Starting phenix.real_space_refine on Sun Mar 10 20:35:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hu7_0273/03_2024/6hu7_0273.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hu7_0273/03_2024/6hu7_0273.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hu7_0273/03_2024/6hu7_0273.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hu7_0273/03_2024/6hu7_0273.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hu7_0273/03_2024/6hu7_0273.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hu7_0273/03_2024/6hu7_0273.pdb" } resolution = 2.8 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= 0.079 sd= 1.306 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: 4 Type Number sf(0) Gaussians S 27 5.16 5 C 3155 2.51 5 N 820 2.21 5 O 888 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 82": "NH1" <-> "NH2" Residue "B PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 127": "NH1" <-> "NH2" Residue "B ARG 151": "NH1" <-> "NH2" Residue "B ARG 152": "NH1" <-> "NH2" Residue "A ARG 82": "NH1" <-> "NH2" Residue "C ARG 39": "NH1" <-> "NH2" Residue "C ARG 82": "NH1" <-> "NH2" Residue "C ARG 82": "NH1" <-> "NH2" Residue "D ARG 150": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4890 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1218 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 12, 'TRANS': 139} Chain: "A" Number of atoms: 1190 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 147, 1171 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 12, 'TRANS': 134} Conformer: "B" Number of residues, atoms: 147, 1171 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 12, 'TRANS': 134} bond proxies already assigned to first conformer: 1185 Chain: "C" Number of atoms: 1218 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 151, 1207 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 12, 'TRANS': 138} Conformer: "B" Number of residues, atoms: 151, 1207 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 12, 'TRANS': 138} bond proxies already assigned to first conformer: 1230 Chain: "D" Number of atoms: 1207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1207 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 12, 'TRANS': 138} Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain: "G" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 21 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Chain: "H" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 21 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG A 127 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 127 " occ=0.50 residue: pdb=" N AARG C 82 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 82 " occ=0.50 Time building chain proxies: 4.41, per 1000 atoms: 0.90 Number of scatterers: 4890 At special positions: 0 Unit cell: (107.712, 117.216, 81.312, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 27 16.00 O 888 8.00 N 820 7.00 C 3155 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.75 Conformation dependent library (CDL) restraints added in 1.2 seconds 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1176 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 0 sheets defined 73.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'B' and resid 6 through 10 Processing helix chain 'B' and resid 12 through 17 Processing helix chain 'B' and resid 18 through 19 No H-bonds generated for 'chain 'B' and resid 18 through 19' Processing helix chain 'B' and resid 20 through 24 Processing helix chain 'B' and resid 26 through 43 removed outlier: 3.585A pdb=" N ARG B 39 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N GLU B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ALA B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 75 removed outlier: 3.718A pdb=" N GLY B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL B 74 " --> pdb=" O THR B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 110 removed outlier: 3.654A pdb=" N ASP B 83 " --> pdb=" O PRO B 79 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR B 88 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY B 94 " --> pdb=" O ASN B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 128 Processing helix chain 'A' and resid 6 through 10 Processing helix chain 'A' and resid 20 through 24 removed outlier: 3.822A pdb=" N PHE A 24 " --> pdb=" O SER A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 38 Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 49 through 76 removed outlier: 