Starting phenix.real_space_refine on Wed Jan 17 20:42:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fjb_29221/01_2024/8fjb_29221.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fjb_29221/01_2024/8fjb_29221.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fjb_29221/01_2024/8fjb_29221.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fjb_29221/01_2024/8fjb_29221.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fjb_29221/01_2024/8fjb_29221.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fjb_29221/01_2024/8fjb_29221.pdb" } resolution = 3.06 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= -0.000 sd= 1.000 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 24 5.16 5 C 3980 2.51 5 N 1095 2.21 5 O 1231 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 232": "OE1" <-> "OE2" Residue "B ASP 98": "OD1" <-> "OD2" Residue "E ASP 73": "OD1" <-> "OD2" Residue "E TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 144": "OE1" <-> "OE2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "D TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 188": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 6330 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2230 Classifications: {'peptide': 273} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 260} Chain breaks: 1 Chain: "B" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 829 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 93} Chain: "C" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 76 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "E" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1555 Classifications: {'peptide': 207} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 196} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Link IDs: {'PCIS': 4, 'PTRANS': 8, 'TRANS': 201} Time building chain proxies: 3.79, per 1000 atoms: 0.60 Number of scatterers: 6330 At special positions: 0 Unit cell: (139.4, 107.1, 72.25, 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 24 16.00 O 1231 8.00 N 1095 7.00 C 3980 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 259 " distance=2.03 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 80 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 145 " - pdb=" SG CYS E 201 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 195 " 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: 2.11 Conformation dependent library (CDL) restraints added in 1.3 seconds 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1494 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 17 sheets defined 14.2% alpha, 46.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 56 through 85 removed outlier: 3.773A pdb=" N TRP A 60 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 151 removed outlier: 3.559A pdb=" N LYS A 146 " --> pdb=" O THR A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 162 Processing helix chain 'A' and resid 162 through 175 Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 253 through 255 No H-bonds generated for 'chain 'A' and resid 253 through 255' Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.656A pdb=" N GLU E 31 " --> pdb=" O THR E 28 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 28 through 32' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'E' and resid 190 through 197 removed outlier: 3.682A pdb=" N THR E 196 " --> pdb=" O SER E 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 128 removed outlier: 3.991A pdb=" N SER D 128 " --> pdb=" O GLU D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 190 removed outlier: 3.818A pdb=" N HIS D 190 " --> pdb=" O ASP D 186 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 47 removed outlier: 6.752A pdb=" N GLY A 26 " --> pdb=" O PHE A 33 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ARG A 35 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA A 24 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASP A 37 " --> pdb=" O PHE A 22 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N