Starting phenix.real_space_refine on Sun May 11 02:04:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t04_40934/05_2025/8t04_40934.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t04_40934/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8t04_40934/05_2025/8t04_40934.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t04_40934/05_2025/8t04_40934.map" model { file = "/net/cci-nas-00/data/ceres_data/8t04_40934/05_2025/8t04_40934.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t04_40934/05_2025/8t04_40934.cif" } resolution = 2.98 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= 0.088 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.01, per 1000 atoms: 0.73 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: 1.84 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.98 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: 2.02 Time building geometry restraints manager: 2.12 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: 0.03 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.000 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.410 ------------------------------------------------------------------------------- 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 (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: -1.07 (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 TRP 0.030 0.003 TRP C 110 HIS 0.007 0.002 HIS C 52 PHE 0.021 0.002 PHE B 69 TYR 0.028 0.003 TYR D 91 ARG 0.006 0.001 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.18540 ( 379) hydrogen bonds : angle 8.76850 ( 1047) metal coordination : bond 0.11773 ( 6) SS BOND : bond 0.00684 ( 4) SS BOND : angle 1.17853 ( 8) covalent geometry : bond 0.01440 ( 7058) covalent geometry : angle 1.82850 ( 9564) *********************** 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 : 0.700 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: 0.8822 time to fit residues: 108.7992 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 : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.4032 r_free = 0.4032 target = 0.174925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.123978 restraints weight = 6983.152| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.35 r_work: 0.3296 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 7068 Z= 0.164 Angle : 0.607 6.250 9572 Z= 0.318 Chirality : 0.045 0.161 1054 Planarity : 0.005 0.035 1156 Dihedral : 12.411 138.992 1136 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.13 % Allowed : 11.17 % Favored : 85.69 % 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: 0.47 (0.30), residues: 840 helix: 1.16 (0.28), residues: 288 sheet: 0.05 (0.36), residues: 230 loop : -0.10 (0.40), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 110 HIS 0.006 0.002 HIS E 52 PHE 0.021 0.002 PHE A 42 TYR 0.010 0.001 TYR D 91 ARG 0.002 0.000 ARG B 93 Details of bonding type rmsd hydrogen bonds : bond 0.04365 ( 379) hydrogen bonds : angle 5.30403 ( 1047) metal coordination : bond 0.00578 ( 6) SS BOND : bond 0.00080 ( 4) SS BOND : angle 0.63773 ( 8) covalent geometry : bond 0.00383 ( 7058) covalent geometry : angle 0.60661 ( 9564) *********************** 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 125 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.781 Fit side-chains REVERT: A 27 LYS cc_start: 0.7607 (ttmt) cc_final: 0.6704 (mptt) REVERT: A 61 MET cc_start: 0.7767 (mtm) cc_final: 0.7563 (mtp) REVERT: A 138 LYS cc_start: 0.6578 (mttt) cc_final: 0.6146 (mppt) REVERT: B 27 LYS cc_start: 0.7614 (ttmt) cc_final: 0.6725 (mptt) REVERT: B 138 LYS cc_start: 0.6596 (mttt) cc_final: 0.6128 (mppt) REVERT: C 83 MET cc_start: 0.7296 (mmt) cc_final: 0.6754 (mmt) REVERT: C 107 MET cc_start: 0.9101 (OUTLIER) cc_final: 0.8730 (pmm) REVERT: D 63 SER cc_start: 0.8468 (m) cc_final: 0.8160 (p) REVERT: D 65 SER cc_start: 0.8309 (m) cc_final: 0.8018 (p) REVERT: E 83 MET cc_start: 0.7324 (mmt) cc_final: 0.6782 (mmt) REVERT: F 4 MET cc_start: 0.7383 (mmm) cc_final: 0.6904 (mmm) REVERT: F 65 SER cc_start: 0.8278 (m) cc_final: 0.8061 (p) outliers start: 23 outliers final: 9 residues processed: 117 average time/residue: 1.0978 time to fit residues: 135.9292 Evaluate side-chains 101 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 MET 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 