Starting phenix.real_space_refine on Thu Nov 14 20:21:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t04_40934/11_2024/8t04_40934.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t04_40934/11_2024/8t04_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t04_40934/11_2024/8t04_40934.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t04_40934/11_2024/8t04_40934.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t04_40934/11_2024/8t04_40934.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t04_40934/11_2024/8t04_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 4.67, per 1000 atoms: 0.68 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: 1.87 Conformation dependent library (CDL) restraints added in 1.1 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: 0.95 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: 2.00 Time building geometry restraints manager: 2.13 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: 0.00 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: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 21.480 Find NCS groups from input model: 0.210 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:13.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.890 ------------------------------------------------------------------------------- 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 : 0.014 0.111 7058 Z= 0.933 Angle : 1.828 16.817 9564 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 *********************** 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 : 0.531 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: 0.7791 time to fit residues: 95.8801 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 : 0.542 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6498 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 7058 Z= 0.246 Angle : 0.607 6.250 9564 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 *********************** 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 : 0.792 Fit side-chains REVERT: A 27 LYS cc_start: 0.5541 (ttmt) cc_final: 0.4737 (mptt) REVERT: A 61 MET cc_start: 0.6037 (mtm) cc_final: 0.5782 (mtp) REVERT: A 138 LYS cc_start: 0.4657 (mttt) cc_final: 0.4277 (mppt) REVERT: B 27 LYS cc_start: 0.6849 (ttmt) cc_final: 0.5897 (mptt) REVERT: B 138 LYS cc_start: 0.5899 (mttt) cc_final: 0.5402 (mppt) REVERT: C 61 TYR cc_start: 0.7789 (m-80) cc_final: 0.7535 (m-80) REVERT: C 83 MET cc_start: 0.5718 (mmt) cc_final: 0.5360 (mmt) REVERT: C 107 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.7886 (pmm) REVERT: C 112 GLN cc_start: 0.7186 (mt0) cc_final: 0.6874 (mm110) REVERT: D 63 SER cc_start: 0.7191 (m) cc_final: 0.6780 (p) REVERT: D 65 SER cc_start: 0.6895 (m) cc_final: 0.6514 (p) REVERT: E 83 MET cc_start: 0.6976 (mmt) cc_final: 0.6423 (mmt) REVERT: F 4 MET cc_start: 0.6779 (mmm) cc_final: 0.6387 (mmm) REVERT: F 65 SER cc_start: 0.7940 (m) cc_final: 0.7630 (p) outliers start: 23 outliers final: 9 residues processed: 117 average time/residue: 1.1823 time to fit residues: 146.2363 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 : 0.978 ------------------------------------------------------------------------------- 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 41 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 50 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7058 Z= 0.199 Angle : 0.537 6.170 9564 Z= 0.281 Chirality : 0.043 0.145 1054 Planarity : 0.004 0.034 1156 Dihedral : 11.250 136.676 1136 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.28 