PHE A 22 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG A 111 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N HIS A 114 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ALA A 125 " --> pdb=" O HIS A 114 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N TYR A 116 " --> pdb=" O TYR A 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 189 through 194 removed outlier: 5.740A pdb=" N PHE A 241 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 189 through 194 removed outlier: 5.740A pdb=" N PHE A 241 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 223 Processing sheet with id=AA5, first strand: chain 'B' and resid 6 through 11 removed outlier: 5.814A pdb=" N PHE B 62 " --> pdb=" O GLY B 29 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 6 through 11 removed outlier: 5.814A pdb=" N PHE B 62 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER B 55 " --> pdb=" O TYR B 63 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 44 through 45 Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'E' and resid 11 through 12 removed outlier: 7.030A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.892A pdb=" N VAL E 107 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 125 through 129 removed outlier: 6.278A pdb=" N TYR E 181 " --> pdb=" O ASP E 149 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 125 through 129 removed outlier: 6.278A pdb=" N TYR E 181 " --> pdb=" O ASP E 149 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 156 through 159 removed outlier: 3.543A pdb=" N LYS E 214 " --> pdb=" O CYS E 201 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 4 through 7 removed outlier: 6.283A pdb=" N THR D 69 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 10.552A pdb=" N GLN D 27 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 10.096A pdb=" N SER D 67 " --> pdb=" O GLN D 27 " (cutoff:3.500A) removed outlier: 11.757A pdb=" N ILE D 29 " --> pdb=" O SER D 65 " (cutoff:3.500A) removed outlier: 11.586A pdb=" N SER D 65 " --> pdb=" O ILE D 29 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.775A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 115 through 119 removed outlier: 3.555A pdb=" N VAL D 134 " --> pdb=" O PHE D 119 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N TYR D 174 " --> pdb=" O ASN D 139 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 154 through 155 326 hydrogen bonds defined for protein. 852 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: 1.91 Time building geometry restraints manager: 2.32 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: 2070 1.34 - 1.46: 1646 1.46 - 1.58: 2739 1.58 - 1.70: 0 1.70 - 1.82: 34 Bond restraints: 6489 Sorted by residual: bond pdb=" CG GLN D 90 " pdb=" CD GLN D 90 " ideal model delta sigma weight residual 1.516 1.479 0.037 2.50e-02 1.60e+03 2.14e+00 bond pdb=" CB PRO A 210 " pdb=" CG PRO A 210 " ideal model delta sigma weight residual 1.506 1.455 0.051 3.90e-02 6.57e+02 1.74e+00 bond pdb=" CG ARG A 6 " pdb=" CD ARG A 6 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.70e+00 bond pdb=" CG ASP A 137 " pdb=" OD1 ASP A 137 " ideal model delta sigma weight residual 1.249 1.224 0.025 1.90e-02 2.77e+03 1.69e+00 bond pdb=" CB ASP A 137 " pdb=" CG ASP A 137 " ideal model delta sigma weight residual 1.516 1.484 0.032 2.50e-02 1.60e+03 1.64e+00 ... (remaining 6484 not shown) Histogram of bond angle deviations from ideal: 99.18 - 106.14: 167 106.14 - 113.11: 3456 113.11 - 120.08: 2199 120.08 - 127.05: 2889 127.05 - 134.02: 100 Bond angle restraints: 8811 Sorted by residual: angle pdb=" C SER D 93 " pdb=" N THR D 94 " pdb=" CA THR D 94 " ideal model delta sigma weight residual 121.80 132.01 -10.21 2.44e+00 1.68e-01 1.75e+01 angle pdb=" N ASP A 196 " pdb=" CA ASP A 196 " pdb=" C ASP A 196 " ideal model delta sigma weight residual 111.28 114.81 -3.53 1.09e+00 8.42e-01 1.05e+01 angle pdb=" C VAL A 194 " pdb=" N SER A 195 " pdb=" CA SER A 195 " ideal model delta sigma weight residual 121.53 128.72 -7.19 2.25e+00 