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 65 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 68 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 67 optimal weight: 7.9990 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4061 r_free = 0.4061 target = 0.177164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.126990 restraints weight = 7036.651| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.32 r_work: 0.3333 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7068 Z= 0.122 Angle : 0.524 6.140 9572 Z= 0.275 Chirality : 0.042 0.144 1054 Planarity : 0.004 0.035 1156 Dihedral : 11.104 135.004 1136 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.32 % Allowed : 14.71 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.04 (0.31), residues: 840 helix: 1.78 (0.28), residues: 296 sheet: 0.36 (0.37), residues: 230 loop : 0.02 (0.40), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 110 HIS 0.005 0.001 HIS E 52 PHE 0.016 0.001 PHE A 39 TYR 0.009 0.001 TYR D 91 ARG 0.003 0.000 ARG A 168 Details of bonding type rmsd hydrogen bonds : bond 0.03836 ( 379) hydrogen bonds : angle 4.84210 ( 1047) metal coordination : bond 0.00203 ( 6) SS BOND : bond 0.00082 ( 4) SS BOND : angle 0.41226 ( 8) covalent geometry : bond 0.00276 ( 7058) covalent geometry : angle 0.52375 ( 9564) *********************** 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 121 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.843 Fit side-chains REVERT: A 27 LYS cc_start: 0.7672 (ttmt) cc_final: 0.6808 (mptt) REVERT: A 138 LYS cc_start: 0.6755 (mttt) cc_final: 0.6316 (tppt) REVERT: B 27 LYS cc_start: 0.7673 (ttmt) cc_final: 0.6834 (mptt) REVERT: B 138 LYS cc_start: 0.6734 (mttt) cc_final: 0.6327 (tppt) REVERT: C 83 MET cc_start: 0.7359 (mmt) cc_final: 0.7097 (mmm) REVERT: E 83 MET cc_start: 0.7347 (mmt) cc_final: 0.7069 (mmm) REVERT: F 61 ARG cc_start: 0.7218 (ptp-170) cc_final: 0.7008 (ptp-170) outliers start: 17 outliers final: 5 residues processed: 113 average time/residue: 1.1683 time to fit residues: 140.2426 Evaluate side-chains 99 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 94 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 4 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 46 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4041 r_free = 0.4041 target = 0.175369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.124473 restraints weight = 7103.557| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.37 r_work: 0.3317 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2676 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= 0.129 Angle : 0.515 6.116 9572 Z= 0.269 Chirality : 0.042 0.142 1054 Planarity : 0.004 0.032 1156 Dihedral : 10.994 134.907 1136 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.72 % Allowed : 13.62 % Favored : 83.65 % 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: 1.16 (0.31), residues: 840 helix: 2.00 (0.28), residues: 296 sheet: 0.45 (0.37), residues: 230 loop : -0.07 (0.39), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 110 HIS 0.004 0.001 HIS E 52 PHE 0.017 0.002 PHE B 170 TYR 0.009 0.001 TYR D 91 ARG 0.003 0.000 ARG A 168 Details of bonding type rmsd hydrogen bonds : bond 0.03813 ( 379) hydrogen bonds : angle 4.73304 ( 1047) metal coordination : bond 0.00205 ( 6) SS BOND : bond 0.00067 ( 4) SS BOND : angle 0.42039 ( 8) covalent geometry : bond 0.00296 ( 7058) covalent geometry : angle 0.51532 ( 9564) *********************** 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 113 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.727 Fit side-chains REVERT: A 27 LYS cc_start: 0.7750 (ttmt) cc_final: 0.6835 (mptt) REVERT: A 29 ARG cc_start: 0.8155 (mtp180) cc_final: 0.7916 (mtp85) REVERT: A 138 LYS cc_start: 0.6740 (mttt) cc_final: 0.6326 (tppt) REVERT: A 200 LYS cc_start: 0.8150 (mttt) cc_final: 0.7938 (mttt) REVERT: B 27 LYS cc_start: 0.7748 (ttmt) cc_final: 0.6835 (mptt) REVERT: B 29 ARG cc_start: 0.8128 (mtp180) cc_final: 0.7902 (mtp85) REVERT: B 138 LYS cc_start: 0.6757 (mttt) cc_final: 0.6347 (tppt) REVERT: C 83 MET cc_start: 0.7381 (mmt) cc_final: 0.7134 (mmm) REVERT: E 83 MET cc_start: 0.7385 (mmt) cc_final: 0.7136 (mmm) REVERT: F 61 ARG cc_start: 0.7392 (ptp-170) cc_final: 0.7181 (ptp-170) outliers start: 20 outliers final: 8 residues processed: 105 average time/residue: 1.1480 time to fit residues: 127.7006 Evaluate side-chains 97 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain D residue 5 THR 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 72 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 21 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4047 r_free = 0.4047 target = 0.175544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.125096 restraints weight = 6984.817| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.34 r_work: 0.3300 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2802 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= 0.140 Angle : 0.523 6.109 9572 Z= 0.272 Chirality : 0.042 0.140 1054 Planarity : 0.004 0.032 1156 Dihedral : 10.666 137.646 1136 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.45 % Allowed : 14.85 % Favored : 82.70 % 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: 1.13 (0.30), residues: 840 helix: 2.04 (0.28), residues: 296 sheet: 0.63 (0.38), residues: 220 loop : -0.32 (0.38), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 110 HIS 0.003 0.001 HIS F 49 PHE 0.024 0.002 PHE B 42 TYR 0.010 0.001 TYR D 91 ARG 0.002 0.000 ARG A 168 Details of bonding type rmsd hydrogen bonds : bond 0.03889 ( 379) hydrogen bonds : angle 4.72073 ( 1047) metal coordination : bond 0.00218 ( 6) SS BOND : bond 0.00078 ( 4) SS BOND : angle 0.39918 ( 8) covalent geometry : bond 0.00325 ( 7058) covalent geometry : angle 0.52294 ( 9564) *********************** 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 109 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.744 Fit side-chains REVERT: A 27 LYS cc_start: 0.7688 (ttmt) cc_final: 0.6777 (mptt) REVERT: A 29 ARG cc_start: 0.8200 (mtp180) cc_final: 0.7941 (mtp85) REVERT: A 138 LYS cc_start: 0.6751 (mttt) cc_final: 0.6337 (tppt) REVERT: A 200 LYS cc_start: 0.8140 (mttt) cc_final: 0.7902 (mtpt) REVERT: B 27 LYS cc_start: 0.7679 (ttmt) cc_final: 0.6787 (mptt) REVERT: B 29 ARG cc_start: 0.8127 (mtp180) cc_final: 0.7888 (mtp85) REVERT: B 138 LYS cc_start: 0.6748 (mttt) cc_final: 0.6340 (tppt) REVERT: C 83 MET cc_start: 0.7462 (mmt) cc_final: 0.7153 (mmm) REVERT: C 107 MET cc_start: 0.8995 (ptp) cc_final: 0.8768 (pmm) REVERT: E 83 MET cc_start: 0.7466 (mmt) cc_final: 0.7143 (mmm) REVERT: F 61 ARG cc_start: 0.7446 (ptp-170) cc_final: 0.7246 (ptp-170) outliers start: 18 outliers final: 13 residues processed: 103 average time/residue: 1.1558 time to fit residues: 125.7895 Evaluate side-chains 103 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 HIS Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 21 ILE 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 52 HIS Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 21 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 7 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 5 optimal weight: 0.1980 chunk 10 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.4043 r_free = 0.4043 target = 0.175113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.124508 restraints weight = 7002.847| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.34 r_work: 0.3291 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2899 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= 0.148 Angle : 0.525 6.119 9572 Z= 0.273 Chirality : 0.042 0.141 1054 Planarity : 0.004 0.031 1156 Dihedral : 10.473 134.829 1136 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.72 % Allowed : 15.26 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.30), residues: 840 helix: 2.05 (0.28), residues: 296 sheet: 0.61 (0.37), residues: 220 loop : -0.43 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 110 HIS 0.004 0.001 HIS D 49 PHE 0.017 0.002 PHE B 42 TYR 0.010 0.001 TYR D 91 ARG 0.002 0.000 ARG B 168 Details of bonding type rmsd hydrogen bonds : bond 0.03933 ( 379) hydrogen bonds : angle 4.74623 ( 1047) metal coordination : bond 0.00230 ( 6) SS BOND : bond 0.00080 ( 4) SS BOND : angle 0.41551 ( 8) covalent geometry : bond 0.00346 ( 7058) covalent geometry : angle 0.52516 ( 9564) *********************** 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 113 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.752 Fit side-chains REVERT: A 29 ARG