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 (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: 0.95 (0.31), residues: 840 helix: 1.70 (0.28), residues: 296 sheet: 0.32 (0.37), residues: 230 loop : -0.02 (0.40), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 110 HIS 0.005 0.001 HIS E 52 PHE 0.017 0.002 PHE A 39 TYR 0.009 0.001 TYR D 91 ARG 0.003 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.770 Fit side-chains REVERT: A 27 LYS cc_start: 0.5655 (ttmt) cc_final: 0.4832 (mptt) REVERT: A 61 MET cc_start: 0.6303 (mtm) cc_final: 0.6102 (mtp) REVERT: A 138 LYS cc_start: 0.4892 (mttt) cc_final: 0.4494 (tppt) REVERT: B 27 LYS cc_start: 0.6935 (ttmt) cc_final: 0.5986 (mptt) REVERT: B 138 LYS cc_start: 0.6078 (mttt) cc_final: 0.5559 (mppt) REVERT: C 17 THR cc_start: 0.5453 (p) cc_final: 0.5117 (m) REVERT: C 61 TYR cc_start: 0.7839 (m-80) cc_final: 0.7582 (m-80) REVERT: C 83 MET cc_start: 0.5841 (mmt) cc_final: 0.5580 (mmm) REVERT: C 107 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.7923 (pmm) REVERT: C 112 GLN cc_start: 0.7225 (mt0) cc_final: 0.6883 (mm110) REVERT: D 61 ARG cc_start: 0.5522 (ptp-170) cc_final: 0.5199 (ptp-170) REVERT: D 63 SER cc_start: 0.7058 (m) cc_final: 0.6754 (p) REVERT: E 83 MET cc_start: 0.7019 (mmt) cc_final: 0.6750 (mmm) REVERT: F 23 CYS cc_start: 0.7512 (t) cc_final: 0.7129 (t) REVERT: F 61 ARG cc_start: 0.6905 (ptp-170) cc_final: 0.6636 (ptp-170) outliers start: 18 outliers final: 6 residues processed: 116 average time/residue: 1.2070 time to fit residues: 147.8961 Evaluate side-chains 105 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 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 73 optimal weight: 7.9990 chunk 56 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6510 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7058 Z= 0.213 Angle : 0.531 6.176 9564 Z= 0.275 Chirality : 0.043 0.144 1054 Planarity : 0.004 0.033 1156 Dihedral : 10.982 136.990 1136 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.00 % Allowed : 13.35 % 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: 1.01 (0.30), residues: 840 helix: 1.88 (0.28), residues: 296 sheet: 0.44 (0.38), residues: 220 loop : -0.22 (0.38), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 110 HIS 0.005 0.001 HIS E 52 PHE 0.017 0.002 PHE A 39 TYR 0.010 0.001 TYR F 91 ARG 0.002 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.693 Fit side-chains REVERT: A 27 LYS cc_start: 0.5649 (ttmt) cc_final: 0.4792 (mptt) REVERT: A 29 ARG cc_start: 0.6309 (mtp180) cc_final: 0.5922 (mtp85) REVERT: A 138 LYS cc_start: 0.4854 (mttt) cc_final: 0.4495 (tppt) REVERT: B 27 LYS cc_start: 0.6944 (ttmt) cc_final: 0.5956 (mptt) REVERT: B 29 ARG cc_start: 0.7431 (mtp180) cc_final: 0.7131 (mtp85) REVERT: B 138 LYS cc_start: 0.6090 (mttt) cc_final: 0.5570 (mppt) REVERT: C 61 TYR cc_start: 0.7833 (m-80) cc_final: 0.7541 (m-80) REVERT: C 83 MET cc_start: 0.5834 (mmt) cc_final: 0.5581 (mmm) REVERT: C 107 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.7911 (pmm) REVERT: C 112 GLN cc_start: 0.7220 (mt0) cc_final: 0.6863 (mm110) REVERT: C 117 THR cc_start: 0.8691 (p) cc_final: 0.8255 (t) REVERT: D 61 ARG cc_start: 0.5614 (ptp-170) cc_final: 0.5256 (ptp-170) REVERT: D 63 SER cc_start: 0.7091 (m) cc_final: 0.6785 (p) REVERT: E 83 MET cc_start: 0.7024 (mmt) cc_final: 0.6764 (mmm) REVERT: E 107 MET cc_start: 0.8972 (ptp) cc_final: 0.8660 (pmm) REVERT: F 61 ARG cc_start: 0.7139 (ptp-170) cc_final: 0.6857 (ptp-170) outliers start: 22 outliers final: 11 residues processed: 117 average time/residue: 