1.98e-01 1.02e+01 angle pdb=" C TYR D 92 " pdb=" N SER D 93 " pdb=" CA SER D 93 " ideal model delta sigma weight residual 121.54 115.81 5.73 1.91e+00 2.74e-01 9.01e+00 angle pdb=" C ASP A 137 " pdb=" CA ASP A 137 " pdb=" CB ASP A 137 " ideal model delta sigma weight residual 110.45 116.23 -5.78 2.15e+00 2.16e-01 7.22e+00 ... (remaining 8806 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 3557 17.89 - 35.79: 245 35.79 - 53.68: 40 53.68 - 71.58: 14 71.58 - 89.47: 6 Dihedral angle restraints: 3862 sinusoidal: 1533 harmonic: 2329 Sorted by residual: dihedral pdb=" CA THR D 94 " pdb=" C THR D 94 " pdb=" N PRO D 95 " pdb=" CA PRO D 95 " ideal model delta harmonic sigma weight residual 0.00 -25.14 25.14 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA ILE D 29 " pdb=" C ILE D 29 " pdb=" N SER D 30 " pdb=" CA SER D 30 " ideal model delta harmonic sigma weight residual -180.00 -161.95 -18.05 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" C ASP A 137 " pdb=" N ASP A 137 " pdb=" CA ASP A 137 " pdb=" CB ASP A 137 " ideal model delta harmonic sigma weight residual -122.60 -131.62 9.02 0 2.50e+00 1.60e-01 1.30e+01 ... (remaining 3859 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 824 0.068 - 0.137: 114 0.137 - 0.205: 9 0.205 - 0.274: 1 0.274 - 0.342: 1 Chirality restraints: 949 Sorted by residual: chirality pdb=" CB ILE B 1 " pdb=" CA ILE B 1 " pdb=" CG1 ILE B 1 " pdb=" CG2 ILE B 1 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" CA ASP A 137 " pdb=" N ASP A 137 " pdb=" C ASP A 137 " pdb=" CB ASP A 137 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA ILE D 97 " pdb=" N ILE D 97 " pdb=" C ILE D 97 " pdb=" CB ILE D 97 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.52e-01 ... (remaining 946 not shown) Planarity restraints: 1138 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 95 " -0.043 5.00e-02 4.00e+02 6.51e-02 6.78e+00 pdb=" N PRO D 96 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO D 96 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 96 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 194 " -0.009 2.00e-02 2.50e+03 1.77e-02 3.13e+00 pdb=" C VAL A 194 " 0.031 2.00e-02 2.50e+03 pdb=" O VAL A 194 " -0.012 2.00e-02 2.50e+03 pdb=" N SER A 195 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 94 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.83e+00 pdb=" N PRO D 95 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO D 95 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 95 " 0.021 5.00e-02 4.00e+02 ... (remaining 1135 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 132 2.69 - 3.24: 5410 3.24 - 3.79: 8981 3.79 - 4.35: 12444 4.35 - 4.90: 22199 Nonbonded interactions: 49166 Sorted by model distance: nonbonded pdb=" OE1 GLU D 188 " pdb=" NH1 ARG D 212 " model vdw 2.135 2.520 nonbonded pdb=" OG1 THR E 200 " pdb=" O LYS E 214 " model vdw 2.257 2.440 nonbonded pdb=" OG SER D 14 " pdb=" OD2 ASP D 17 " model vdw 2.270 2.440 nonbonded pdb=" O LEU D 126 " pdb=" NZ LYS D 184 " model vdw 2.291 2.520 nonbonded pdb=" OE1 GLU C 4 " pdb=" OH TYR E 32 " model vdw 2.296 2.440 ... (remaining 49161 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.040 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: 9.380 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 20.510 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 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 : 0.006 0.051 6489 Z= 0.390 Angle : 0.683 10.209 8811 Z= 0.362 Chirality : 0.049 0.342 949 Planarity : 0.005 0.065 1138 Dihedral : 13.228 89.472 2347 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.66 % Favored : 97.21 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.51 % 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: -1.47 (0.28), residues: 788 helix: -0.94 (0.47), residues: 96 sheet: 0.03 (0.28), residues: 330 loop : -1.97 (0.28), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 244 HIS 0.005 0.001 HIS C 5 PHE 0.029 0.002 PHE B 70 TYR 0.024 0.002 TYR E 33 ARG 0.008 0.001 