cc_start: 0.8222 (mtp180) cc_final: 0.7970 (mtp85) REVERT: A 138 LYS cc_start: 0.6686 (mttt) cc_final: 0.6198 (mppt) REVERT: A 200 LYS cc_start: 0.8161 (mttt) cc_final: 0.7961 (mtpt) REVERT: B 29 ARG cc_start: 0.8130 (mtp180) cc_final: 0.7881 (mtp85) REVERT: B 138 LYS cc_start: 0.6685 (mttt) cc_final: 0.6207 (mppt) REVERT: C 83 MET cc_start: 0.7437 (mmt) cc_final: 0.7165 (mmm) REVERT: C 107 MET cc_start: 0.8999 (ptp) cc_final: 0.8770 (pmm) REVERT: D 4 MET cc_start: 0.7455 (mmm) cc_final: 0.7222 (tpp) REVERT: D 61 ARG cc_start: 0.7227 (ptp-170) cc_final: 0.6722 (ttp-170) REVERT: E 83 MET cc_start: 0.7456 (mmt) cc_final: 0.7173 (mmm) outliers start: 20 outliers final: 16 residues processed: 106 average time/residue: 1.1117 time to fit residues: 124.9504 Evaluate side-chains 105 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 5 THR Chi-restraints excluded: chain D residue 21 ILE 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 21 ILE 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 7 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 53 optimal weight: 0.0000 chunk 0 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- 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 = 0.4065 r_free = 0.4065 target = 0.177439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.126942 restraints weight = 6953.485| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.34 r_work: 0.3325 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7068 Z= 0.117 Angle : 0.497 6.010 9572 Z= 0.260 Chirality : 0.041 0.141 1054 Planarity : 0.004 0.031 1156 Dihedral : 10.064 129.497 1136 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.86 % Allowed : 15.94 % Favored : 81.20 % 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: 1.21 (0.30), residues: 840 helix: 2.24 (0.28), residues: 296 sheet: 0.70 (0.37), residues: 220 loop : -0.45 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 55 HIS 0.003 0.001 HIS C 52 PHE 0.015 0.001 PHE A 39 TYR 0.008 0.001 TYR D 91 ARG 0.002 0.000 ARG A 168 Details of bonding type rmsd hydrogen bonds : bond 0.03689 ( 379) hydrogen bonds : angle 4.57202 ( 1047) metal coordination : bond 0.00156 ( 6) SS BOND : bond 0.00104 ( 4) SS BOND : angle 0.47077 ( 8) covalent geometry : bond 0.00264 ( 7058) covalent geometry : angle 0.49748 ( 9564) *********************** 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 116 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.760 Fit side-chains REVERT: A 29 ARG cc_start: 0.8206 (mtp180) cc_final: 0.7960 (mtp85) REVERT: A 138 LYS cc_start: 0.6678 (mttt) cc_final: 0.6283 (tppt) REVERT: B 138 LYS cc_start: 0.6691 (mttt) cc_final: 0.6292 (tppt) REVERT: C 83 MET cc_start: 0.7455 (mmt) cc_final: 0.7147 (mmm) REVERT: C 107 MET cc_start: 0.8988 (ptp) cc_final: 0.8733 (pmm) REVERT: D 61 ARG cc_start: 0.7319 (ptp-170) cc_final: 0.6846 (ttp-170) REVERT: E 83 MET cc_start: 0.7466 (mmt) cc_final: 0.7150 (mmm) REVERT: F 61 ARG cc_start: 0.7270 (ptp-170) cc_final: 0.6921 (ttp-170) outliers start: 21 outliers final: 15 residues processed: 111 average time/residue: 1.1056 time to fit residues: 130.3888 Evaluate side-chains 106 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 0.3980 chunk 45 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 50 optimal weight: 0.0770 chunk 77 optimal weight: 2.9990 overall best weight: 0.8942 ------------------------------------------------------------------------------- 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 = 0.4046 r_free = 0.4046 target = 0.175646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.125279 restraints weight = 7054.758| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.35 r_work: 0.3299 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3098 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= 0.142 Angle : 0.520 6.083 9572 Z= 0.271 Chirality : 0.042 0.143 1054 Planarity : 0.004 0.031 1156 Dihedral : 10.092 127.032 1136 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.86 % Allowed : 16.62 % Favored : 80.52 % 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: 1.14 (0.30), residues: 840 helix: 2.04 (0.28), residues: 308 sheet: 0.77 (0.37), residues: 220 loop : -0.53 (0.37), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 55 HIS 0.004 0.001 HIS F 49 PHE 0.020 0.002 