1.0863 time to fit residues: 135.0629 Evaluate side-chains 112 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.796 ------------------------------------------------------------------------------- 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 3 THR Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain D residue 12 SER 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6524 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 : 0.004 0.026 7058 Z= 0.253 Angle : 0.550 6.172 9564 Z= 0.284 Chirality : 0.043 0.143 1054 Planarity : 0.004 0.032 1156 Dihedral : 10.785 138.635 1136 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.13 % Allowed : 14.44 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.30), residues: 840 helix: 1.89 (0.28), residues: 296 sheet: 0.46 (0.37), residues: 220 loop : -0.40 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 110 HIS 0.004 0.001 HIS C 52 PHE 0.017 0.002 PHE A 39 TYR 0.011 0.001 TYR D 91 ARG 0.002 0.000 ARG A 168 *********************** 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 122 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.781 Fit side-chains REVERT: A 27 LYS cc_start: 0.5623 (ttmt) cc_final: 0.4753 (mptt) REVERT: A 138 LYS cc_start: 0.4788 (mttt) cc_final: 0.4349 (mppt) REVERT: B 27 LYS cc_start: 0.6895 (ttmt) cc_final: 0.5946 (mptt) REVERT: B 29 ARG cc_start: 0.7503 (mtp180) cc_final: 0.7247 (mtp85) REVERT: B 138 LYS cc_start: 0.6014 (mttt) cc_final: 0.5500 (mppt) REVERT: C 3 THR cc_start: 0.6165 (OUTLIER) cc_final: 0.5907 (t) REVERT: C 61 TYR cc_start: 0.7814 (m-80) cc_final: 0.7580 (m-80) REVERT: C 83 MET cc_start: 0.5905 (mmt) cc_final: 0.5613 (mmm) REVERT: C 112 GLN cc_start: 0.7259 (mt0) cc_final: 0.6877 (mm110) REVERT: D 61 ARG cc_start: 0.5777 (ptp-170) cc_final: 0.5424 (ptp-170) REVERT: D 63 SER cc_start: 0.7039 (m) cc_final: 0.6767 (p) REVERT: E 83 MET cc_start: 0.7106 (mmt) cc_final: 0.6804 (mmm) REVERT: E 107 MET cc_start: 0.8894 (ptp) cc_final: 0.8459 (pmm) REVERT: F 61 ARG cc_start: 0.7123 (ptp-170) cc_final: 0.6843 (ptp-170) outliers start: 23 outliers final: 15 residues processed: 113 average time/residue: 1.1339 time to fit residues: 135.9241 Evaluate side-chains 112 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 THR 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 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 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 26 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6506 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7058 Z= 0.194 Angle : 0.512 6.058 9564 Z= 0.266 Chirality : 0.042 0.141 1054 Planarity : 0.004 0.031 1156 Dihedral : 10.406 134.701 1136 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.13 % Allowed : 15.67 % 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: 1.10 (0.30), residues: 840 helix: 2.10 (0.28), residues: 296 sheet: 0.57 (0.37), residues: 220 loop : -0.41 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 55 HIS 0.004 0.001 HIS E 52 PHE 0.025 0.002 PHE B 42 TYR 0.009 0.001 TYR D 91 ARG 0.003 0.000 ARG B 168 *********************** 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 120 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.775 Fit side-chains REVERT: A 29 ARG cc_start: 0.6286 (mtp180) cc_final: 0.5988 (mtp85) REVERT: A 138 LYS cc_start: 0.4772 (mttt) cc_final: 0.4345 (mppt) REVERT: B 27 LYS cc_start: 0.6879 (ttmt) cc_final: 0.5922 (mptt) REVERT: B 29 ARG cc_start: 0.7437 (mtp180) cc_final: 0.7134 (mtp85) REVERT: B 138 LYS cc_start: 0.5997 (mttt) cc_final: 0.5493 (mppt) REVERT: C 3 THR cc_start: 0.6198 (OUTLIER) cc_final: 0.5937 (t) REVERT: C 61 TYR cc_start: 0.7818 (m-80) cc_final: 0.7580 (m-80) REVERT: C 83 MET cc_start: 0.6011 (mmt) cc_final: 0.5711 (mmm) REVERT: C 112 GLN cc_start: 0.7361 (mt0) cc_final: 0.6996 (mm110) REVERT: D 61 ARG cc_start: 0.5775 (ptp-170) cc_final: 0.5433 (ptp-170) REVERT: D 63 SER cc_start: 0.6909 (m) cc_final: 0.6685 (p) REVERT: E 83 MET cc_start: 0.7105 (mmt) cc_final: 0.6802 (mmm) REVERT: E 107 MET cc_start: 0.8917 (ptp) cc_final: 0.8436 (pmm) REVERT: F 61 ARG cc_start: 0.7126 (ptp-170) cc_final: 0.6864 (ptp-170) outliers start: 23 outliers final: 14 residues processed: 113 average time/residue: 1.1437 time to fit residues: 137.0081 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 : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 THR 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 0.8980 chunk 45 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 0.0970 chunk 66 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7058 Z= 0.167 Angle : 0.498 6.030 9564 Z= 0.259 Chirality : 0.041 0.142 1054 Planarity : 0.004 0.031 1156 Dihedral : 10.047 128.565 1136 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.00 % Allowed : 16.62 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.30), residues: 840 helix: 2.29 (0.28), residues: 296 sheet: 0.69 (0.37), residues: 220 loop : -0.41 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 55 HIS 0.004 0.001 HIS E 52 PHE 0.020 0.002 PHE B 42 TYR 0.009 0.001 TYR D 91 ARG 0.002 0.000 ARG A 168 *********************** 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 119 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.763 Fit side-chains REVERT: A 27 LYS cc_start: 0.5574 (mtpt) cc_final: 0.4691 (mptt) REVERT: A 29 ARG cc_start: 0.6386 (mtp180) cc_final: 0.6137 (mtp85) REVERT: A 138 LYS cc_start: 0.4760 (mttt) cc_final: 0.4420 (tppt) REVERT: B 27 LYS cc_start: 0.6879 (ttmt) cc_final: 0.5966 (mptt) REVERT: B 29 ARG cc_start: 0.7440 (mtp180) cc_final: 0.7134 (mtp85) REVERT: B 138 LYS cc_start: 0.5996 (mttt) cc_final: 0.5518 (mppt) REVERT: C 61 TYR cc_start: 0.7801 (m-80) cc_final: 0.7544 (m-80) REVERT: C 83 MET cc_start: 0.6024 (mmt) cc_final: 0.5695 (mmm) REVERT: C 107 MET cc_start: 0.8397 (ptp) cc_final: 0.7914 (pmm) REVERT: C 112 GLN cc_start: 0.7452 (mt0) cc_final: 0.7041 (mm110) REVERT: D 4 MET cc_start: 0.5753 (mmm) cc_final: 0.5505 (tpp) REVERT: D 61 ARG cc_start: 0.5809 (ptp-170) cc_final: 0.5509 (ptp-170) REVERT: E 83 MET cc_start: 0.7125 (mmt) cc_final: 0.6808 (mmm) REVERT: F 61 ARG cc_start: 0.7110 (ptp-170) cc_final: 0.6870 (ptp-170) outliers start: 22 outliers final: 16 residues processed: 114 average time/residue: 1.1033 time to fit residues: 133.3557 Evaluate side-chains 108 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 23 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 50 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 7 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 75 optimal weight: 0.0060 chunk 69 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6510 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7058 Z= 0.212 Angle : 0.526 6.068 9564 Z= 0.273 Chirality : 0.042 0.143 1054 Planarity : 0.004 0.031 1156 Dihedral : 10.096 126.937 1136 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.45 % Allowed : 17.30 % 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 (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 (0.30), residues: 840 helix: 2.06 (0.28), residues: 308 sheet: 0.73 (0.38), residues: 220 loop : -0.48 (0.37), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 55 HIS 0.004 0.001 HIS E 52 PHE 0.016 0.001 PHE A 39 TYR 0.010 0.001 TYR D 91 ARG 0.002 0.000 ARG A 168 *********************** 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 116 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.703 Fit side-chains REVERT: A 27 LYS cc_start: 0.5677 (mtpt) cc_final: 0.4838 (mptt) REVERT: A 29 ARG cc_start: 0.6429 (mtp180) cc_final: 0.6172 (mtp85) REVERT: A 138 LYS cc_start: 0.4778 (mttt) cc_final: 0.4350 (mppt) REVERT: B 29 ARG cc_start: 0.7486 (mtp180) cc_final: 0.7227 (mtp85) REVERT: B 138 LYS cc_start: 0.6010 (mttt) cc_final: 0.5517 (mppt) REVERT: C 61 TYR cc_start: 0.7795 (m-80) cc_final: 0.7559 (m-80) REVERT: C 83 MET cc_start: 0.5994 (mmt) cc_final: 0.5669 (mmm) REVERT: C 112 GLN cc_start: 0.7436 (mt0) cc_final: 0.7026 (mm110) REVERT: D 4 MET cc_start: 0.5686 (mmm) cc_final: 0.5284 (tpp) REVERT: D 61 ARG cc_start: 0.5850 (ptp-170) cc_final: 0.5537 (ptp-170) REVERT: E 83 MET cc_start: 0.7118 (mmt) cc_final: 0.6791 (mmm) REVERT: F 61 ARG cc_start: 0.7123 (ptp-170) cc_final: 0.6876 (ptp-170) outliers start: 18 outliers final: 13 residues processed: 112 average time/residue: 1.1346 time to fit residues: 134.5511 Evaluate side-chains 104 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.796 ------------------------------------------------------------------------------- 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 52 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6501 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7058 Z= 0.186 Angle : 0.517 6.014 9564 Z= 0.267 Chirality : 0.042 0.143 1054 Planarity : 0.004 0.031 1156 Dihedral : 9.934 125.028 1136 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.59 % Allowed : 17.57 % 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: 1.24 (0.30), residues: 840 helix: 2.12 (0.28), residues: 308 sheet: 0.82 (0.38), residues: 220 loop : -0.47 (0.37), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 55 HIS 0.004 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 *********************** 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: 19 poor density : 97 time to evaluate : 0.735 Fit side-chains REVERT: A 27 LYS cc_start: 0.5678 (mtpt) cc_final: 0.4818 (mptt) REVERT: A 29 ARG cc_start: 0.6439 (mtp180) cc_final: 0.6185 (mtp85) REVERT: A 138 LYS cc_start: 0.4768 (mttt) cc_final: 0.4353 (mppt) REVERT: B 27 LYS cc_start: 0.6935 (mtpt) cc_final: 0.5873 (mptt) REVERT: B 138 LYS cc_start: 0.6005 (mttt) cc_final: 0.5508 (mppt) REVERT: C 3 THR cc_start: 0.6069 (OUTLIER) cc_final: 0.5829 (p) REVERT: C 61 TYR cc_start: 0.7779 (m-80) cc_final: 0.7485 (m-80) REVERT: C 66 LYS cc_start: 0.6682 (ttmm) cc_final: 0.6191 (ttmm) REVERT: C 83 MET cc_start: 0.6001 (mmt) cc_final: 0.5674 (mmm) REVERT: C 107 MET cc_start: 0.8419 (ptp) cc_final: 0.7911 (pmm) REVERT: C 112 GLN cc_start: 0.7303 (mt0) cc_final: 0.6903 (mm110) REVERT: C 117 THR cc_start: 0.8753 (p) cc_final: 0.8367 (t) REVERT: D 4 MET cc_start: 0.5693 (mmm) cc_final: 0.5305 (tpp) REVERT: D 61 ARG cc_start: 0.5895 (ptp-170) cc_final: 0.5585 (ptp-170) REVERT: E 66 LYS cc_start: 0.7420 (ttmm) cc_final: 0.6691 (ttmm) REVERT: E 83 MET cc_start: 0.7116 (mmt) cc_final: 0.6787 (mmm) REVERT: E 107 MET cc_start: 0.8831 (ptp) cc_final: 0.8571 (pmm) REVERT: F 61 ARG cc_start: 0.7120 (ptp-170) cc_final: 0.6887 (ptp-170) outliers start: 19 outliers final: 14 residues processed: 111 average time/residue: 1.1585 time to fit residues: 136.1749 Evaluate side-chains 108 