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.747 Fit side-chains REVERT: B 19 LYS cc_start: 0.8774 (mmtt) cc_final: 0.7978 (mtpp) REVERT: B 34 ASP cc_start: 0.8409 (m-30) cc_final: 0.8206 (m-30) REVERT: B 38 ASP cc_start: 0.8283 (m-30) cc_final: 0.7975 (m-30) REVERT: D 82 ASP cc_start: 0.8671 (m-30) cc_final: 0.8433 (m-30) REVERT: D 144 GLU cc_start: 0.8558 (mp0) cc_final: 0.8344 (mp0) REVERT: D 190 HIS cc_start: 0.8933 (m90) cc_final: 0.8649 (m90) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.2930 time to fit residues: 31.4063 Evaluate side-chains 82 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 139 ASN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6489 Z= 0.218 Angle : 0.550 11.479 8811 Z= 0.285 Chirality : 0.044 0.229 949 Planarity : 0.005 0.053 1138 Dihedral : 4.348 17.520 881 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.29 % Allowed : 5.18 % Favored : 94.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.51 % 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: 788 helix: 0.29 (0.52), residues: 98 sheet: 0.64 (0.28), residues: 351 loop : -1.25 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 244 HIS 0.003 0.001 HIS B 51 PHE 0.013 0.001 PHE B 70 TYR 0.017 0.001 TYR E 33 ARG 0.010 0.001 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 0.669 Fit side-chains REVERT: A 108 ARG cc_start: 0.8010 (mmm-85) cc_final: 0.7709 (mmm160) REVERT: B 19 LYS cc_start: 0.8819 (mmtt) cc_final: 0.8016 (mtpp) REVERT: B 34 ASP cc_start: 0.8373 (m-30) cc_final: 0.8148 (m-30) REVERT: B 38 ASP cc_start: 0.8157 (m-30) cc_final: 0.7849 (m-30) REVERT: D 144 GLU cc_start: 0.8509 (mp0) cc_final: 0.8302 (mp0) outliers start: 2 outliers final: 2 residues processed: 88 average time/residue: 0.2592 time to fit residues: 28.1547 Evaluate side-chains 86 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 84 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 59 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 ASN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6489 Z= 0.277 Angle : 0.548 12.232 8811 Z= 0.282 Chirality : 0.044 0.188 949 Planarity : 0.004 0.050 1138 Dihedral : 4.334 18.448 881 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.86 % Allowed : 7.77 % Favored : 91.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.51 % 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: 0.19 (0.29), residues: 788 helix: 0.60 (0.53), residues: 98 sheet: 1.05 (0.28), residues: 347 loop : -1.01 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 244 HIS 0.003 0.001 HIS D 190 PHE 0.013 0.002 PHE B 70 TYR 0.016 0.001 TYR E 33 ARG 0.009 0.000 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 0.729 Fit side-chains REVERT: A 108 ARG cc_start: 0.8040 (mmm-85) cc_final: 0.7734 (mmm160) REVERT: B 19 LYS cc_start: 0.8818 (mmtt) cc_final: 0.8023 (mtpp) REVERT: B 34 ASP cc_start: 0.8365 (m-30) cc_final: 0.8162 (m-30) REVERT: B 38 ASP cc_start: 0.8209 (m-30) cc_final: 0.7928 (m-30) REVERT: D 144 GLU cc_start: 0.8533 (mp0) cc_final: 0.8327 (mp0) REVERT: D 188 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8585 (mm-30) outliers start: 6 outliers final: 5 residues processed: 86 average time/residue: 0.2731 time to fit residues: 28.8242 Evaluate side-chains 84 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 79 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 203 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 69 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 6489 Z= 0.330 Angle : 0.559 12.425 8811 Z= 0.287 Chirality : 0.045 0.168 949 Planarity : 0.004 0.049 1138 Dihedral : 4.418 22.344 881 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.01 % Allowed : 10.36 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.51 % 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: 0.43 (0.30), residues: 788 helix: 0.73 (0.53), residues: 98 sheet: 1.24 (0.28), residues: 345 loop : -0.86 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 244 HIS 0.004 0.001 HIS C 5 PHE 0.013 0.002 PHE D 140 TYR 