3.545A pdb=" N LEU A 76 " --> pdb=" O VAL A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 111 removed outlier: 3.507A pdb=" N ASP A 83 " --> pdb=" O PRO A 79 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET A 93 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLY A 94 " --> pdb=" O ASN A 90 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 97 " --> pdb=" O MET A 93 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 100 " --> pdb=" O LYS A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 128 Processing helix chain 'C' and resid 6 through 10 Processing helix chain 'C' and resid 12 through 17 removed outlier: 3.588A pdb=" N LEU C 16 " --> pdb=" O THR C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 43 removed outlier: 3.639A pdb=" N ARG C 39 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLU C 40 " --> pdb=" O ALA C 36 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ALA C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 76 Processing helix chain 'C' and resid 78 through 91 removed outlier: 3.523A pdb=" N LEU C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL C 85 " --> pdb=" O SER C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 111 removed outlier: 3.831A pdb=" N LYS C 96 " --> pdb=" O ASN C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 128 removed outlier: 3.573A pdb=" N ARG C 127 " --> pdb=" O GLY C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 133 Processing helix chain 'D' and resid 6 through 10 Processing helix chain 'D' and resid 20 through 24 removed outlier: 3.760A pdb=" N PHE D 24 " --> pdb=" O SER D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 38 Processing helix chain 'D' and resid 38 through 43 Processing helix chain 'D' and resid 49 through 76 removed outlier: 3.553A pdb=" N GLY D 73 " --> pdb=" O ALA D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 91 removed outlier: 3.505A pdb=" N ASP D 83 " --> pdb=" O PRO D 79 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER D 87 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 109 removed outlier: 4.131A pdb=" N LYS D 96 " --> pdb=" O ASN D 92 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU D 97 " --> pdb=" O MET D 93 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR D 109 " --> pdb=" O ILE D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 128 removed outlier: 3.570A pdb=" N THR D 128 " --> pdb=" O VAL D 124 " (cutoff:3.500A) 299 hydrogen bonds defined for protein. 857 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.09 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1564 1.34 - 1.46: 1067 1.46 - 1.57: 2360 1.57 - 1.69: 0 1.69 - 1.81: 39 Bond restraints: 5030 Sorted by residual: bond pdb=" CG LEU A 97 " pdb=" CD2 LEU A 97 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.58e+00 bond pdb=" CG LEU C 30 " pdb=" CD1 LEU C 30 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.16e+00 bond pdb=" CG LEU D 97 " pdb=" CD2 LEU D 97 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.78e+00 bond pdb=" CB GLU B 8 " pdb=" CG GLU B 8 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.11e+00 bond pdb=" CB ARG A 98 " pdb=" CG ARG A 98 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.04e+00 ... (remaining 5025 not shown) Histogram of bond angle deviations from ideal: 99.31 - 106.26: 216 106.26 - 113.22: 2775 113.22 - 120.17: 1890 120.17 - 127.12: 1911 127.12 - 134.08: 92 Bond angle restraints: 6884 Sorted by residual: angle pdb=" CA TYR A 38 " pdb=" CB TYR A 38 " pdb=" CG TYR A 38 " ideal model delta sigma weight residual 113.90 107.49 6.41 1.80e+00 3.09e-01 1.27e+01 angle pdb=" CA TYR C 132 " pdb=" CB TYR C 132 " pdb=" CG TYR C 132 " ideal model delta sigma weight residual 113.90 108.31 5.59 1.80e+00 3.09e-01 9.65e+00 angle pdb=" CA TYR D 38 " pdb=" CB TYR D 38 " pdb=" CG TYR D 38 " ideal model delta sigma weight residual 113.90 108.53 5.37 1.80e+00 3.09e-01 8.89e+00 angle pdb=" C VAL C 148 " pdb=" N VAL C 149 " pdb=" CA VAL C 149 " ideal model delta sigma weight residual 121.97 126.98 -5.01 1.80e+00 3.09e-01 7.75e+00 angle pdb=" C MET D 1 " pdb=" N ASP D 2 " pdb=" CA ASP D 2 " ideal model delta sigma weight residual 122.46 126.24 -3.78 1.41e+00 5.03e-01 7.20e+00 ... (remaining 6879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.70: 2873 15.70 - 31.39: 92 31.39 - 47.08: 27 47.08 - 62.78: 1 62.78 - 78.47: 5 Dihedral angle restraints: 2998 sinusoidal: 1194 harmonic: 1804 Sorted by residual: dihedral pdb=" CA LEU A 143 " pdb=" C LEU A 143 " pdb=" N PRO A 144 " pdb=" CA PRO A 144 " ideal model delta harmonic sigma weight residual 180.00 154.27 25.73 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA LEU D 108 " pdb=" C LEU D 108 " pdb=" N THR D 109 " pdb=" CA THR D 109 " ideal model delta harmonic sigma weight residual 180.00 159.50 20.50 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA LEU B 143 " pdb=" C LEU B 143 " pdb=" N PRO B 144 " pdb=" CA PRO B 144 " ideal model delta harmonic sigma weight residual 180.00 160.98 19.02 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 2995 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 537 0.047 - 0.094: 203 0.094 - 0.141: 42 0.141 - 0.187: 7 0.187 - 0.234: 1 Chirality restraints: 790 Sorted by residual: chirality pdb=" CG LEU A 97 " pdb=" CB LEU A 97 " pdb=" CD1 LEU A 97 " pdb=" CD2 LEU A 97 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA HIS A 47 " pdb=" N HIS A 47 " pdb=" C HIS A 47 " pdb=" CB HIS A 47 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.81e-01 chirality pdb=" CB THR D 109 " pdb=" CA THR D 109 " pdb=" OG1 THR D 109 " pdb=" CG2 THR D 109 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.39e-01 ... (remaining 787 not shown) Planarity restraints: 872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 18 " -0.026 2.00e-02 2.50e+03 2.28e-02 9.12e+00 pdb=" CG PHE C 18 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE C 18 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE C 18 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE C 18 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 18 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE C 18 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 132 " 0.025 2.00e-02 2.50e+03 2.05e-02 8.44e+00 pdb=" CG TYR C 132 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR C 132 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR C 132 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR C 132 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR C 132 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR C 132 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 132 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 38 " -0.028 2.00e-02 2.50e+03 1.89e-02 7.11e+00 pdb=" CG TYR A 38 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR A 38 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR A 38 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 38 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 38 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 38 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 38 " -0.006 2.00e-02 2.50e+03 ... (remaining 869 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 71 2.68 - 3.24: 4989 3.24 - 3.79: 7768 3.79 - 4.35: 10897 4.35 - 4.90: 17311 Nonbonded interactions: 41036 Sorted by model distance: nonbonded pdb=" NH1 ARG B 150 " pdb=" O LEU C 143 " model vdw 2.130 2.520 nonbonded pdb=" OD1 ASP A 2 " pdb=" N ILE A 3 " model vdw 2.165 2.520 nonbonded pdb=" O THR B 146 " pdb=" OG1 THR B 147 " model vdw 2.273 2.440 nonbonded pdb=" O PHE D 24 " pdb=" NH1 ARG D 98 " model vdw 2.283 2.520 nonbonded pdb=" OD1 ASP A 83 " pdb=" N LEU A 84 " model vdw 2.314 2.520 ... (remaining 41031 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' and (resid 1 through 27 or resid 29 through 81 or resid 83 through 12 \ 6 or resid 128 through 147)) selection = (chain 'B' and (resid 1 through 27 or resid 29 through 81 or resid 83 through 12 \ 6 or resid 128 through 147)) selection = (chain 'C' and (resid 1 through 27 or resid 29 through 81 or resid 83 through 12 \ 6 or resid 128 through 147)) selection = (chain 'D' and (resid 1 through 27 or resid 29 through 81 or resid 83 through 12 \ 6 or resid 128 through 147)) } ncs_group { reference = chain 'G' selection = chain 'H' } 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=0.50 max=1.00 mean=0.99 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: 5.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 26.090 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 18.280 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.020 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:13.