107 MET cc_start: 0.9024 (ptp) cc_final: 0.8761 (pmm) REVERT: D 61 ARG cc_start: 0.7248 (ptp-170) cc_final: 0.7020 (ptp-170) REVERT: E 83 MET cc_start: 0.7363 (mmt) cc_final: 0.7110 (mmm) REVERT: F 61 ARG cc_start: 0.7419 (ptp-170) cc_final: 0.7196 (ptp-170) outliers start: 18 outliers final: 8 residues processed: 115 average time/residue: 0.4628 time to fit residues: 56.2801 Evaluate side-chains 106 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 72 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 76 optimal weight: 0.3980 chunk 58 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4062 r_free = 0.4062 target = 0.177005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.126892 restraints weight = 7037.392| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.34 r_work: 0.3323 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7068 Z= 0.111 Angle : 0.501 6.034 9572 Z= 0.260 Chirality : 0.041 0.140 1054 Planarity : 0.004 0.032 1156 Dihedral : 10.454 137.159 1136 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.32 % Allowed : 15.80 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.30), residues: 840 helix: 2.18 (0.28), residues: 296 sheet: 0.49 (0.37), residues: 220 loop : -0.29 (0.38), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 168 TYR 0.008 0.001 TYR F 91 PHE 0.019 0.002 PHE B 42 TRP 0.011 0.001 TRP E 55 HIS 0.004 0.001 HIS C 52 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 7058) covalent geometry : angle 0.50063 ( 9564) SS BOND : bond 0.00071 ( 4) SS BOND : angle 0.44587 ( 8) hydrogen bonds : bond 0.03644 ( 379) hydrogen bonds : angle 4.62665 ( 1047) metal coordination : bond 0.00158 ( 6) *********************** 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 113 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.265 Fit side-chains REVERT: A 29 ARG cc_start: 0.8139 (mtp180) cc_final: 0.7893 (mtp85) REVERT: A 138 LYS cc_start: 0.6721 (mttt) cc_final: 0.6315 (tppt) REVERT: B 27 LYS cc_start: 0.7650 (ttmt) cc_final: 0.6783 (mptt) REVERT: B 29 ARG cc_start: 0.8093 (mtp180) cc_final: 0.7886 (mtp85) REVERT: B 138 LYS cc_start: 0.6679 (mttt) cc_final: 0.6282 (tppt) REVERT: C 83 MET cc_start: 0.7374 (mmt) cc_final: 0.7075 (mmm) REVERT: E 83 MET cc_start: 0.7428 (mmt) cc_final: 0.7112 (mmm) outliers start: 17 outliers final: 10 residues processed: 107 average time/residue: 0.5441 time to fit residues: 61.4303 Evaluate side-chains 103 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 52 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.4024 r_free = 0.4024 target = 0.173127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.122911 restraints weight = 7106.166| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.33 r_work: 0.3267 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7068 Z= 0.187 Angle : 0.563 6.177 9572 Z= 0.291 Chirality : 0.044 0.141 1054 Planarity : 0.004 0.031 1156 Dihedral : 10.678 134.819 1136 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.68 % Allowed : 16.49 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.30), residues: 840 helix: 1.98 (0.28), residues: 296 sheet: 0.47 (0.37), residues: 220 loop : -0.44 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 45 TYR 0.012 0.002 TYR D 91 PHE 0.021 0.002 PHE A 42 TRP 0.015 0.001 TRP E 110 HIS 0.004 0.001 HIS F 49 Details of bonding type rmsd covalent geometry : bond 0.00446 ( 7058) covalent geometry : angle 0.56322 ( 9564) SS BOND : bond 0.00088 ( 4) SS BOND : angle 0.38168 ( 8) hydrogen bonds : bond 0.04212 ( 379) hydrogen bonds : angle 4.86738 ( 1047) metal coordination : bond 0.00298 ( 6) *********************** 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 124 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.267 Fit side-chains REVERT: A 27 LYS cc_start: 0.7647 (mtpt) cc_final: 0.6678 (mptt) REVERT: A 41 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8319 (ttt) REVERT: A 138 LYS cc_start: 0.6723 (mttt) cc_final: 0.6239 (mppt) REVERT: B 27 LYS cc_start: 0.7658 (ttmt) cc_final: 0.6763 (mptt) REVERT: B 29 ARG