Starting phenix.real_space_refine on Tue Feb 13 11:08:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vaf_31839/02_2024/7vaf_31839.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vaf_31839/02_2024/7vaf_31839.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vaf_31839/02_2024/7vaf_31839.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vaf_31839/02_2024/7vaf_31839.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vaf_31839/02_2024/7vaf_31839.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vaf_31839/02_2024/7vaf_31839.pdb" } resolution = 3.11 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= 0.002 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 40 5.16 5 C 3629 2.51 5 N 899 2.21 5 O 1057 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 10": "OE1" <-> "OE2" Residue "H TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 56": "OD1" <-> "OD2" Residue "H GLU 82": "OE1" <-> "OE2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 88": "OD1" <-> "OD2" Residue "L PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 159": "OE1" <-> "OE2" Residue "A PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 115": "OD1" <-> "OD2" Residue "A ASP 152": "OD1" <-> "OD2" Residue "A GLU 308": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 5625 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1669 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 15, 'TRANS': 205} Chain: "L" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1684 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 9, 'TRANS': 206} Chain: "A" Number of atoms: 2272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2272 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 16, 'TRANS': 280} Time building chain proxies: 3.59, per 1000 atoms: 0.64 Number of scatterers: 5625 At special positions: 0 Unit cell: (85.905, 75.945, 141.93, 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 40 16.00 O 1057 8.00 N 899 7.00 C 3629 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 203 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.03 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: 1.76 Conformation dependent library (CDL) restraints added in 901.9 milliseconds 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1360 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 10 sheets defined 36.8% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.568A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 85 through 89 removed outlier: 4.153A pdb=" N LEU L 89 " --> pdb=" O ALA L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 132 Processing helix chain 'L' and resid 190 through 195 removed outlier: 3.578A pdb=" N HIS L 194 " --> pdb=" O GLU L 190 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN L 195 " --> pdb=" O TYR L 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 190 through 195' Processing helix chain 'A' and resid 23 through 44 Processing helix chain 'A' and resid 48 through 57 Processing helix chain 'A' and resid 59 through 71 removed outlier: 3.706A pdb=" N VAL A 63 " --> pdb=" O LYS A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 84 Processing helix chain 'A' and resid 86 through 98 Processing helix chain 'A' and resid 102 through 109 removed outlier: 3.768A pdb=" N ASN A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 141 removed outlier: 3.819A pdb=" N SER A 119 " --> pdb=" O ASP A 115 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE A 120 " --> pdb=" O MET A 116 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY A 132 " --> pdb=" O PHE A 128 " (cutoff:3.500A) Proline residue: A 135 - end of helix removed outlier: 3.921A pdb=" N TYR A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 154 removed outlier: 3.510A pdb=" N LYS A 153 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL A 154 " --> pdb=" O LYS A 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 150 through 154' Processing helix chain 'A' and resid 156 through 180 Proline residue: A 169 - end of helix Processing helix chain 'A' and resid 183 through 211 removed outlier: 3.555A pdb=" N GLY A 190 " --> pdb=" O TYR A 186 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER A 199 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL A 200 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 