PHE A 42 TYR 0.010 0.001 TYR D 91 ARG 0.002 0.000 ARG A 168 Details of bonding type rmsd hydrogen bonds : bond 0.03909 ( 379) hydrogen bonds : angle 4.64892 ( 1047) metal coordination : bond 0.00211 ( 6) SS BOND : bond 0.00103 ( 4) SS BOND : angle 0.44388 ( 8) covalent geometry : bond 0.00331 ( 7058) covalent geometry : angle 0.52054 ( 9564) *********************** 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 113 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.789 Fit side-chains REVERT: A 29 ARG cc_start: 0.8198 (mtp180) cc_final: 0.7954 (mtp85) REVERT: A 138 LYS cc_start: 0.6689 (mttt) cc_final: 0.6214 (mppt) REVERT: B 29 ARG cc_start: 0.8143 (mtp180) cc_final: 0.7921 (mtp85) REVERT: B 138 LYS cc_start: 0.6685 (mttt) cc_final: 0.6213 (mppt) REVERT: C 83 MET cc_start: 0.7456 (mmt) cc_final: 0.7148 (mmm) REVERT: C 107 MET cc_start: 0.8993 (ptp) cc_final: 0.8736 (pmm) REVERT: D 61 ARG cc_start: 0.7295 (ptp-170) cc_final: 0.6900 (ttp-170) REVERT: E 66 LYS cc_start: 0.7095 (ttpt) cc_final: 0.6893 (ttmm) REVERT: E 83 MET cc_start: 0.7474 (mmt) cc_final: 0.7159 (mmm) outliers start: 21 outliers final: 15 residues processed: 110 average time/residue: 1.0719 time to fit residues: 124.9789 Evaluate side-chains 103 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 5 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 54 optimal weight: 0.0040 chunk 75 optimal weight: 0.3980 chunk 30 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 44 optimal weight: 0.0870 chunk 2 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 overall best weight: 0.3770 ------------------------------------------------------------------------------- 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 = 0.4057 r_free = 0.4057 target = 0.176927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.126549 restraints weight = 7011.042| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.37 r_work: 0.3350 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7068 Z= 0.099 Angle : 0.484 5.904 9572 Z= 0.253 Chirality : 0.040 0.140 1054 Planarity : 0.004 0.031 1156 Dihedral : 9.665 122.621 1136 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.91 % Allowed : 18.26 % 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 (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: 1.39 (0.30), residues: 840 helix: 2.33 (0.28), residues: 308 sheet: 0.89 (0.37), residues: 220 loop : -0.49 (0.37), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 55 HIS 0.003 0.001 HIS C 52 PHE 0.013 0.001 PHE A 39 TYR 0.008 0.001 TYR D 71 ARG 0.002 0.000 ARG A 168 Details of bonding type rmsd hydrogen bonds : bond 0.03518 ( 379) hydrogen bonds : angle 4.42791 ( 1047) metal coordination : bond 0.00104 ( 6) SS BOND : bond 0.00143 ( 4) SS BOND : angle 0.50875 ( 8) covalent geometry : bond 0.00214 ( 7058) covalent geometry : angle 0.48386 ( 9564) *********************** 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 116 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.700 Fit side-chains REVERT: A 23 SER cc_start: 0.7903 (p) cc_final: 0.7679 (m) REVERT: A 27 LYS cc_start: 0.7746 (ttpt) cc_final: 0.6853 (mptt) REVERT: A 29 ARG cc_start: 0.8152 (mtp180) cc_final: 0.7918 (mtp85) REVERT: A 138 LYS cc_start: 0.6719 (mttt) cc_final: 0.6341 (tppt) REVERT: B 23 SER cc_start: 0.7906 (p) cc_final: 0.7672 (m) REVERT: B 27 LYS cc_start: 0.7742 (ttpt) cc_final: 0.6854 (mptt) REVERT: B 29 ARG cc_start: 0.8085 (mtp180) cc_final: 0.7873 (mtp85) REVERT: B 83 MET cc_start: 0.8297 (mmp) cc_final: 0.7973 (mmp) REVERT: B 138 LYS cc_start: 0.6717 (mttt) cc_final: 0.6353 (tppt) REVERT: C 16 GLN cc_start: 0.7285 (mm-40) cc_final: 0.7068 (mm-40) REVERT: C 66 LYS cc_start: 0.7617 (ttmm) cc_final: 0.6872 (ttmm) REVERT: C 83 MET cc_start: 0.7442 (mmt) cc_final: 0.7142 (mmm) REVERT: D 61 ARG cc_start: 0.7303 (ptp-170) cc_final: 0.7035 (ttp-170) REVERT: E 16 GLN cc_start: 0.7306 (mm-40) cc_final: 0.7101 (mm-40) REVERT: E 83 MET cc_start: 0.7475 (mmt) cc_final: 0.7169 (mmm) outliers start: 14 outliers final: 10 residues processed: 111 average time/residue: 1.0592 time to fit residues: 124.5082 Evaluate side-chains 109 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER 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 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 