cc_start: 0.8208 (mtp180) cc_final: 0.7976 (mtp85) REVERT: B 138 LYS cc_start: 0.6729 (mttt) cc_final: 0.6242 (mppt) REVERT: C 83 MET cc_start: 0.7439 (mmt) cc_final: 0.7169 (mmm) REVERT: C 107 MET cc_start: 0.9022 (ptp) cc_final: 0.8744 (pmm) REVERT: E 83 MET cc_start: 0.7454 (mmt) cc_final: 0.7161 (mmm) outliers start: 27 outliers final: 14 residues processed: 117 average time/residue: 0.5334 time to fit residues: 66.0651 Evaluate side-chains 110 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 72 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 43 optimal weight: 0.0270 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.7238 ------------------------------------------------------------------------------- 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 = 0.4048 r_free = 0.4048 target = 0.175879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.125965 restraints weight = 7049.785| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.33 r_work: 0.3309 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7068 Z= 0.128 Angle : 0.514 6.040 9572 Z= 0.266 Chirality : 0.042 0.141 1054 Planarity : 0.004 0.031 1156 Dihedral : 10.258 131.556 1136 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.81 % Allowed : 15.94 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.30), residues: 840 helix: 2.16 (0.28), residues: 296 sheet: 0.63 (0.37), residues: 220 loop : -0.44 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 168 TYR 0.009 0.001 TYR D 91 PHE 0.021 0.002 PHE A 42 TRP 0.015 0.001 TRP E 55 HIS 0.003 0.001 HIS C 52 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 7058) covalent geometry : angle 0.51356 ( 9564) SS BOND : bond 0.00098 ( 4) SS BOND : angle 0.48326 ( 8) hydrogen bonds : bond 0.03774 ( 379) hydrogen bonds : angle 4.65694 ( 1047) metal coordination : bond 0.00178 ( 6) *********************** 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 126 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 0.282 Fit side-chains REVERT: A 27 LYS cc_start: 0.7711 (mtpt) cc_final: 0.6728 (mptt) REVERT: A 29 ARG cc_start: 0.8135 (mtp180) cc_final: 0.7871 (mtp85) REVERT: A 138 LYS cc_start: 0.6700 (mttt) cc_final: 0.6226 (mppt) REVERT: B 29 ARG cc_start: 0.8176 (mtp180) cc_final: 0.7955 (mtp85) REVERT: B 138 LYS cc_start: 0.6710 (mttt) cc_final: 0.6234 (mppt) REVERT: C 83 MET cc_start: 0.7460 (mmt) cc_final: 0.7159 (mmm) REVERT: C 107 MET cc_start: 0.8964 (ptp) cc_final: 0.8739 (pmm) REVERT: D 61 ARG cc_start: 0.7236 (ptp-170) cc_final: 0.7032 (ttp-170) REVERT: E 83 MET cc_start: 0.7462 (mmt) cc_final: 0.7146 (mmm) REVERT: F 61 ARG cc_start: 0.7293 (ptp-170) cc_final: 0.6891 (ttp-170) outliers start: 28 outliers final: 17 residues processed: 116 average time/residue: 0.4982 time to fit residues: 60.9924 Evaluate side-chains 111 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 89 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 67 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 46 optimal weight: 0.1980 chunk 41 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 52 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4060 r_free = 0.4060 target = 0.176781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.126822 restraints weight = 7122.710| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.35 r_work: 0.3317 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7068 Z= 0.114 Angle : 0.497 5.986 9572 Z= 0.260 Chirality : 0.041 0.143 1054 Planarity : 0.004 0.032 1156 Dihedral : 9.949 126.672 1136 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.13 % Allowed : 17.17 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.30), residues: 840 helix: 2.18 (0.28), residues: 308 sheet: 0.70 (0.37), residues: 220 loop : -0.48 (0.37), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 168 TYR 0.008 0.001 TYR D 71 PHE 0.024 0.001 PHE B 42 TRP 0.018 0.001 TRP E 55 HIS 0.003 0.001 HIS E 52 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 7058) covalent geometry : angle 0.49734 ( 9564) SS BOND : bond 0.00113 ( 4) SS BOND : angle 0.49022 ( 8) hydrogen bonds : bond 0.03694 ( 379) hydrogen bonds : angle 4.52671 ( 1047) metal coordination : bond 0.00142 ( 6) *********************** 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 123 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.282 Fit side-chains REVERT: A 27 LYS cc_start: 0.7725 (mtpt) cc_final: 0.6716 (mptt) REVERT: A 29 ARG cc_start: 0.8131 (mtp180) cc_final: 0.7916 (mtp85) REVERT: A 138 LYS cc_start: 0.6708 (mttt) cc_final: 0.6303 (tppt) REVERT: B 23 SER cc_start: 0.7881 (p) cc_final: 0.7643 (m) REVERT: B 27 LYS cc_start: 0.7668 (mtpt) cc_final: 0.6693 (mptt) REVERT: B 29 ARG cc_start: 0.8152 (mtp180) cc_final: 0.7906 (mtp85) REVERT: B 138 LYS cc_start: 0.6724 (mttt) cc_final: 0.6295 (mppt) REVERT: C 83 MET cc_start: 0.7478 (mmt) cc_final: 0.7158 (mmm) REVERT: C 107 MET cc_start: 0.8966 (ptp) cc_final: 0.8722 (pmm) REVERT: C 117 THR cc_start: 0.8967 (p) cc_final: 0.8512 (t) REVERT: E 66 LYS cc_start: 0.7108 (ttpt) cc_final: 0.6902 (ttmm) REVERT: E 83 MET cc_start: 0.7489 (mmt) cc_final: 0.7159 (mmm) REVERT: E 117 THR cc_start: 0.8970 (p) cc_final: 0.8518 (t) outliers start: 23 outliers final: 16 residues processed: 118 average time/residue: 0.5035 time to fit residues: 62.7286 Evaluate side-chains 111 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain C residue 52 HIS Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain E residue 52 HIS Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 89 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 78 optimal weight: 7.9990 chunk 15 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 72 optimal weight: 0.3980 chunk 57 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4054 r_free = 0.4054 target = 0.176255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.126376 restraints weight = 7042.597| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.33 r_work: 0.3315 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7068 Z= 0.125 Angle : 0.514 6.025 9572 Z= 0.268 Chirality : 0.041 0.143 1054 Planarity : 0.004 0.031 1156 Dihedral : 9.889 124.589 1136 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.54 % Allowed : 17.30 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.30), residues: 840 helix: 2.17 (0.28), residues: 308 sheet: 0.71 (0.37), residues: 230 loop : -0.47 (0.38), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 168 TYR 0.009 0.001 TYR D 91 PHE 0.022 0.002 PHE B 170 TRP 0.021 0.001 TRP E 55 HIS 0.003 0.001 HIS F 49 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 7058) covalent geometry : angle 0.51395 ( 9564) SS BOND : bond 0.00115 ( 4) SS BOND : angle 0.46965 ( 8) hydrogen bonds : bond 0.03787 ( 379) hydrogen bonds : angle 4.57005 ( 1047) metal coordination : bond 0.00170 ( 6) *********************** 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 126 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 0.272 Fit side-chains REVERT: A 27 LYS cc_start: 0.7743 (mtpt) cc_final: 0.6744 (mptt) REVERT: A 29 ARG cc_start: 0.8134 (mtp180) cc_final: 0.7912 (mtp85) REVERT: A 138 LYS cc_start: 0.6757 (mttt) cc_final: 0.6372 (tppt) REVERT: B 9 LEU cc_start: 0.7842 (mp) cc_final: 0.7564 (pp) REVERT: B 23 SER cc_start: 0.7904 (p) cc_final: 0.7667 (m) REVERT: B 27 LYS cc_start: 0.7713 (mtpt) cc_final: 0.6732 (mptt) REVERT: B 138 LYS cc_start: 0.6746 (mttt) cc_final: 0.6376 (tppt) REVERT: C 66 LYS cc_start: 0.7626 (ttmm) cc_final: 0.6811 (ttmm) REVERT: C 83 MET cc_start: 0.7482 (mmt) cc_final: 0.7163 (mmm) REVERT: C 107 MET cc_start: 0.8978 (ptp) cc_final: 0.8747 (pmm) REVERT: C 117 THR cc_start: 0.8970 (p) cc_final: 0.8513 (t) REVERT: E 83 MET cc_start: 0.7497 (mmt) cc_final: 0.7174 (mmm) REVERT: E 117 THR cc_start: 0.8969 (p) cc_final: 0.8528 (t) outliers start: 26 outliers final: 15 residues processed: 122 average time/residue: 0.4966 time to fit residues: 64.1683 Evaluate side-chains 110 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain C residue 52 HIS Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 52 