244 Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 247 through 260 removed outlier: 3.810A pdb=" N PHE A 260 " --> pdb=" O MET A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 274 removed outlier: 4.271A pdb=" N CYS A 266 " --> pdb=" O ASN A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 311 removed outlier: 3.546A pdb=" N LYS A 311 " --> pdb=" O TYR A 307 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.503A pdb=" N GLU H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY H 57 " --> pdb=" O ASN H 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.503A pdb=" N GLU H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N TYR H 100 " --> pdb=" O PHE H 108 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N PHE H 108 " --> pdb=" O TYR H 100 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 128 through 132 removed outlier: 4.050A pdb=" N GLY H 147 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N CYS H 148 " --> pdb=" O SER H 187 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N SER H 187 " --> pdb=" O CYS H 148 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL H 150 " --> pdb=" O MET H 185 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N MET H 185 " --> pdb=" O VAL H 150 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N THR H 184 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA H 176 " --> pdb=" O THR H 184 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER H 186 " --> pdb=" O PHE H 174 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 159 through 161 Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.744A pdb=" N LEU L 11 " --> pdb=" O GLU L 110 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 19 through 21 removed outlier: 3.950A pdb=" N VAL L 19 " --> pdb=" O ILE L 81 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE L 81 " --> pdb=" O VAL L 19 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 40 through 43 removed outlier: 6.613A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 119 through 123 removed outlier: 3.826A pdb=" N ASN L 143 " --> pdb=" O TYR L 178 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N TYR L 178 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 158 through 159 270 hydrogen bonds defined for protein. 753 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: 1.51 Time building geometry restraints manager: 1.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1711 1.34 - 1.46: 1379 1.46 - 1.58: 2608 1.58 - 1.70: 0 1.70 - 1.82: 63 Bond restraints: 5761 Sorted by residual: bond pdb=" N ALA H 16 " pdb=" CA ALA H 16 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.67e+00 bond pdb=" CA ALA H 16 " pdb=" CB ALA H 16 " ideal model delta sigma weight residual 1.530 1.514 0.016 1.69e-02 3.50e+03 8.66e-01 bond pdb=" CA VAL A 154 " pdb=" CB VAL A 154 " ideal model delta sigma weight residual 1.526 1.539 -0.013 1.55e-02 4.16e+03 7.53e-01 bond pdb=" CB ASN H 55 " pdb=" CG ASN H 55 " ideal model delta sigma weight residual 1.516 1.536 -0.020 2.50e-02 1.60e+03 6.48e-01 bond pdb=" CB GLU L 159 " pdb=" CG GLU L 159 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 6.00e-01 ... (remaining 5756 not shown) Histogram of bond angle deviations from ideal: 99.59 - 106.48: 199 106.48 - 113.37: 3188 113.37 - 120.27: 1968 120.27 - 127.16: 2407 127.16 - 134.05: 65 Bond angle restraints: 7827 Sorted by residual: angle pdb=" C TRP L 56 " pdb=" N ALA L 57 " pdb=" CA ALA L 57 " ideal model delta sigma weight residual 121.54 126.44 -4.90 1.91e+00 2.74e-01 6.59e+00 angle pdb=" C PRO L 8 " pdb=" N SER L 9 " pdb=" CA SER L 9 " ideal model delta sigma weight residual 121.54 126.38 -4.84 1.91e+00 2.74e-01 6.43e+00 angle pdb=" C ALA H 16 " pdb=" CA ALA H 16 " pdb=" CB ALA H 16 " ideal model delta sigma weight residual 110.42 115.20 -4.78 1.99e+00 2.53e-01 5.76e+00 angle pdb=" C MET A 112 " pdb=" N LYS A 113 " pdb=" CA LYS A 113 " ideal model delta sigma weight residual 121.54 125.49 -3.95 1.91e+00 2.74e-01 4.28e+00 angle pdb=" CA CYS L 94 " pdb=" CB CYS L 94 " pdb=" SG CYS L 94 " ideal model delta sigma weight residual 114.40 119.11 -4.71 2.30e+00 1.89e-01 4.20e+00 ... (remaining 7822 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.73: 3095 16.73 - 33.45: 279 33.45 - 50.18: 