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain C residue 3 THR 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 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 36 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 65 optimal weight: 0.4980 chunk 6 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 51 optimal weight: 0.0670 chunk 69 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6487 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7058 Z= 0.162 Angle : 0.513 5.965 9564 Z= 0.265 Chirality : 0.041 0.143 1054 Planarity : 0.004 0.031 1156 Dihedral : 9.733 122.249 1136 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.18 % Allowed : 18.12 % 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 (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: 2.21 (0.28), residues: 308 sheet: 0.92 (0.37), residues: 220 loop : -0.46 (0.37), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 55 HIS 0.003 0.001 HIS C 52 PHE 0.024 0.001 PHE B 170 TYR 0.010 0.001 TYR E 109 ARG 0.002 0.000 ARG A 168 ********************** 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 116 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.720 Fit side-chains REVERT: A 27 LYS cc_start: 0.5721 (mtpt) cc_final: 0.4821 (mptt) REVERT: A 29 ARG cc_start: 0.6438 (mtp180) cc_final: 0.6186 (mtp85) REVERT: A 138 LYS cc_start: 0.4758 (mttt) cc_final: 0.4420 (tppt) REVERT: B 27 LYS cc_start: 0.6944 (mtpt) cc_final: 0.5853 (mptt) REVERT: B 29 ARG cc_start: 0.7421 (mtp180) cc_final: 0.7080 (mtp85) REVERT: B 138 LYS cc_start: 0.6043 (mttt) cc_final: 0.5646 (tppt) REVERT: C 3 THR cc_start: 0.6110 (m) cc_final: 0.5897 (p) REVERT: C 61 TYR cc_start: 0.7773 (m-80) cc_final: 0.7544 (m-80) REVERT: C 83 MET cc_start: 0.6007 (mmt) cc_final: 0.5675 (mmm) REVERT: C 107 MET cc_start: 0.8451 (ptp) cc_final: 0.8238 (pmm) REVERT: C 112 GLN cc_start: 0.7393 (mt0) cc_final: 0.6962 (mm110) REVERT: C 117 THR cc_start: 0.8820 (p) cc_final: 0.8476 (t) REVERT: D 4 MET cc_start: 0.5667 (mmm) cc_final: 0.5302 (tpp) REVERT: D 61 ARG cc_start: 0.5892 (ptp-170) cc_final: 0.5602 (ptp-170) REVERT: E 83 MET cc_start: 0.7125 (mmt) cc_final: 0.6787 (mmm) REVERT: E 117 THR cc_start: 0.9031 (p) cc_final: 0.8624 (t) REVERT: F 61 ARG cc_start: 0.7131 (ptp-170) cc_final: 0.6926 (ptp-170) outliers start: 16 outliers final: 11 residues processed: 113 average time/residue: 1.0968 time to fit residues: 131.6271 Evaluate side-chains 105 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 72 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 70 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 59 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.4051 r_free = 0.4051 target = 0.175523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.125126 restraints weight = 6956.834| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.34 r_work: 0.3303 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7058 Z= 0.203 Angle : 0.532 6.137 9564 Z= 0.274 Chirality : 0.042 0.149 1054 Planarity : 0.004 0.031 1156 Dihedral : 9.789 121.138 1136 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.32 % Allowed : 18.39 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.30), residues: 840 helix: 2.10 (0.28), residues: 308 sheet: 0.95 (0.37), residues: 220 loop : -0.48 (0.37), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 55 HIS 0.004 0.001 HIS F 49 PHE 0.024 0.002 PHE B 170 TYR 0.010 0.001 TYR D 91 ARG 0.002 0.000 ARG B 168 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2702.88 seconds wall clock time: 52 minutes 3.80 seconds (3123.80 seconds total)