Starting phenix.real_space_refine on Fri Jul 19 05:55:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t07_40937/07_2024/8t07_40937_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t07_40937/07_2024/8t07_40937.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t07_40937/07_2024/8t07_40937.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t07_40937/07_2024/8t07_40937.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t07_40937/07_2024/8t07_40937_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t07_40937/07_2024/8t07_40937_neut.cif" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.066 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 44 5.16 5 C 4352 2.51 5 N 1090 2.21 5 O 1222 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 90": "OE1" <-> "OE2" Residue "B PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 90": "OE1" <-> "OE2" Residue "C ARG 60": "NH1" <-> "NH2" Residue "D ASP 70": "OD1" <-> "OD2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 60": "NH1" <-> "NH2" Residue "F ASP 70": "OD1" <-> "OD2" Residue "F TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 6710 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1586 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 190} Chain: "B" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1586 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 190} Chain: "C" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 936 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "D" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "E" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 936 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "F" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.92, per 1000 atoms: 0.73 Number of scatterers: 6710 At special positions: 0 Unit cell: (87.15, 110.39, 104.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 44 16.00 O 1222 8.00 N 1090 7.00 C 4352 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 59 " distance=2.03 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 59 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 97 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 97 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 2.57 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 184 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 48 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 180 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 184 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 48 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 180 " 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1572 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 12 sheets defined 44.0% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 5 through 14 removed outlier: 3.586A pdb=" N LEU A 9 " --> pdb=" O VAL A 5 " (cutoff:3.500A) Proline residue: A 11 - end of helix Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 18 through 28 Processing helix chain 'A' and resid 30 through 50 Processing helix chain 'A' and resid 55 through 59 removed outlier: 3.701A pdb=" N CYS A 59 " --> pdb=" O SER A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 87 removed outlier: 3.620A pdb=" N LEU A 66 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 85 " --> pdb=" O SER A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 111 Processing helix chain 'A' and resid 115 through 141 Proline residue: A 121 - end of helix Processing helix chain 'A' and resid 146 through 153 Processing helix chain 'A' and resid 153 through 170 Processing helix chain 'A' and resid 171 through 174 Processing helix chain 'A' and resid 177 through 195 removed outlier: 3.513A pdb=" N SER A 181 " --> pdb=" O THR A 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 14 Proline residue: B 11 - end of helix Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 18 through 28 Processing helix chain 'B' and resid 30 through 50 Processing helix chain 'B' and resid 55 through 59 removed outlier: 3.702A pdb=" N CYS B 59 " --> pdb=" O SER B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 87 removed outlier: 3.620A pdb=" N LEU B 66 " --> pdb=" O ARG B 62 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 111 Processing helix chain 'B' and resid 115 through 141 Proline residue: B 121 - end of helix Processing helix chain 'B' and