56 50.18 - 66.91: 6 66.91 - 83.64: 7 Dihedral angle restraints: 3443 sinusoidal: 1317 harmonic: 2126 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 94 " pdb=" CB CYS L 94 " ideal model delta sinusoidal sigma weight residual 93.00 166.24 -73.24 1 1.00e+01 1.00e-02 6.83e+01 dihedral pdb=" CB CYS H 148 " pdb=" SG CYS H 148 " pdb=" SG CYS H 203 " pdb=" CB CYS H 203 " ideal model delta sinusoidal sigma weight residual 93.00 138.20 -45.20 1 1.00e+01 1.00e-02 2.84e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 66.55 26.45 1 1.00e+01 1.00e-02 1.00e+01 ... (remaining 3440 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 535 0.028 - 0.057: 240 0.057 - 0.085: 74 0.085 - 0.113: 52 0.113 - 0.142: 10 Chirality restraints: 911 Sorted by residual: chirality pdb=" CA ILE H 104 " pdb=" N ILE H 104 " pdb=" C ILE H 104 " pdb=" CB ILE H 104 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CB THR A 268 " pdb=" CA THR A 268 " pdb=" OG1 THR A 268 " pdb=" CG2 THR A 268 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA VAL L 120 " pdb=" N VAL L 120 " pdb=" C VAL L 120 " pdb=" CB VAL L 120 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 908 not shown) Planarity restraints: 964 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR H 125 " 0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO H 126 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO H 126 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO H 126 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN L 85 " 0.006 2.00e-02 2.50e+03 1.16e-02 1.36e+00 pdb=" CD GLN L 85 " -0.020 2.00e-02 2.50e+03 pdb=" OE1 GLN L 85 " 0.008 2.00e-02 2.50e+03 pdb=" NE2 GLN L 85 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 48 " -0.006 2.00e-02 2.50e+03 8.72e-03 1.33e+00 pdb=" CG PHE A 48 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE A 48 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 48 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A 48 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 48 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 48 " 0.000 2.00e-02 2.50e+03 ... (remaining 961 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1281 2.79 - 3.32: 5356 3.32 - 3.85: 9073 3.85 - 4.37: 10154 4.37 - 4.90: 17991 Nonbonded interactions: 43855 Sorted by model distance: nonbonded pdb=" O LEU A 138 " pdb=" OG SER A 142 " model vdw 2.264 2.440 nonbonded pdb=" OE1 GLN L 6 " pdb=" OG1 THR L 107 " model vdw 2.287 2.440 nonbonded pdb=" NE2 GLN L 96 " pdb=" O LEU L 100 " model vdw 2.321 2.520 nonbonded pdb=" OD1 ASN A 106 " pdb=" OG SER A 119 " model vdw 2.321 2.440 nonbonded pdb=" OG SER L 126 " pdb=" OE1 GLU L 128 " model vdw 2.349 2.440 ... (remaining 43850 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: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.970 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 18.690 Find NCS groups from input model: 0.150 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 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 : 0.002 0.028 5761 Z= 0.143 Angle : 0.561 6.923 7827 Z= 0.275 Chirality : 0.041 0.142 911 Planarity : 0.003 0.036 964 Dihedral : 13.384 83.635 2074 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: 0.32 (0.32), residues: 728 helix: 1.38 (0.34), residues: 245 sheet: 0.71 (0.39), residues: 194 loop : -1.17 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 56 HIS 0.003 0.000 HIS H 35 PHE 0.020 0.001 PHE A 48 TYR 0.011 0.001 TYR L 55 ARG 0.001 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 0.647 Fit side-chains REVERT: L 20 THR cc_start: 0.8750 (p) cc_final: 0.8519 (p) REVERT: L 129 GLN cc_start: 0.8601 (tp-100) cc_final: 0.8335 (tp40) REVERT: L 139 CYS cc_start: 0.6902 (p) cc_final: 0.6461 (p) REVERT: L 153 TRP cc_start: 0.8296 (m100) cc_final: 0.7897 (m100) REVERT: L 180 MET cc_start: 0.8417 (ttt) cc_final: 0.7946 (ttt) REVERT: A 59 LYS cc_start: 0.7783 (tttm) cc_final: 0.7362 (ttmt) REVERT: A 143 LYS cc_start: 0.8221 (tttm) cc_final: 0.7955 (mmtt) REVERT: A 239 ILE cc_start: 0.9301 (mm) cc_final: 0.9096 (mm) REVERT: A 298 LEU cc_start: 0.8742 (mt) cc_final: 0.8514 (mt) REVERT: A 299 LEU cc_start: 0.8865 (tp) cc_final: 0.8471 (tp) REVERT: A 307 TYR cc_start: 0.8253 (t80) cc_final: 0.8006 (t80) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.1298 