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 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 : 0.008 0.071 5030 Z= 0.520 Angle : 0.781 9.018 6884 Z= 0.411 Chirality : 0.050 0.234 790 Planarity : 0.007 0.060 872 Dihedral : 9.806 78.470 1822 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.50 % Allowed : 2.69 % Favored : 96.81 % Rotamer: Outliers : 0.36 % Allowed : 0.36 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.47 (0.28), residues: 602 helix: -3.23 (0.16), residues: 405 sheet: None (None), residues: 0 loop : 0.50 (0.43), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 102 HIS 0.014 0.004 HIS A 47 PHE 0.053 0.003 PHE C 18 TYR 0.050 0.006 TYR C 132 ARG 0.011 0.002 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.716 Fit side-chains REVERT: B 61 CYS cc_start: 0.8966 (t) cc_final: 0.8723 (t) REVERT: B 82 ARG cc_start: 0.6554 (mtp180) cc_final: 0.5565 (ptt-90) REVERT: B 117 GLU cc_start: 0.8095 (tt0) cc_final: 0.7722 (tp30) REVERT: A 64 GLU cc_start: 0.6708 (tp30) cc_final: 0.6467 (mm-30) REVERT: A 117 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8486 (mm-30) REVERT: A 141 SER cc_start: 0.8697 (m) cc_final: 0.8441 (m) REVERT: C 83 ASP cc_start: 0.7576 (m-30) cc_final: 0.7194 (m-30) REVERT: C 113 GLU cc_start: 0.7977 (pm20) cc_final: 0.7764 (mp0) REVERT: D 64 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7845 (mm-30) REVERT: D 78 ASP cc_start: 0.7218 (t0) cc_final: 0.6891 (t0) REVERT: D 96 LYS cc_start: 0.8524 (mtpp) cc_final: 0.8281 (mtpt) REVERT: D 136 ASN cc_start: 0.7122 (p0) cc_final: 0.6851 (p0) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 1.4686 time to fit residues: 183.2106 Evaluate side-chains 95 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 30 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 28 optimal weight: 0.0570 chunk 34 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 HIS B 57 GLN B 75 ASN B 90 ASN B 104 HIS A 47 HIS A 52 HIS A 57 GLN A 75 ASN C 52 HIS C 75 ASN D 47 HIS D 52 HIS D 90 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5030 Z= 0.198 Angle : 0.646 9.396 6884 Z= 0.322 Chirality : 0.041 0.258 790 Planarity : 0.006 0.043 872 Dihedral : 5.122 22.786 670 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.50 % Allowed : 1.51 % Favored : 97.98 % Rotamer: Outliers : 2.19 % Allowed : 7.66 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.11 (0.33), residues: 602 helix: -0.20 (0.24), residues: 412 sheet: None (None), residues: 0 loop : 1.19 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 102 HIS 0.007 0.002 HIS A 47 PHE 0.031 0.002 PHE C 18 TYR 0.024 0.003 TYR C 132 ARG 0.004 0.001 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 0.606 Fit side-chains REVERT: B 76 LEU cc_start: 0.6570 (OUTLIER) cc_final: 0.5974 (tt) REVERT: B 117 GLU cc_start: 0.7896 (tt0) cc_final: 0.7528 (mm-30) REVERT: A 8 GLU cc_start: 0.8598 (pt0) cc_final: 0.8355 (pt0) REVERT: A 32 ASP cc_start: 0.8753 (m-30) cc_final: 0.8479 (m-30) REVERT: A 75 ASN cc_start: 0.7059 (m110) cc_final: 0.6779 (m110) REVERT: A 79 PRO cc_start: 0.7617 (Cg_endo) cc_final: 0.7404 (Cg_exo) REVERT: C 83 ASP cc_start: 0.7410 (m-30) cc_final: 0.7021 (m-30) REVERT: C 113 GLU cc_start: 0.8017 (pm20) cc_final: 0.7735 (mp0) REVERT: C 117 GLU cc_start: 0.7687 (pp20) cc_final: 0.7459 (pp20) REVERT: D 64 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7641 (mm-30) REVERT: D 98 ARG cc_start: 0.8173 (ptt90) cc_final: 0.7957 (ptt-90) outliers start: 10 outliers final: 4 residues processed: 105 average time/residue: 1.4265 time to fit residues: 154.6911 Evaluate side-chains 96 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 91 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 142 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 4.9990 chunk 16 optimal weight: 0.0040 chunk 44 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 0.1980 chunk 53 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5030 Z= 0.158 Angle : 0.562 9.761 6884 Z= 0.273 Chirality : 0.038 0.204 790 Planarity : 0.005 0.039 872 Dihedral : 4.579 20.159 670 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.50 % Allowed : 1.68 % Favored : 97.82 % Rotamer: Outliers : 1.28 % Allowed : 10.40 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.67 (0.34), residues: 602 helix: 1.13 (0.25), residues: 416 sheet: None (None), residues: 0 loop : 1.43 (0.48), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 102 HIS 0.002 0.001 HIS D 47 PHE 0.023 0.001 PHE C 18 TYR 0.022 0.002 TYR C 132 ARG 0.005 0.001 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 0.576 Fit side-chains REVERT: B 14 GLU cc_start: 0.8902 (mp0) cc_final: 0.8513 (mt-10) REVERT: B 64 