0.016 0.002 TYR E 33 ARG 0.008 0.000 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 0.765 Fit side-chains REVERT: A 108 ARG cc_start: 0.8069 (mmm-85) cc_final: 0.7759 (mmm160) REVERT: A 113 TYR cc_start: 0.7810 (m-80) cc_final: 0.7582 (m-80) REVERT: A 253 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7649 (pm20) REVERT: B 19 LYS cc_start: 0.8800 (mmtt) cc_final: 0.8001 (mtpp) REVERT: B 34 ASP cc_start: 0.8357 (m-30) cc_final: 0.8151 (m-30) REVERT: D 159 ASN cc_start: 0.8853 (p0) cc_final: 0.8385 (p0) REVERT: D 188 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8576 (mm-30) outliers start: 7 outliers final: 5 residues processed: 83 average time/residue: 0.2654 time to fit residues: 27.2815 Evaluate side-chains 84 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 253 GLN Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain D residue 33 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 42 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 25 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6489 Z= 0.221 Angle : 0.515 11.807 8811 Z= 0.264 Chirality : 0.043 0.152 949 Planarity : 0.004 0.049 1138 Dihedral : 4.244 21.501 881 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.01 % Allowed : 11.08 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.51 % 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: 0.61 (0.30), residues: 788 helix: 0.88 (0.53), residues: 98 sheet: 1.41 (0.29), residues: 339 loop : -0.77 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 244 HIS 0.004 0.001 HIS D 190 PHE 0.010 0.001 PHE A 33 TYR 0.014 0.001 TYR E 33 ARG 0.005 0.000 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 0.725 Fit side-chains REVERT: A 108 ARG cc_start: 0.8058 (mmm-85) cc_final: 0.7754 (mmm160) REVERT: A 113 TYR cc_start: 0.7736 (m-80) cc_final: 0.7439 (m-80) REVERT: B 19 LYS cc_start: 0.8746 (mmtt) cc_final: 0.7964 (mtpp) REVERT: B 34 ASP cc_start: 0.8346 (m-30) cc_final: 0.8124 (m-30) REVERT: D 159 ASN cc_start: 0.8839 (p0) cc_final: 0.8372 (p0) REVERT: D 188 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8547 (mm-30) outliers start: 7 outliers final: 4 residues processed: 80 average time/residue: 0.2676 time to fit residues: 26.5848 Evaluate side-chains 81 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 77 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain E residue 194 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 67 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 61 optimal weight: 0.3980 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 ASN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 6489 Z= 0.299 Angle : 0.539 12.057 8811 Z= 0.276 Chirality : 0.044 0.153 949 Planarity : 0.004 0.047 1138 Dihedral : 4.312 22.997 881 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.01 % Allowed : 11.08 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.51 % 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: 0.67 (0.30), residues: 788 helix: 0.84 (0.52), residues: 98 sheet: 1.43 (0.28), residues: 339 loop : -0.68 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 244 HIS 0.004 0.001 HIS D 190 PHE 0.012 0.002 PHE D 140 TYR 0.015 0.001 TYR E 33 ARG 0.006 0.000 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 76 time to evaluate : 0.799 Fit side-chains REVERT: A 108 ARG cc_start: 0.8057 (mmm-85) cc_final: 0.7750 (mmm160) REVERT: A 113 TYR cc_start: 0.7818 (m-80) cc_final: 0.7407 (m-80) REVERT: A 253 GLN cc_start: 0.8254 (pt0) cc_final: 0.7528 (pm20) REVERT: B 19 LYS cc_start: 0.8745 (mmtt) cc_final: 0.7962 (mtpp) REVERT: B 34 ASP cc_start: 0.8372 (m-30) cc_final: 0.8154 (m-30) REVERT: E 199 TYR cc_start: 0.7464 (m-80) cc_final: 0.7189 (m-80) REVERT: D 159 ASN cc_start: 0.8839 (p0) cc_final: 0.8400 (p0) REVERT: D 188 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8562 (mm-30) outliers start: 7 outliers final: 6 residues processed: 81 average time/residue: 0.2536 time to fit residues: 25.7113 Evaluate side-chains 81 