time to fit residues: 39.6476 Evaluate side-chains 174 residues out of total 641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5761 Z= 0.316 Angle : 0.646 8.540 7827 Z= 0.320 Chirality : 0.045 0.153 911 Planarity : 0.004 0.035 964 Dihedral : 3.980 14.744 781 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 2.65 % Allowed : 11.70 % Favored : 85.65 % 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: 0.44 (0.32), residues: 728 helix: 1.61 (0.34), residues: 243 sheet: 0.76 (0.39), residues: 190 loop : -1.17 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.006 0.001 HIS H 35 PHE 0.018 0.002 PHE A 48 TYR 0.020 0.002 TYR L 55 ARG 0.003 0.000 ARG L 216 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 181 time to evaluate : 0.699 Fit side-chains REVERT: H 156 GLU cc_start: 0.7493 (tp30) cc_final: 0.6983 (tp30) REVERT: L 129 GLN cc_start: 0.8621 (tp-100) cc_final: 0.8214 (tp-100) REVERT: L 165 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8637 (mp) REVERT: L 168 TRP cc_start: 0.9283 (m-90) cc_final: 0.8676 (m-90) REVERT: A 59 LYS cc_start: 0.7856 (tttm) cc_final: 0.7524 (ttmt) outliers start: 17 outliers final: 15 residues processed: 191 average time/residue: 0.1348 time to fit residues: 35.2939 Evaluate side-chains 183 residues out of total 641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 167 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 130 LEU Chi-restraints excluded: chain L residue 165 LEU Chi-restraints excluded: chain L residue 183 THR Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 187 THR Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 267 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 52 optimal weight: 0.3980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 5 GLN L 31 ASN ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 GLN L 85 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5761 Z= 0.270 Angle : 0.614 7.802 7827 Z= 0.305 Chirality : 0.044 0.145 911 Planarity : 0.004 0.036 964 Dihedral : 4.087 15.343 781 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 2.96 % Allowed : 17.32 % Favored : 79.72 % 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: 0.41 (0.32), residues: 728 helix: 1.63 (0.34), residues: 244 sheet: 0.74 (0.40), residues: 186 loop : -1.22 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 168 HIS 0.004 0.001 HIS H 35 PHE 0.020 0.002 PHE A 285 TYR 0.018 0.001 TYR H 183 ARG 0.001 0.000 ARG L 160 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 175 time to evaluate : 0.641 Fit side-chains REVERT: H 156 GLU cc_start: 0.7493 (tp30) cc_final: 0.6997 (tp30) REVERT: L 31 ASN cc_start: 0.8459 (t0) cc_final: 0.8220 (t0) REVERT: L 129 GLN cc_start: 0.8772 (tp-100) cc_final: 0.8347 (tp-100) REVERT: L 159 GLU cc_start: 0.7072 (mm-30) cc_final: 0.6598 (mm-30) REVERT: L 162 ASN cc_start: 0.8037 (m110) cc_final: 0.7827 (t0) REVERT: L 168 TRP cc_start: 0.9333 (m-90) cc_final: 0.8760 (m-90) REVERT: L 180 MET cc_start: 0.8851 (ttt) cc_final: 0.8244 (ttt) REVERT: A 59 LYS cc_start: 0.7846 (tttm) cc_final: 0.7604 (ttmt) outliers start: 19 outliers final: 15 residues processed: 185 average time/residue: 0.1328 time to fit residues: 33.5510 Evaluate side-chains 182 residues out of total 641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 167 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 43 GLN Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 130 LEU Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 294 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 43 optimal weight: 9.9990 chunk 65 optimal weight: 0.0870 chunk 69 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 5 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5761 Z= 0.217 Angle : 0.608 7.781 7827 Z= 0.299 Chirality : 0.043 0.146 911 Planarity : 0.004 0.033 964 Dihedral : 4.038 15.177 781 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 3.12 % Allowed : 19.19 % Favored : 77.69 % 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: 0.37 (0.32), residues: 728 helix: 1.65 (0.34), residues: 243 sheet: 0.70 (0.40), residues: 186 loop : -1.26 (0.36), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 153 HIS 0.003 0.001 HIS H 35 PHE 0.012 0.001 PHE H 154 TYR 0.015 0.001 TYR H 183 ARG 0.001 