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 11 optimal weight: 0.0980 chunk 34 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 80 optimal weight: 0.0970 chunk 47 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.4083 r_free = 0.4083 target = 0.178935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.128409 restraints weight = 7088.767| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.37 r_work: 0.3346 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7068 Z= 0.109 Angle : 0.499 6.019 9572 Z= 0.259 Chirality : 0.041 0.149 1054 Planarity : 0.004 0.031 1156 Dihedral : 9.558 119.754 1136 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.32 % Allowed : 18.53 % 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 (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: 1.41 (0.30), residues: 840 helix: 2.36 (0.28), residues: 308 sheet: 0.96 (0.37), residues: 220 loop : -0.54 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 55 HIS 0.006 0.001 HIS E 52 PHE 0.022 0.002 PHE A 42 TYR 0.009 0.001 TYR D 91 ARG 0.002 0.000 ARG A 168 Details of bonding type rmsd hydrogen bonds : bond 0.03628 ( 379) hydrogen bonds : angle 4.43078 ( 1047) metal coordination : bond 0.00125 ( 6) SS BOND : bond 0.00135 ( 4) SS BOND : angle 0.46476 ( 8) covalent geometry : bond 0.00242 ( 7058) covalent geometry : angle 0.49931 ( 9564) ********************** 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 118 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.719 Fit side-chains REVERT: A 23 SER cc_start: 0.7891 (p) cc_final: 0.7683 (m) REVERT: A 27 LYS cc_start: 0.7758 (ttpt) cc_final: 0.6871 (mptt) REVERT: A 29 ARG cc_start: 0.8206 (mtp180) cc_final: 0.7965 (mtp85) REVERT: A 138 LYS cc_start: 0.6731 (mttt) cc_final: 0.6357 (tppt) REVERT: B 27 LYS cc_start: 0.7763 (ttpt) cc_final: 0.6878 (mptt) REVERT: B 29 ARG cc_start: 0.8114 (mtp180) cc_final: 0.7891 (mtp85) REVERT: B 83 MET cc_start: 0.8353 (mmp) cc_final: 0.7990 (mmp) REVERT: B 138 LYS cc_start: 0.6723 (mttt) cc_final: 0.6351 (tppt) REVERT: C 16 GLN cc_start: 0.7273 (mm-40) cc_final: 0.7058 (mm-40) REVERT: C 66 LYS cc_start: 0.7627 (ttmm) cc_final: 0.6902 (ttmm) REVERT: C 83 MET cc_start: 0.7435 (mmt) cc_final: 0.7108 (mmm) REVERT: D 61 ARG cc_start: 0.7258 (ptp-170) cc_final: 0.6982 (ttp-170) REVERT: E 16 GLN cc_start: 0.7310 (mm-40) cc_final: 0.7110 (mm-40) REVERT: E 66 LYS cc_start: 0.7650 (ttmm) cc_final: 0.6893 (ttmm) REVERT: E 83 MET cc_start: 0.7470 (mmt) cc_final: 0.7167 (mmm) outliers start: 17 outliers final: 12 residues processed: 113 average time/residue: 1.0581 time to fit residues: 126.7448 Evaluate side-chains 111 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B 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 52 SER Chi-restraints excluded: chain D residue 63 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 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 69 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4041 r_free = 0.4041 target = 0.175162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.124462 restraints weight = 7023.200| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.39 r_work: 0.3326 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3368 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= 0.124 Angle : 0.513 6.081 9572 Z= 0.266 Chirality : 0.041 0.145 1054 Planarity : 0.004 0.031 1156 Dihedral : 9.573 118.421 1136 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.04 % Allowed : 18.80 % 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 (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: 1.34 (0.30), residues: 840 helix: 2.23 (0.28), residues: 308 sheet: 1.00 (0.37), residues: 220 loop : -0.56 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 55 HIS 0.007 0.001 HIS E 52 PHE 0.017 0.001 PHE B 46 TYR 0.010 0.001 TYR D 91 ARG 0.002 0.000 ARG A 168 Details of bonding type rmsd hydrogen bonds : bond 0.03757 ( 379) hydrogen bonds : angle 4.49949 ( 1047) metal coordination : bond 0.00166 ( 6) SS BOND : bond 0.00120 ( 4) SS BOND : angle 0.44780 ( 8) covalent geometry : bond 0.00285 ( 7058) covalent geometry : angle 0.51321 ( 9564) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4531.10 seconds wall clock time: 79 minutes 3.09 seconds (4743.09 seconds total)