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 75 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain D residue 33 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 6489 Z= 0.253 Angle : 0.520 11.715 8811 Z= 0.266 Chirality : 0.043 0.148 949 Planarity : 0.004 0.047 1138 Dihedral : 4.234 23.192 881 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.15 % Allowed : 11.22 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.51 % 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: 0.76 (0.30), residues: 788 helix: 0.88 (0.52), residues: 98 sheet: 1.50 (0.28), residues: 338 loop : -0.62 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 244 HIS 0.003 0.001 HIS D 190 PHE 0.010 0.001 PHE D 140 TYR 0.014 0.001 TYR E 33 ARG 0.005 0.000 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 78 time to evaluate : 0.682 Fit side-chains REVERT: A 108 ARG cc_start: 0.8009 (mmm-85) cc_final: 0.7687 (mmm160) REVERT: A 113 TYR cc_start: 0.7761 (m-80) cc_final: 0.7207 (m-80) REVERT: A 253 GLN cc_start: 0.8381 (pt0) cc_final: 0.7749 (pm20) REVERT: B 19 LYS cc_start: 0.8738 (mmtt) cc_final: 0.7963 (mtpp) REVERT: B 34 ASP cc_start: 0.8376 (m-30) cc_final: 0.8149 (m-30) REVERT: E 199 TYR cc_start: 0.7428 (m-80) cc_final: 0.7163 (m-80) REVERT: D 159 ASN cc_start: 0.8851 (p0) cc_final: 0.8427 (p0) REVERT: D 188 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8606 (mm-30) outliers start: 8 outliers final: 7 residues processed: 83 average time/residue: 0.2585 time to fit residues: 26.6829 Evaluate side-chains 84 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain D residue 126 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 22 optimal weight: 0.0030 chunk 14 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 chunk 58 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 64 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6489 Z= 0.184 Angle : 0.487 10.946 8811 Z= 0.249 Chirality : 0.042 0.135 949 Planarity : 0.004 0.046 1138 Dihedral : 4.020 20.448 881 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.01 % Allowed : 11.37 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.51 % 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: 788 helix: 0.99 (0.53), residues: 98 sheet: 1.59 (0.29), residues: 338 loop : -0.54 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 244 HIS 0.003 0.001 HIS D 190 PHE 0.009 0.001 PHE A 33 TYR 0.014 0.001 TYR E 33 ARG 0.004 0.000 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 1.738 Fit side-chains REVERT: A 108 ARG cc_start: 0.8013 (mmm-85) cc_final: 0.7694 (mmm160) REVERT: A 113 TYR cc_start: 0.7689 (m-80) cc_final: 0.7142 (m-80) REVERT: A 253 GLN cc_start: 0.8478 (pt0) cc_final: 0.7827 (pm20) REVERT: B 19 LYS cc_start: 0.8734 (mmtt) cc_final: 0.7955 (mtpp) REVERT: B 34 ASP cc_start: 0.8395 (m-30) cc_final: 0.8169 (m-30) REVERT: E 199 TYR cc_start: 0.7373 (m-80) cc_final: 0.7120 (m-80) REVERT: D 159 ASN cc_start: 0.8833 (p0) cc_final: 0.8427 (p0) REVERT: D 188 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8605 (mm-30) REVERT: D 212 ARG cc_start: 0.8262 (ttp80) cc_final: 0.7751 (ttp80) outliers start: 7 outliers final: 7 residues processed: 83 average time/residue: 0.2775 time to fit residues: 31.4476 Evaluate side-chains 85 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 78 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain D residue 126 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 71 optimal weight: 9.9990 chunk 41 optimal weight: 0.3980 chunk 30 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 44 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 148 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6489 Z= 0.181 Angle : 0.487 11.041 8811 Z= 0.249 Chirality : 0.042 0.135 949 Planarity : 0.004 0.045 1138 Dihedral : 3.972 18.693 881 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.15 % Allowed : 11.80 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.51 % 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: 0.96 (0.30), residues: 788 helix: 1.06 (0.53), residues: 98 sheet: 1.57 (0.29), residues: 337 loop : -0.42 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 244 HIS 0.003 0.001 HIS D 190 PHE 0.009 0.001 PHE A 33 TYR 0.013 0.001 TYR E 33 ARG 0.004 0.000 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 0.748 Fit side-chains REVERT: A 108 ARG cc_start: 0.8008 (mmm-85) cc_final: 0.7686 (mmm160) REVERT: A 113 TYR cc_start: 0.7704 (m-80) cc_final: 0.7160 (m-80) REVERT: A 253 GLN cc_start: 0.8492 (pt0) cc_final: 0.7896 (pm20) REVERT: B 19 LYS cc_start: 0.8721 (mmtt) cc_final: 0.7926 (mtpp) REVERT: B 34 ASP cc_start: 0.8403 (m-30) cc_final: 0.8190 (m-30) REVERT: E 199 TYR cc_start: 0.7379 (m-80) cc_final: 0.7124 (m-80) REVERT: D 159 ASN cc_start: 0.8861 (p0) cc_final: 0.8420 (p0) REVERT: D 188 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8604 (mm-30) REVERT: D 212 ARG cc_start: 0.8245 (ttp80) cc_final: 0.7728 (ttp80) outliers start: 8 outliers final: 6 residues processed: 84 average time/residue: 0.2115 time to fit residues: 22.4150 Evaluate side-chains 84 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain D residue 126 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 34 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 65 optimal weight: 0.3980 chunk 18 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 6489 Z= 0.264 Angle : 0.523 12.015 8811 Z= 0.266 Chirality : 0.043 0.149 949 Planarity : 0.004 0.045 1138 Dihedral : 4.139 20.299 881 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.01 % Allowed : 11.65 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.51 % 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: 1.00 (0.30), residues: 788 helix: 0.99 (0.52), residues: 98 sheet: 1.55 (0.28), residues: 342 loop : -0.34 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 244 HIS 0.003 0.001 HIS D 190 PHE 0.010 0.001 PHE D 140 TYR 0.015 0.001 TYR E 33 ARG 0.004 0.000 ARG A 6 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 76 time to evaluate : 0.768 Fit side-chains REVERT: A 108 ARG cc_start: 0.8011 (mmm-85) cc_final: 0.7687 (mmm160) REVERT: A 113 TYR cc_start: 0.7792 (m-80) cc_final: 0.7204 (m-80) REVERT: A 253 GLN cc_start: 0.8528 (pt0) cc_final: 0.7951 (pm20) REVERT: B 19 LYS cc_start: 0.8749 (mmtt) cc_final: 0.7951 (mtpp) REVERT: B 34 ASP cc_start: 0.8422 (m-30) cc_final: 0.8204 (m-30) REVERT: E 199 TYR cc_start: 0.7414 (m-80) cc_final: 0.7154 (m-80) REVERT: D 159 ASN cc_start: 0.8873 (p0) cc_final: 0.8440 (p0) REVERT: D 188 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8581 (mm-30) outliers start: 7 outliers final: 7 residues processed: 80 average time/residue: 0.3403 time to fit residues: 34.4052 Evaluate side-chains 82 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 75 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain D residue 126 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 44 optimal weight: 0.0980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 176 GLN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.110764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.071424 restraints weight = 9307.856| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 2.92 r_work: 0.2639 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2484 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6489 Z= 0.193 Angle : 0.493 11.560 8811 Z= 0.251 Chirality : 0.042 0.136 949 Planarity : 0.004 0.045 1138 Dihedral : 4.011 18.956 881 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.01 % Allowed : 11.51 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.51 % 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: 1.03 (0.30), residues: 788 helix: 1.02 (0.53), residues: 98 sheet: 1.59 (0.28), residues: 342 loop : -0.33 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 167 HIS 0.003 0.001 HIS D 190 PHE 0.009 0.001 PHE A 33 TYR 0.013 0.001 TYR E 33 ARG 0.004 0.000 ARG A 6 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1834.87 seconds wall clock time: 35 minutes 32.28 seconds (2132.28 seconds total)