0.000 ARG L 36 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 175 time to evaluate : 0.610 Fit side-chains REVERT: H 156 GLU cc_start: 0.7447 (tp30) cc_final: 0.6961 (tp30) REVERT: L 129 GLN cc_start: 0.8780 (tp-100) cc_final: 0.8340 (tp-100) REVERT: L 153 TRP cc_start: 0.8169 (m100) cc_final: 0.7946 (m100) REVERT: L 168 TRP cc_start: 0.9314 (m-90) cc_final: 0.8794 (m-90) REVERT: L 180 MET cc_start: 0.8865 (ttt) cc_final: 0.8260 (ttt) REVERT: A 59 LYS cc_start: 0.7843 (tttm) cc_final: 0.7586 (ttmt) outliers start: 20 outliers final: 14 residues processed: 186 average time/residue: 0.1349 time to fit residues: 34.3564 Evaluate side-chains 185 residues out of total 641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 171 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 130 LEU Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 187 THR Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 183 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 59 optimal weight: 0.0060 chunk 48 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 62 optimal weight: 8.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 31 ASN L 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5761 Z= 0.200 Angle : 0.602 7.293 7827 Z= 0.296 Chirality : 0.043 0.145 911 Planarity : 0.003 0.034 964 Dihedral : 4.001 15.155 781 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 3.28 % Allowed : 19.66 % Favored : 77.07 % 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: 0.34 (0.32), residues: 728 helix: 1.56 (0.34), residues: 245 sheet: 0.71 (0.40), residues: 183 loop : -1.24 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 153 HIS 0.003 0.001 HIS H 35 PHE 0.012 0.001 PHE L 140 TYR 0.016 0.001 TYR A 289 ARG 0.002 0.000 ARG L 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 182 time to evaluate : 0.677 Fit side-chains REVERT: L 42 TYR cc_start: 0.8874 (m-80) cc_final: 0.8656 (m-80) REVERT: L 129 GLN cc_start: 0.8692 (tp-100) cc_final: 0.8215 (tp-100) REVERT: L 168 TRP cc_start: 0.9312 (m-90) cc_final: 0.8801 (m-90) REVERT: L 180 MET cc_start: 0.8884 (ttt) cc_final: 0.8281 (ttt) REVERT: A 59 LYS cc_start: 0.7829 (tttm) cc_final: 0.7575 (ttmt) REVERT: A 289 TYR cc_start: 0.8988 (t80) cc_final: 0.8691 (t80) outliers start: 21 outliers final: 17 residues processed: 195 average time/residue: 0.1355 time to fit residues: 36.0812 Evaluate side-chains 189 residues out of total 641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 172 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 130 LEU Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 187 THR Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 121 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 5 GLN L 6 GLN L 31 ASN ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 5761 Z= 0.404 Angle : 0.703 8.786 7827 Z= 0.354 Chirality : 0.047 0.164 911 Planarity : 0.004 0.033 964 Dihedral : 4.461 16.896 781 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 4.99 % Allowed : 19.81 % Favored : 75.20 % 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: 0.13 (0.32), residues: 728 helix: 1.27 (0.34), residues: 246 sheet: 0.60 (0.40), residues: 186 loop : -1.28 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP L 168 HIS 0.005 0.001 HIS H 35 PHE 0.020 0.002 PHE H 154 TYR 0.021 0.002 TYR H 183 ARG 0.002 0.000 ARG L 160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 183 time to evaluate : 0.678 Fit side-chains REVERT: L 44 GLN cc_start: 0.9166 (OUTLIER) cc_final: 0.8473 (tt0) REVERT: L 129 GLN cc_start: 0.8592 (tp-100) cc_final: 0.8322 (tp40) REVERT: L 168 TRP cc_start: 0.9349 (m-90) cc_final: 0.8867 (m-90) REVERT: A 283 PHE cc_start: 0.8806 (t80) cc_final: 0.8594 (t80) REVERT: A 289 TYR cc_start: 0.9062 (t80) cc_final: 0.8741 (t80) outliers start: 32 outliers final: 23 residues processed: 202 average time/residue: 0.1372 time to fit residues: 37.7121 Evaluate side-chains 193 residues out of total 641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 169 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 43 GLN Chi-restraints excluded: chain L residue 44 GLN Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 130 LEU Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain L residue 183 THR Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 