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7766 (tp30) REVERT: B 76 LEU cc_start: 0.6759 (OUTLIER) cc_final: 0.6153 (tt) REVERT: B 117 GLU cc_start: 0.7832 (tt0) cc_final: 0.7534 (mm-30) REVERT: A 75 ASN cc_start: 0.6866 (m110) cc_final: 0.6534 (m110) REVERT: C 83 ASP cc_start: 0.7396 (m-30) cc_final: 0.7171 (m-30) REVERT: D 64 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7591 (mm-30) REVERT: D 98 ARG cc_start: 0.8002 (ptt90) cc_final: 0.7760 (ptt-90) outliers start: 5 outliers final: 2 residues processed: 100 average time/residue: 1.4029 time to fit residues: 145.1099 Evaluate side-chains 89 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 86 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain D residue 93 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 0.4980 chunk 53 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN A 99 GLN D 104 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5030 Z= 0.182 Angle : 0.560 9.588 6884 Z= 0.272 Chirality : 0.038 0.190 790 Planarity : 0.005 0.037 872 Dihedral : 4.456 18.268 670 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.50 % Allowed : 1.68 % Favored : 97.82 % Rotamer: Outliers : 1.82 % Allowed : 12.23 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.06 (0.34), residues: 602 helix: 1.47 (0.25), residues: 415 sheet: None (None), residues: 0 loop : 1.44 (0.47), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 102 HIS 0.003 0.001 HIS B 104 PHE 0.022 0.001 PHE C 18 TYR 0.021 0.002 TYR C 132 ARG 0.004 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 0.613 Fit side-chains REVERT: B 14 GLU cc_start: 0.8941 (mp0) cc_final: 0.8556 (mt-10) REVERT: B 22 ASP cc_start: 0.8621 (OUTLIER) cc_final: 0.8364 (p0) REVERT: B 64 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7839 (tp30) REVERT: B 76 LEU cc_start: 0.6725 (OUTLIER) cc_final: 0.6120 (tt) REVERT: B 117 GLU cc_start: 0.7890 (tt0) cc_final: 0.7584 (mm-30) REVERT: A 75 ASN cc_start: 0.6848 (m110) cc_final: 0.6593 (m110) REVERT: C 83 ASP cc_start: 0.7372 (m-30) cc_final: 0.7015 (m-30) REVERT: D 64 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7585 (mm-30) outliers start: 8 outliers final: 3 residues processed: 93 average time/residue: 1.4241 time to fit residues: 136.9321 Evaluate side-chains 89 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 84 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 143 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 14 optimal weight: 0.0170 chunk 19 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 overall best weight: 0.9220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5030 Z= 0.192 Angle : 0.555 9.443 6884 Z= 0.270 Chirality : 0.038 0.169 790 Planarity : 0.005 0.037 872 Dihedral : 4.384 16.556 670 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.18 % Favored : 97.48 % Rotamer: Outliers : 2.37 % Allowed : 12.77 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.44 (0.35), residues: 602 helix: 1.77 (0.26), residues: 409 sheet: None (None), residues: 0 loop : 1.58 (0.47), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 62 HIS 0.004 0.001 HIS B 104 PHE 0.021 0.001 PHE C 18 TYR 0.021 0.002 TYR C 132 ARG 0.003 0.001 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 0.687 Fit side-chains REVERT: B 14 GLU cc_start: 0.8675 (mp0) cc_final: 0.8454 (mt-10) REVERT: B 22 ASP cc_start: 0.8609 (OUTLIER) cc_final: 0.8299 (p0) REVERT: B 64 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7773 (tp30) REVERT: B 76 LEU cc_start: 0.6779 (OUTLIER) cc_final: 0.6128 (tt) REVERT: B 97 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8593 (tm) REVERT: A 75 ASN cc_start: 0.6963 (m110) cc_final: 0.6689 (m110) REVERT: C 83 ASP cc_start: 0.7395 (m-30) cc_final: 0.7048 (m-30) REVERT: D 64 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7600 (mm-30) outliers start: 11 outliers final: 4 residues processed: 93 average time/residue: 1.4512 time to fit residues: 139.5387 Evaluate side-chains 90 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 83 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 146 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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: 0.8210 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5030 Z= 0.192 Angle : 0.551 9.233 6884 Z= 0.267 Chirality : 0.038 0.161 790 Planarity : 0.005 0.037 872 Dihedral : 4.340 15.473 670 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.35 % Favored : 97.31 % Rotamer: Outliers : 2.37 % Allowed : 12.96 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.61 (0.35), residues: 602 helix: 1.88 (0.26), residues: 408 sheet: None (None), residues: 0 loop : 1.69 (0.47), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 62 HIS 0.004 0.001 HIS B 104 PHE 0.020 0.001 PHE C 18 TYR 0.019 0.002 TYR C 132 ARG 0.003 0.000 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 88 time to evaluate : 0.563 Fit side-chains REVERT: B 22 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8315 (p0) REVERT: B 64 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7895 (tp30) REVERT: B 76 LEU cc_start: 0.6762 (OUTLIER) cc_final: 0.6104 (tt) REVERT: B 97 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8609 (tm) REVERT: A 75 ASN cc_start: 0.6969 (m110) cc_final: 0.6741 (m110) REVERT: C 83 ASP cc_start: 0.7415 (m-30) cc_final: 0.6968 (m-30) REVERT: D 64 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7607 (mm-30) outliers start: 11 outliers final: 4 residues processed: 96 average time/residue: 1.4482 time to fit residues: 143.9407 Evaluate side-chains 93 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 86 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 146 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 17 optimal weight: 0.1980 chunk 11 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.8193 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5030 Z= 0.161 Angle : 0.538 9.276 6884 Z= 0.260 Chirality : 0.037 0.156 790 Planarity : 0.005 0.035 872 Dihedral : 4.248 15.115 670 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.52 % Favored : 97.14 % Rotamer: Outliers : 2.19 % Allowed : 13.14 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.69 (0.35), residues: 602 helix: 1.97 (0.26), residues: 411 sheet: None (None), residues: 0 loop : 1.63 (0.47), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 62 HIS 0.003 0.001 HIS B 104 PHE 0.017 0.001 PHE C 18 TYR 0.017 0.001 TYR C 132 ARG 0.002 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 0.572 Fit side-chains REVERT: B 22 ASP cc_start: 0.8661 (OUTLIER) cc_final: 0.8344 (p0) REVERT: B 64 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7880 (tp30) REVERT: B 76 LEU cc_start: 0.6708 (OUTLIER) cc_final: 0.6061 (tt) REVERT: A 75 ASN cc_start: 0.7006 (m110) cc_final: 0.6730 (m110) REVERT: C 83 ASP cc_start: 0.7404 (m-30) cc_final: 0.6974 (m-30) outliers start: 10 outliers final: 4 residues processed: 95 average time/residue: 1.3116 time to fit residues: 129.1065 Evaluate side-chains 92 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 146 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 28 optimal weight: 0.0030 chunk 5 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- 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: 0.8195 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5030 Z= 0.167 Angle : 0.542 9.156 6884 Z= 0.261 Chirality : 0.037 0.150 790 Planarity : 0.005 0.035 872 Dihedral : 4.208 14.945 670 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.02 % Favored : 97.65 % Rotamer: Outliers : 2.19 % Allowed : 12.77 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.77 (0.35), residues: 602 helix: 2.00 (0.26), residues: 412 sheet: None (None), residues: 0 loop : 1.72 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 62 HIS 0.003 0.001 HIS B 104 PHE 0.018 0.001 PHE C 18 TYR 0.018 0.001 TYR C 132 ARG 0.003 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 0.517 Fit side-chains REVERT: B 22 ASP cc_start: 0.8695 (OUTLIER) cc_final: 0.8409 (p0) REVERT: B 64 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7895 (tp30) REVERT: B 76 LEU cc_start: 0.6723 (OUTLIER) cc_final: 0.6085 (tt) REVERT: B 83 ASP cc_start: 0.7985 (m-30) cc_final: 0.7208 (p0) REVERT: B 113 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7844 (mp0) REVERT: A 75 ASN cc_start: 0.6950 (m110) cc_final: 0.6728 (m110) REVERT: C 28 ARG cc_start: 0.7970 (mmm160) cc_final: 0.7382 (tpm170) REVERT: C 83 ASP cc_start: 0.7410 (m-30) cc_final: 0.6980 (m-30) outliers start: 10 outliers final: 6 residues processed: 93 average time/residue: 1.3472 time to fit residues: 129.8543 Evaluate side-chains 92 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 146 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 56 optimal weight: 0.4980 chunk 26 optimal weight: 0.5980 chunk 38 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.8189 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5030 Z= 