resid 146 through 153 Processing helix chain 'B' and resid 153 through 170 Processing helix chain 'B' and resid 171 through 174 Processing helix chain 'B' and resid 177 through 195 removed outlier: 3.513A pdb=" N SER B 181 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 67 No H-bonds generated for 'chain 'C' and resid 65 through 67' Processing helix chain 'C' and resid 75 through 77 No H-bonds generated for 'chain 'C' and resid 75 through 77' Processing helix chain 'C' and resid 88 through 91 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'E' and resid 65 through 67 No H-bonds generated for 'chain 'E' and resid 65 through 67' Processing helix chain 'E' and resid 75 through 77 No H-bonds generated for 'chain 'E' and resid 75 through 77' Processing helix chain 'E' and resid 88 through 91 Processing helix chain 'F' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.952A pdb=" N VAL C 36 " --> pdb=" O HIS C 52 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N HIS C 52 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TRP C 38 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.710A pdb=" N TYR C 109 " --> pdb=" O ARG C 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AA5, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.060A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE D 33 " --> pdb=" O HIS D 49 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N HIS D 49 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.060A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.952A pdb=" N VAL E 36 " --> pdb=" O HIS E 52 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N HIS E 52 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TRP E 38 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.709A pdb=" N TYR E 109 " --> pdb=" O ARG E 99 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AB2, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.060A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE F 33 " --> pdb=" O HIS F 49 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N HIS F 49 " --> pdb=" O ILE F 33 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.060A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) 382 hydrogen bonds defined for protein. 1014 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.09 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1243 1.33 - 1.46: 1814 1.46 - 1.58: 3759 1.58 - 1.70: 0 1.70 - 1.82: 72 Bond restraints: 6888 Sorted by residual: bond pdb=" C ARG B 93 " pdb=" N SER B 94 " ideal model delta sigma weight residual 1.335 1.423 -0.088 1.30e-02 5.92e+03 4.61e+01 bond pdb=" N ARG C 68 " pdb=" CA ARG C 68 " ideal model delta sigma weight residual 1.458 1.502 -0.044 1.00e-02 1.00e+04 1.97e+01 bond pdb=" N ARG E 68 " pdb=" CA ARG E 68 " ideal model delta sigma weight residual 1.458 1.502 -0.044 1.00e-02 1.00e+04 1.96e+01 bond pdb=" C ALA B 86 " pdb=" N ASP B 87 " ideal model delta sigma weight residual 1.330 1.277 0.053 1.30e-02 5.92e+03 1.69e+01 bond pdb=" N SER D 7 " pdb=" CA SER D 7 " ideal model delta sigma weight residual 1.463 1.488 -0.025 6.90e-03 2.10e+04 1.34e+01 ... (remaining 6883 not shown) Histogram of bond angle deviations from ideal: 99.70 - 106.72: 211 106.72 - 113.73: 3670 113.73 - 120.75: 3080 120.75 - 127.77: 2310 127.77 - 134.78: 67 Bond angle restraints: 9338 Sorted by residual: angle pdb=" CA GLY D 66 " pdb=" C GLY D 66 " pdb=" O GLY D 66 " ideal model delta sigma weight residual 122.23 118.61 3.62 6.90e-01 2.10e+00 2.76e+01 angle pdb=" CA GLY F 66 " pdb=" C GLY F 66 " pdb=" O GLY F 66 " ideal model delta sigma weight residual 122.23 118.65 3.58 6.90e-01 2.10e+00 2.69e+01 angle pdb=" CA GLY E 113 " pdb=" C GLY E 113 " pdb=" O GLY E 113 " ideal model delta sigma weight residual 122.29 118.11 4.18 8.10e-01 1.52e+00 2.67e+01 angle pdb=" CA GLY C 113 " pdb=" C GLY C 113 " pdb=" O GLY C 113 " ideal model delta sigma weight residual 122.29 118.11 4.18 8.10e-01 1.52e+00 2.66e+01 angle pdb=" C PHE E 54 " pdb=" N TRP E 55 " pdb=" CA TRP E 55 " ideal model delta sigma weight residual 120.38 127.28 -6.90 1.37e+00 5.33e-01 2.54e+01 ... (remaining 9333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.92: 3542 13.92 - 27.85: 371 27.85 - 41.77: 87 41.77 - 55.70: 20 55.70 - 69.62: 14 Dihedral angle restraints: 4034 sinusoidal: 1574 harmonic: 2460 Sorted by residual: dihedral pdb=" CB CYS B 50 " pdb=" SG CYS B 50 " pdb=" SG CYS B 59 " pdb=" CB CYS B 59 " ideal model delta sinusoidal sigma weight residual 93.00 151.19 -58.19 1 1.00e+01 1.00e-02 4.54e+01 dihedral pdb=" CB CYS A 50 " pdb=" SG CYS A 50 " pdb=" SG CYS A 59 " pdb=" CB CYS A 59 " ideal model delta sinusoidal sigma weight residual 93.00 151.16 -58.16 1 1.00e+01 1.00e-02 4.54e+01 dihedral pdb=" CA LEU B 58 " pdb=" C LEU B 58 " pdb=" N CYS B 59 " pdb=" CA CYS B 59 " ideal model delta harmonic sigma weight residual -180.00 -153.40 -26.60 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 4031 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 395 0.043 - 0.086: 310 0.086 - 0.129: 221 0.129 - 0.172: 90 0.172 - 0.215: 20 Chirality restraints: 1036 Sorted by residual: chirality pdb=" CA ILE F 33 " pdb=" N ILE F 33 " pdb=" C ILE F 33 " pdb=" CB ILE F 33 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA ILE D 33 " pdb=" N ILE D 33 " pdb=" C ILE D 33 " pdb=" CB ILE D 33 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA ILE C 84 " pdb=" N ILE C 84 " pdb=" C ILE C 84 " pdb=" CB ILE C 84 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1033 not shown) Planarity restraints: 1148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 86 " -0.019 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" C ALA A 86 " 0.067 2.00e-02 2.50e+03 pdb=" O ALA A 86 " -0.024 2.00e-02 2.50e+03 pdb=" N ASP A 87 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 86 " 0.018 2.00e-02 2.50e+03 3.64e-02 1.32e+01 pdb=" C ALA B 86 " -0.063 2.00e-02 2.50e+03 pdb=" O ALA B 86 " 0.023 2.00e-02 2.50e+03 pdb=" N ASP B 87 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 93 " 0.010 2.00e-02 2.50e+03 2.15e-02 4.62e+00 pdb=" C ARG B 93 " -0.037 2.00e-02 2.50e+03 pdb=" O ARG B 93 " 0.015 2.00e-02 2.50e+03 pdb=" N SER B 94 " 0.012 2.00e-02 2.50e+03 ... (remaining 1145 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 1664 2.87 - 3.38: 6811 3.38 - 3.89: 11017 3.89 - 4.39: 13006 4.39 - 4.90: 22414 Nonbonded interactions: 54912 Sorted by model distance: nonbonded pdb=" O PRO B 91 " pdb=" OG1 THR B 95 " model vdw 2.368 2.440 nonbonded pdb=" NH2 ARG E 99 " pdb=" OD2 ASP E 108 " model vdw 2.394 2.520 nonbonded pdb=" NH2 ARG C 99 " pdb=" OD2 ASP C 108 " model vdw 2.395 2.520 nonbonded pdb=" O ILE B 104 " pdb=" OG1 THR B 108 " model vdw 2.486 2.440 nonbonded pdb=" O ILE A 104 " pdb=" OG1 THR A 108 " model vdw 2.487 2.440 ... (remaining 54907 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 4.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.080 Process input model: 25.020 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.088 6888 Z= 0.887 Angle : 1.710 7.637 9338 Z= 1.277 Chirality : 0.080 0.215 1036 Planarity : 0.004 0.039 1148 Dihedral : 12.725 69.621 2450 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 0.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.27 % Allowed : 5.74 % Favored : 93.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.27), residues: 840 helix: -1.20 (0.24), residues: 302 sheet: -0.35 (0.34), residues: 182 loop : -0.63 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP E 110 HIS 0.007 0.002 HIS A 180 PHE 0.029 0.003 PHE B 46 TYR 0.024 0.003 TYR A 144 ARG 0.003 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 151 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.7361 (mmm160) cc_final: 0.7048 (mtm-85) REVERT: A 138 LYS cc_start: 0.7683 (mptt) cc_final: 0.7028 (mtpp) REVERT: B 29 ARG cc_start: 0.7380 (mmm160) cc_final: 0.7130 (mtm-85) REVERT: B 138 LYS cc_start: 0.7669 (mptt) cc_final: 0.7017 (mtpp) REVERT: C 48 GLU cc_start: 0.7563 (tt0) cc_final: 0.7358 (tt0) REVERT: C 94 THR cc_start: 0.7716 (p) cc_final: 0.7253 (p) REVERT: D 14 SER cc_start: 0.7686 (p) cc_final: 0.7309 (m) REVERT: E 94 THR cc_start: 0.7710 (p) cc_final: 0.7262 (p) REVERT: F 45 ARG cc_start: 0.7436 (mtp85) cc_final: 0.7225 (mtp85) outliers start: 2 outliers final: 2 residues processed: 151 average time/residue: 0.2050 time to fit residues: 40.0776 Evaluate side-chains 118 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 116 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain F residue 61 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN B 92 GLN D 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6888 Z= 0.225 Angle : 0.595 6.276 9338 Z= 0.313 