187 THR Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 205 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5761 Z= 0.225 Angle : 0.658 7.769 7827 Z= 0.325 Chirality : 0.045 0.181 911 Planarity : 0.004 0.029 964 Dihedral : 4.280 18.020 781 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 3.43 % Allowed : 23.09 % Favored : 73.48 % 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: 0.22 (0.32), residues: 728 helix: 1.40 (0.34), residues: 245 sheet: 0.63 (0.39), residues: 192 loop : -1.28 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 168 HIS 0.003 0.001 HIS H 35 PHE 0.014 0.001 PHE H 154 TYR 0.015 0.001 TYR H 183 ARG 0.001 0.000 ARG L 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 188 time to evaluate : 0.660 Fit side-chains REVERT: L 42 TYR cc_start: 0.8945 (m-80) cc_final: 0.8725 (m-80) REVERT: L 44 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.8373 (tt0) REVERT: L 129 GLN cc_start: 0.8741 (tp-100) cc_final: 0.8509 (tp40) REVERT: L 168 TRP cc_start: 0.9278 (m-90) cc_final: 0.8789 (m-90) REVERT: L 180 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8085 (ttt) REVERT: L 212 LYS cc_start: 0.6877 (mmmt) cc_final: 0.6557 (tppt) REVERT: A 46 MET cc_start: 0.7504 (OUTLIER) cc_final: 0.6949 (ptt) REVERT: A 115 ASP cc_start: 0.8364 (t0) cc_final: 0.8038 (t0) REVERT: A 289 TYR cc_start: 0.8987 (t80) cc_final: 0.8680 (t80) outliers start: 22 outliers final: 15 residues processed: 201 average time/residue: 0.1387 time to fit residues: 37.9723 Evaluate side-chains 198 residues out of total 641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 180 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 44 GLN Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 128 GLU Chi-restraints excluded: chain L residue 130 LEU Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain L residue 183 THR Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 187 THR Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 183 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 5 GLN L 6 GLN ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5761 Z= 0.238 Angle : 0.664 7.907 7827 Z= 0.327 Chirality : 0.045 0.175 911 Planarity : 0.004 0.028 964 Dihedral : 4.232 17.824 781 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 3.59 % Allowed : 23.56 % Favored : 72.85 % 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: 0.16 (0.32), residues: 728 helix: 1.45 (0.34), residues: 245 sheet: 0.57 (0.39), residues: 186 loop : -1.37 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 168 HIS 0.003 0.001 HIS H 35 PHE 0.012 0.001 PHE H 154 TYR 0.014 0.001 TYR H 183 ARG 0.006 0.000 ARG L 216 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 182 time to evaluate : 0.652 Fit side-chains REVERT: L 44 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.8351 (tt0) REVERT: L 129 GLN cc_start: 0.8758 (tp-100) cc_final: 0.8531 (tp40) REVERT: L 168 TRP cc_start: 0.9289 (m-90) cc_final: 0.8796 (m-90) REVERT: L 180 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8060 (ttt) REVERT: L 212 LYS cc_start: 0.7001 (mmmt) cc_final: 0.6720 (tppt) REVERT: A 289 TYR cc_start: 0.9011 (t80) cc_final: 0.8724 (t80) outliers start: 23 outliers final: 17 residues processed: 195 average time/residue: 0.1320 time to fit residues: 35.4000 Evaluate side-chains 199 residues out of total 641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 180 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 44 GLN Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 128 GLU Chi-restraints excluded: chain L residue 130 LEU Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 187 THR Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 183 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 42 optimal weight: 9.9990 chunk 68 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 5 GLN L 6 GLN ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5761 Z= 0.285 Angle : 0.675 8.481 7827 Z= 0.334 Chirality : 0.046 0.175 911 Planarity : 0.004 0.028 964 Dihedral : 4.289 17.869 781 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 3.59 % Allowed : 23.87 % Favored : 72.54 % 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: 0.08 (0.32), residues: 728 helix: 1.34 (0.34), residues: 246 sheet: 0.50 (0.39), residues: 