0.160 Angle : 0.537 9.025 6884 Z= 0.259 Chirality : 0.037 0.154 790 Planarity : 0.005 0.034 872 Dihedral : 4.184 14.935 670 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.52 % Favored : 97.14 % Rotamer: Outliers : 2.01 % Allowed : 13.32 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.79 (0.35), residues: 602 helix: 2.03 (0.26), residues: 413 sheet: None (None), residues: 0 loop : 1.69 (0.47), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 62 HIS 0.003 0.001 HIS B 104 PHE 0.017 0.001 PHE C 18 TYR 0.017 0.001 TYR C 132 ARG 0.002 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 88 time to evaluate : 0.486 Fit side-chains REVERT: B 22 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.8420 (p0) REVERT: B 64 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7894 (tp30) REVERT: B 76 LEU cc_start: 0.6696 (OUTLIER) cc_final: 0.6066 (tt) REVERT: B 83 ASP cc_start: 0.7980 (m-30) cc_final: 0.7169 (p0) REVERT: B 113 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7864 (mp0) REVERT: A 75 ASN cc_start: 0.6911 (m110) cc_final: 0.6702 (m110) REVERT: C 66 MET cc_start: 0.8329 (mmp) cc_final: 0.8044 (mmp) REVERT: C 83 ASP cc_start: 0.7462 (m-30) cc_final: 0.7042 (m-30) outliers start: 9 outliers final: 6 residues processed: 94 average time/residue: 1.3969 time to fit residues: 135.8951 Evaluate side-chains 93 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 85 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 146 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 4 optimal weight: 0.0670 chunk 36 optimal weight: 0.0170 chunk 28 optimal weight: 0.0980 chunk 37 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 43 optimal weight: 0.0060 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 0.0060 overall best weight: 0.0388 ------------------------------------------------------------------------------- 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: 0.8103 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5030 Z= 0.133 Angle : 0.515 9.081 6884 Z= 0.247 Chirality : 0.036 0.150 790 Planarity : 0.005 0.040 872 Dihedral : 4.000 13.910 670 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.18 % Favored : 97.48 % Rotamer: Outliers : 1.64 % Allowed : 14.42 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.96 (0.35), residues: 602 helix: 2.20 (0.26), residues: 412 sheet: None (None), residues: 0 loop : 1.69 (0.49), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 125 HIS 0.003 0.001 HIS B 104 PHE 0.011 0.001 PHE C 18 TYR 0.011 0.001 TYR C 132 ARG 0.003 0.000 ARG D 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 91 time to evaluate : 0.587 Fit side-chains REVERT: B 76 LEU cc_start: 0.6647 (OUTLIER) cc_final: 0.6118 (tt) REVERT: B 83 ASP cc_start: 0.7987 (m-30) cc_final: 0.7114 (p0) REVERT: A 132 TYR cc_start: 0.8490 (m-80) cc_final: 0.8180 (m-80) REVERT: C 28 ARG cc_start: 0.7996 (mmm160) cc_final: 0.7507 (tpm170) REVERT: C 83 ASP cc_start: 0.7457 (m-30) cc_final: 0.7009 (m-30) REVERT: D 92 ASN cc_start: 0.8671 (m-40) cc_final: 0.8444 (m-40) outliers start: 7 outliers final: 4 residues processed: 97 average time/residue: 1.2756 time to fit residues: 128.5350 Evaluate side-chains 90 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 85 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 146 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN C 47 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.116956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.101233 restraints weight = 14387.735| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.89 r_work: 0.3035 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2934 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2934 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5030 Z= 0.189 Angle : 0.557 8.675 6884 Z= 0.268 Chirality : 0.038 0.139 790 Planarity : 0.005 0.034 872 Dihedral : 4.066 14.841 670 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.18 % Favored : 97.48 % Rotamer: Outliers : 2.01 % Allowed : 14.78 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.03 (0.35), residues: 602 helix: 2.22 (0.26), residues: 412 sheet: None (None), residues: 0 loop : 1.80 (0.48), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 62 HIS 0.004 0.001 HIS D 104 PHE 0.017 0.001 PHE C 18 TYR 0.019 0.002 TYR C 132 ARG 0.004 0.000 ARG A 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3045.70 seconds wall clock time: 54 minutes 37.49 seconds (3277.49 seconds total)