Chirality : 0.042 0.133 1036 Planarity : 0.004 0.034 1148 Dihedral : 5.669 56.570 932 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.37 % Allowed : 11.20 % Favored : 87.43 % 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: 0.30 (0.29), residues: 840 helix: 1.21 (0.29), residues: 302 sheet: -0.60 (0.33), residues: 226 loop : 0.02 (0.38), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 55 HIS 0.003 0.001 HIS D 49 PHE 0.016 0.002 PHE A 69 TYR 0.014 0.002 TYR B 72 ARG 0.003 0.000 ARG E 68 *********************** 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 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 115 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.7400 (mmm160) cc_final: 0.7181 (mtm-85) REVERT: A 35 MET cc_start: 0.8383 (mtm) cc_final: 0.8179 (ttm) REVERT: A 83 MET cc_start: 0.7383 (mmp) cc_final: 0.7182 (mmp) REVERT: A 138 LYS cc_start: 0.7555 (mptt) cc_final: 0.6948 (mtpp) REVERT: B 35 MET cc_start: 0.8288 (mtm) cc_final: 0.8075 (ttm) REVERT: B 138 LYS cc_start: 0.7533 (mptt) cc_final: 0.6933 (mtpp) REVERT: F 103 LYS cc_start: 0.7948 (tttt) cc_final: 0.7616 (tptt) outliers start: 10 outliers final: 9 residues processed: 119 average time/residue: 0.1996 time to fit residues: 31.1682 Evaluate side-chains 120 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 111 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain F residue 61 ARG Chi-restraints excluded: chain F residue 94 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 61 optimal weight: 9.9990 chunk 50 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 66 optimal weight: 0.0670 chunk 73 optimal weight: 0.0170 chunk 25 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 overall best weight: 0.4956 ------------------------------------------------------------------------------- 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: 0.7154 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6888 Z= 0.157 Angle : 0.516 5.789 9338 Z= 0.269 Chirality : 0.041 0.212 1036 Planarity : 0.004 0.031 1148 Dihedral : 5.200 59.068 932 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.78 % Allowed : 12.98 % Favored : 85.25 % 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: 0.89 (0.30), residues: 840 helix: 1.86 (0.29), residues: 304 sheet: -0.28 (0.33), residues: 226 loop : 0.15 (0.38), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 35 HIS 0.004 0.001 HIS E 52 PHE 0.013 0.001 PHE B 43 TYR 0.010 0.001 TYR B 72 ARG 0.003 0.000 ARG E 68 *********************** 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 130 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 117 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.7375 (mmm160) cc_final: 0.7148 (mtm-85) REVERT: A 138 LYS cc_start: 0.7541 (mptt) cc_final: 0.7015 (mtpp) REVERT: B 138 LYS cc_start: 0.7527 (mptt) cc_final: 0.7000 (mtpp) REVERT: C 100 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7436 (tmt90) REVERT: D 103 LYS cc_start: 0.8014 (tttt) cc_final: 0.7662 (tptt) REVERT: E 100 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7434 (tmt90) REVERT: F 103 LYS cc_start: 0.8042 (tttt) cc_final: 0.7711 (tptt) outliers start: 13 outliers final: 8 residues processed: 121 average time/residue: 0.2355 time to fit residues: 37.0730 Evaluate side-chains 118 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 108 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 100 ARG Chi-restraints excluded: chain F residue 61 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 0.1980 chunk 56 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 8 optimal weight: 0.0060 chunk 35 optimal weight: 4.9990 chunk 50 optimal weight: 0.1980 chunk 74 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 39 optimal weight: 9.9990 chunk 70 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN F 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6888 Z= 0.146 Angle : 0.485 6.265 9338 Z= 0.250 Chirality : 0.039 0.129 1036 Planarity : 0.004 0.029 1148 Dihedral : 4.904 57.337 932 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.87 % Allowed : 12.16 % Favored : 84.97 % 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: 1.34 (0.30), residues: 840 helix: 2.21 (0.29), residues: 304 sheet: 0.23 (0.35), residues: 230 loop : 0.19 (0.39), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 35 HIS 