186 loop : -1.37 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 168 HIS 0.004 0.001 HIS H 35 PHE 0.015 0.001 PHE H 154 TYR 0.016 0.001 TYR H 183 ARG 0.005 0.000 ARG L 216 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 183 time to evaluate : 0.647 Fit side-chains REVERT: L 44 GLN cc_start: 0.9124 (OUTLIER) cc_final: 0.8387 (tt0) REVERT: L 129 GLN cc_start: 0.8625 (tp-100) cc_final: 0.8394 (tp40) REVERT: L 168 TRP cc_start: 0.9306 (m-90) cc_final: 0.8818 (m-90) REVERT: L 180 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8118 (ttt) REVERT: L 212 LYS cc_start: 0.6987 (mmmt) cc_final: 0.6676 (tppt) REVERT: A 289 TYR cc_start: 0.9000 (t80) cc_final: 0.8738 (t80) outliers start: 23 outliers final: 18 residues processed: 196 average time/residue: 0.1326 time to fit residues: 35.6452 Evaluate side-chains 203 residues out of total 641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 183 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 43 GLN Chi-restraints excluded: chain L residue 44 GLN Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 128 GLU Chi-restraints excluded: chain L residue 130 LEU Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain L residue 183 THR Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 187 THR Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 183 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 0.4980 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5761 Z= 0.233 Angle : 0.670 8.992 7827 Z= 0.329 Chirality : 0.045 0.170 911 Planarity : 0.004 0.028 964 Dihedral : 4.225 17.431 781 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 3.43 % Allowed : 24.65 % Favored : 71.92 % 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: 0.09 (0.32), residues: 728 helix: 1.38 (0.34), residues: 246 sheet: 0.52 (0.39), residues: 186 loop : -1.40 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 168 HIS 0.004 0.001 HIS H 35 PHE 0.013 0.001 PHE H 154 TYR 0.013 0.001 TYR H 183 ARG 0.005 0.000 ARG L 216 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 191 time to evaluate : 0.657 Fit side-chains REVERT: L 44 GLN cc_start: 0.9114 (OUTLIER) cc_final: 0.8372 (tt0) REVERT: L 129 GLN cc_start: 0.8599 (tp-100) cc_final: 0.8358 (tp40) REVERT: L 168 TRP cc_start: 0.9295 (m-90) cc_final: 0.8816 (m-90) REVERT: L 180 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8046 (ttt) REVERT: L 212 LYS cc_start: 0.7063 (mmmt) cc_final: 0.6766 (tppt) REVERT: A 151 LYS cc_start: 0.8755 (tmtt) cc_final: 0.8475 (tmtt) REVERT: A 289 TYR cc_start: 0.9011 (t80) cc_final: 0.8740 (t80) outliers start: 22 outliers final: 18 residues processed: 204 average time/residue: 0.1301 time to fit residues: 36.5997 Evaluate side-chains 206 residues out of total 641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 186 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 44 GLN Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 128 GLU Chi-restraints excluded: chain L residue 130 LEU Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain L residue 183 THR Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 187 THR Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 183 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 23 optimal weight: 0.0010 chunk 58 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 5 GLN L 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.132317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.102592 restraints weight = 9274.664| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 3.02 r_work: 0.3079 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5761 Z= 0.211 Angle : 0.659 9.451 7827 Z= 0.322 Chirality : 0.045 0.171 911 Planarity : 0.004 0.028 964 Dihedral : 4.146 17.600 781 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 3.28 % Allowed : 24.65 % Favored : 72.07 % 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: 0.14 (0.32), residues: 728 helix: 1.43 (0.34), residues: 246 sheet: 0.56 (0.40), residues: 186 loop : -1.40 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 168 HIS 0.003 0.001 HIS H 35 PHE 0.012 0.001 PHE H 154 TYR 0.012 0.001 TYR L 55 ARG 0.005 0.000 ARG L 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1579.16 seconds wall clock time: 29 minutes 37.32 seconds (1777.32 seconds total)