HIS Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 72 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 42 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 5 optimal weight: 0.0770 chunk 17 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.7942 ------------------------------------------------------------------------------- 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 = 0.4049 r_free = 0.4049 target = 0.175736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.125685 restraints weight = 7045.142| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.34 r_work: 0.3307 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7068 Z= 0.136 Angle : 0.534 6.036 9572 Z= 0.276 Chirality : 0.042 0.145 1054 Planarity : 0.004 0.031 1156 Dihedral : 9.884 123.467 1136 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.45 % Allowed : 18.39 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.30), residues: 840 helix: 2.11 (0.28), residues: 308 sheet: 0.77 (0.37), residues: 220 loop : -0.60 (0.37), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 168 TYR 0.010 0.001 TYR D 91 PHE 0.022 0.002 PHE B 42 TRP 0.025 0.001 TRP E 55 HIS 0.003 0.001 HIS F 49 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 7058) covalent geometry : angle 0.53432 ( 9564) SS BOND : bond 0.00115 ( 4) SS BOND : angle 0.45888 ( 8) hydrogen bonds : bond 0.03863 ( 379) hydrogen bonds : angle 4.63319 ( 1047) metal coordination : bond 0.00195 ( 6) ********************** 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 120 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.264 Fit side-chains REVERT: A 27 LYS cc_start: 0.7748 (mtpt) cc_final: 0.6773 (mptt) REVERT: A 29 ARG cc_start: 0.8174 (mtp180) cc_final: 0.7942 (mtp85) REVERT: A 138 LYS cc_start: 0.6707 (mttt) cc_final: 0.6229 (mppt) REVERT: B 27 LYS cc_start: 0.7731 (mtpt) cc_final: 0.6730 (mptt) REVERT: B 138 LYS cc_start: 0.6708 (mttt) cc_final: 0.6238 (mppt) REVERT: C 66 LYS cc_start: 0.7626 (ttmm) cc_final: 0.6872 (ttmm) REVERT: C 83 MET cc_start: 0.7480 (mmt) cc_final: 0.7166 (mmm) REVERT: C 107 MET cc_start: 0.9027 (ptp) cc_final: 0.8714 (pmm) REVERT: C 117 THR cc_start: 0.8962 (p) cc_final: 0.8505 (t) REVERT: E 66 LYS cc_start: 0.7662 (ttmm) cc_final: 0.6889 (ttmm) REVERT: E 83 MET cc_start: 0.7479 (mmt) cc_final: 0.7159 (mmm) REVERT: E 117 THR cc_start: 0.8962 (p) cc_final: 0.8508 (t) outliers start: 18 outliers final: 15 residues processed: 115 average time/residue: 0.4870 time to fit residues: 59.3985 Evaluate side-chains 111 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 52 HIS Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 52 HIS Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 72 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 3 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 81 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.4048 r_free = 0.4048 target = 0.175357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.124869 restraints weight = 7029.797| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.35 r_work: 0.3300 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7068 Z= 0.149 Angle : 0.545 6.064 9572 Z= 0.282 Chirality : 0.042 0.147 1054 Planarity : 0.004 0.031 1156 Dihedral : 9.928 122.735 1136 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.45 % Allowed : 18.39 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.30), residues: 840 helix: 2.01 (0.28), residues: 308 sheet: 0.70 (0.36), residues: 220 loop : -0.64 (0.37), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 29 TYR 0.011 0.001 TYR C 109 PHE 0.021 0.002 PHE A 42 TRP 0.026 0.001 TRP C 55 HIS 0.004 0.001 HIS F 49 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 7058) covalent geometry : angle 0.54483 ( 9564) SS BOND : bond 0.00120 ( 4) SS BOND : angle 0.43239 ( 8) hydrogen bonds : bond 0.03957 ( 379) hydrogen bonds : angle 4.70018 ( 1047) metal coordination : bond 0.00214 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2153.59 seconds wall clock time: 37 minutes 32.72 seconds (2252.72 seconds total)