0.003 0.001 HIS C 52 PHE 0.012 0.001 PHE A 39 TYR 0.009 0.001 TYR B 72 ARG 0.004 0.000 ARG E 68 *********************** 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 138 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 117 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.7422 (mmm160) cc_final: 0.7203 (mtm-85) REVERT: A 138 LYS cc_start: 0.7479 (mptt) cc_final: 0.6967 (mtpp) REVERT: B 138 LYS cc_start: 0.7474 (mptt) cc_final: 0.6962 (mtpp) REVERT: C 100 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7394 (tmt90) REVERT: E 100 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7388 (tmt90) REVERT: F 103 LYS cc_start: 0.8053 (tttt) cc_final: 0.7717 (tptt) outliers start: 21 outliers final: 11 residues processed: 126 average time/residue: 0.2143 time to fit residues: 35.2479 Evaluate side-chains 125 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 112 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 100 ARG Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 61 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN F 6 GLN F 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6888 Z= 0.246 Angle : 0.527 6.049 9338 Z= 0.273 Chirality : 0.041 0.131 1036 Planarity : 0.004 0.028 1148 Dihedral : 4.770 47.746 932 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.14 % Allowed : 11.89 % Favored : 84.97 % 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: 1.14 (0.29), residues: 840 helix: 2.07 (0.29), residues: 300 sheet: 0.38 (0.35), residues: 218 loop : -0.15 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 110 HIS 0.002 0.001 HIS D 49 PHE 0.015 0.002 PHE B 39 TYR 0.016 0.002 TYR D 91 ARG 0.006 0.000 ARG E 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 110 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.7500 (mptt) cc_final: 0.6949 (mtpp) REVERT: B 138 LYS cc_start: 0.7481 (mptt) cc_final: 0.6976 (mtpp) REVERT: C 100 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7440 (tmt90) REVERT: E 100 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7436 (tmt90) REVERT: E 107 MET cc_start: 0.8469 (ptp) cc_final: 0.7836 (ptp) outliers start: 23 outliers final: 10 residues processed: 122 average time/residue: 0.2061 time to fit residues: 32.6103 Evaluate side-chains 122 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 110 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 100 ARG Chi-restraints excluded: chain F residue 54 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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: 0.7227 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6888 Z= 0.235 Angle : 0.531 6.415 9338 Z= 0.270 Chirality : 0.041 0.135 1036 Planarity : 0.004 0.028 1148 Dihedral : 4.140 22.497 924 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.28 % Allowed : 12.43 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.29), residues: 840 helix: 2.11 (0.29), residues: 288 sheet: 0.48 (0.35), residues: 222 loop : -0.30 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 110 HIS 0.002 0.001 HIS F 49 PHE 0.014 0.001 PHE B 39 TYR 0.014 0.001 TYR D 91 ARG 0.005 0.000 ARG E 68 *********************** 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 134 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 110 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.7510 (mptt) cc_final: 0.6998 (mtpp) REVERT: B 138 LYS cc_start: 0.7492 (mptt) cc_final: 0.6983 (mtpp) REVERT: C 100 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7382 (tmt90) REVERT: E 5 LYS cc_start: 0.8501 (tppt) cc_final: 0.8240 (tptm) REVERT: E 100 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7383 (tmt90) outliers start: 24 outliers final: 11 residues processed: 123 average time/residue: 0.2117 time to fit residues: 33.7554 Evaluate side-chains 120 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 107 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 100 ARG Chi-restraints excluded: chain F residue 33 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 30 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6888 Z= 0.290 Angle : 0.568 8.793 9338 Z= 0.288 Chirality : 0.042 0.130 1036 Planarity : 0.004 0.028 1148 Dihedral : 4.300 26.125 924 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.87 % Allowed : 12.98 % Favored : 84.15 % 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: 0.91 (0.29), residues: 840 helix: 1.96 (0.29), residues: 288 sheet: 0.32 (0.35), residues: 216 loop : -0.33 (0.34), residues: 336 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 0.015 0.002 PHE A 39 TYR 0.017 0.002 TYR F 91 ARG 0.005 0.000 ARG C 68 *********************** 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 128 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 107 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.7518 (mptt) cc_final: 0.6975 (mtpp) REVERT: A 150 TYR cc_start: 0.8220 (m-10) cc_final: 0.7953 (m-10) REVERT: B 138 LYS cc_start: 0.7556 (mptt) cc_final: 0.6994 (mtpp) REVERT: B 150 TYR cc_start: 0.8226 (m-10) cc_final: 0.7962 (m-10) REVERT: C 100 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7320 (tmt90) REVERT: E 5 LYS cc_start: 0.8523 (tppt) cc_final: 0.8268 (tptm) REVERT: E 100 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7328 (tmt90) REVERT: F 11 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.7050 (tt) outliers start: 21 outliers final: 13 residues processed: 121 average time/residue: 0.2567 time to fit residues: 39.7945 Evaluate side-chains 124 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 108 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 100 ARG Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 33 ILE 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: 0.9980 chunk 50 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 73 optimal weight: 8.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6888 Z= 0.219 Angle : 0.531 8.564 9338 Z= 0.267 Chirality : 0.040 0.136 1036 Planarity : 0.004 0.029 1148 Dihedral : 4.152 24.805 924 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.14 % Allowed : 13.25 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.29), residues: 840 helix: 2.09 (0.29), residues: 288 sheet: 0.54 (0.36), residues: 218 loop : -0.46 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 113 HIS 0.002 0.001 HIS C 52 PHE 0.013 0.001 PHE A 39 TYR 0.012 0.001 TYR B 72 ARG 0.006 0.000 ARG E 68 *********************** 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 137 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 114 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.7518 (mptt) cc_final: 0.7004 (mtpp) REVERT: B 138 LYS cc_start: 0.7502 (mptt) cc_final: 0.6980 (mtpp) REVERT: C 100 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7345 (tmt90) REVERT: D 11 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.6959 (tt) REVERT: E 5 LYS cc_start: 0.8530 (tppt) cc_final: 0.8301 (tptm) REVERT: E 48 GLU cc_start: 0.7490 (tt0) cc_final: 0.7048 (pt0) REVERT: E 100 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7344 (tmt90) REVERT: E 115 SER cc_start: 0.8242 (p) cc_final: 0.7837 (t) REVERT: F 11 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.6991 (tt) outliers start: 23 outliers final: 10 residues processed: 128 average time/residue: 0.2147 time to fit residues: 35.6091 Evaluate side-chains 122 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 108 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 100 ARG Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 33 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 2.9990 chunk 44 optimal weight: 0.0970 chunk 32 optimal weight: 0.1980 chunk 57 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 66 optimal weight: 0.4980 chunk 69 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7207 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6888 Z= 0.183 Angle : 0.520 8.429 9338 Z= 0.259 Chirality : 0.040 0.141 1036 Planarity : 0.004 0.029 1148 Dihedral : 4.062 25.631 924 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.32 % Allowed : 13.39 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.29), residues: 840 helix: 2.28 (0.29), residues: 288 sheet: 0.55 (0.36), residues: 218 loop : -0.43 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 113 HIS 0.003 0.001 HIS C 52 PHE 0.012 0.001 PHE B 39 TYR 0.010 0.001 TYR B 72 ARG 0.007 0.000 ARG E 68 *********************** 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 133 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 116 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.7999 (mtm-85) cc_final: 0.7799 (ttm110) REVERT: A 138 LYS cc_start: 0.7495 (mptt) cc_final: 0.6988 (mtpp) REVERT: B 138 LYS cc_start: 0.7497 (mptt) cc_final: 0.6978 (mtpp) REVERT: C 5 LYS cc_start: 0.8583 (tppt) cc_final: 0.8268 (tptp) REVERT: C 100 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7313 (tmt90) REVERT: C 115 SER cc_start: 0.8210 (p) cc_final: 0.7845 (t) REVERT: D 11 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.6977 (tt) REVERT: E 5 LYS cc_start: 0.8541 (tppt) cc_final: 0.8304 (tptm) REVERT: E 48 GLU cc_start: 0.7434 (tt0) cc_final: 0.6994 (pt0) REVERT: E 100 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7319 (tmt90) REVERT: E 115 SER cc_start: 0.8255 (p) cc_final: 0.7897 (t) REVERT: F 4 MET cc_start: 0.7285 (mmm) cc_final: 0.6756 (tpt) REVERT: F 11 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.7025 (tt) outliers start: 17 outliers final: 7 residues processed: 126 average time/residue: 0.2103 time to fit residues: 34.1393 Evaluate side-chains 121 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 110 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 100 ARG Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 33 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 0.7980 chunk 54 optimal weight: 0.0870 chunk 81 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 39 optimal weight: 0.0470 chunk 51 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN B 152 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6888 Z= 0.148 Angle : 0.508 8.251 9338 Z= 0.251 Chirality : 0.040 0.143 1036 Planarity : 0.004 0.028 1148 Dihedral : 3.941 25.543 924 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.91 % Allowed : 14.48 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.29), residues: 840 helix: 2.48 (0.29), residues: 288 sheet: 0.59 (0.36), residues: 218 loop : -0.37 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 113 HIS 0.002 0.001 HIS C 105 PHE 0.011 0.001 PHE B 43 TYR 0.008 0.001 TYR A 150 ARG 0.007 0.000 ARG E 68 ********************** 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 140 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 126 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.7499 (mptt) cc_final: 0.6992 (mtpp) REVERT: B 138 LYS cc_start: 0.7504 (mptt) cc_final: 0.6986 (mtpp) REVERT: C 100 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7312 (tmt90) REVERT: C 115 SER cc_start: 0.8269 (p) cc_final: 0.7941 (t) REVERT: D 11 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.7015 (tt) REVERT: E 5 LYS cc_start: 0.8550 (tppt) cc_final: 0.8322 (tptm) REVERT: E 100 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7300 (tmt90) REVERT: E 115 SER cc_start: 0.8307 (p) cc_final: 0.7973 (t) REVERT: F 4 MET cc_start: 0.7291 (mmm) cc_final: 0.6760 (tpt) REVERT: F 11 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.7019 (tt) outliers start: 14 outliers final: 6 residues processed: 133 average time/residue: 0.1965 time to fit residues: 33.8319 Evaluate side-chains 125 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 115 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 100 ARG Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 33 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 65 optimal weight: 0.0970 chunk 27 optimal weight: 0.0770 chunk 66 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 3 optimal weight: 0.4980 chunk 47 optimal weight: 2.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- 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 = 0.4197 r_free = 0.4197 target = 0.195657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.163658 restraints weight = 7203.473| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 1.68 r_work: 0.3718 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3575 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6888 Z= 0.150 Angle : 0.511 8.157 9338 Z= 0.253 Chirality : 0.040 0.136 1036 Planarity : 0.004 0.028 1148 Dihedral : 3.919 25.592 924 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.91 % Allowed : 15.03 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.29), residues: 840 helix: 2.58 (0.29), residues: 288 sheet: 0.65 (0.36), residues: 218 loop : -0.35 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 113 HIS 0.002 0.001 HIS C 52 PHE 0.012 0.001 PHE A 39 TYR 0.008 0.001 TYR B 72 ARG 0.007 0.000 ARG C 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1801.62 seconds wall clock time: 33 minutes 33.40 seconds (2013.40 seconds total)