Starting phenix.real_space_refine on Wed Feb 12 04:03:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n64_24193/02_2025/7n64_24193.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n64_24193/02_2025/7n64_24193.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n64_24193/02_2025/7n64_24193.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n64_24193/02_2025/7n64_24193.map" model { file = "/net/cci-nas-00/data/ceres_data/7n64_24193/02_2025/7n64_24193.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n64_24193/02_2025/7n64_24193.cif" } resolution = 4.2 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 26 5.16 5 C 4574 2.51 5 N 1194 2.21 5 O 1395 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7189 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2235 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 14, 'TRANS': 262} Chain: "B" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1568 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 11, 'TRANS': 186} Chain: "H" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1687 Classifications: {'peptide': 222} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 209} Chain breaks: 1 Chain: "L" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1604 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 197} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.52, per 1000 atoms: 0.63 Number of scatterers: 7189 At special positions: 0 Unit cell: (99, 79.2, 120.45, 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 26 16.00 O 1395 8.00 N 1194 7.00 C 4574 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 94 " distance=2.03 Simple disulfide: pdb=" SG CYS H 160 " - pdb=" SG CYS H 216 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " NAG-ASN " NAG A1301 " - " ASN A 17 " " NAG A1302 " - " ASN A 165 " " NAG F 1 " - " ASN A 122 " " NAG G 1 " - " ASN B 343 " Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 962.7 milliseconds 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1680 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 17 sheets defined 6.3% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.708A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 390 Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'H' and resid 59 through 63 removed outlier: 3.853A pdb=" N LYS H 63 " --> pdb=" O ASP H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 205 through 209 Processing helix chain 'L' and resid 121 through 127 Processing helix chain 'L' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.300A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 104 removed outlier: 7.424A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 121 removed outlier: 4.168A pdb=" N GLU A 132 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN A 164 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 116 through 121 Processing sheet with id=AA7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.779A pdb=" N SER B 514 " --> pdb=" O TYR B 396 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.685A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'H' and resid 18 through 19 removed outlier: 4.087A pdb=" N SER H 69 " --> pdb=" O TYR H 78 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 47 through 50 removed outlier: 5.264A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR H 92 " --> pdb=" O THR H 123 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 136 through 140 removed outlier: 3.506A pdb=" N LYS H 163 " --> pdb=" O SER H 136 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N TYR H 196 " --> pdb=" O ASP H 164 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER H 199 " --> pdb=" O PHE H 186 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 171 through 174 removed outlier: 3.833A pdb=" N TYR H 214 " --> pdb=" O VAL H 231 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AB6, first strand: chain 'L' and resid 45 through 46 removed outlier: 3.581A pdb=" N GLN L 37 " --> pdb=" O LYS L 45 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 114 through 118 removed outlier: 4.729A pdb=" N SER L 131 " --> pdb=" O LEU L 181 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LEU L 181 " --> pdb=" O SER L 131 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VAL L 133 " --> pdb=" O LEU L 179 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU L 179 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU L 135 " --> pdb=" O SER L 177 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N SER L 177 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ASN L 137 " --> pdb=" O LEU L 175 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU L 175 " --> pdb=" O ASN L 137 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE L 139 " --> pdb=" O TYR L 173 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 144 through 149 187 hydrogen bonds defined for protein. 444 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: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1932 1.33 - 1.45: 1675 1.45 - 1.57: 3736 1.57 - 1.70: 0 1.70 - 1.82: 32 Bond restraints: 7375 Sorted by residual: bond pdb=" N GLN L 3 " pdb=" CA GLN L 3 " ideal model delta sigma weight residual 1.452 1.504 -0.051 1.22e-02 6.72e+03 1.76e+01 bond pdb=" C ALA L 111 " pdb=" N ALA L 112 " ideal model delta sigma weight residual 1.333 1.240 0.093 2.74e-02 1.33e+03 1.14e+01 bond pdb=" N GLN L 100 " pdb=" CA GLN L 100 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.17e-02 7.31e+03 9.83e+00 bond pdb=" C ALA B 520 " pdb=" N PRO B 521 " ideal model delta sigma weight residual 1.331 1.369 -0.038 1.27e-02 6.20e+03 9.03e+00 bond pdb=" N ARG A 237 " pdb=" CA ARG A 237 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.13e-02 7.83e+03 8.78e+00 ... (remaining 7370 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 9485 2.24 - 4.48: 497 4.48 - 6.72: 44 6.72 - 8.97: 7 8.97 - 11.21: 2 Bond angle restraints: 10035 Sorted by residual: angle pdb=" CA ALA B 520 " pdb=" C ALA B 520 " pdb=" N PRO B 521 " ideal model delta sigma weight residual 117.47 123.32 -5.85 1.16e+00 7.43e-01 2.55e+01 angle pdb=" C ILE L 106 " pdb=" N LYS L 107 " pdb=" CA LYS L 107 " ideal model delta sigma weight residual 121.54 129.56 -8.02 1.91e+00 2.74e-01 1.76e+01 angle pdb=" C TYR A 204 " pdb=" N SER A 205 " pdb=" CA SER A 205 " ideal model delta sigma weight residual 122.10 116.05 6.05 1.66e+00 3.63e-01 1.33e+01 angle pdb=" N GLN L 124 " pdb=" CA GLN L 124 " pdb=" C GLN L 124 " ideal model delta sigma weight residual 111.07 107.30 3.77 1.07e+00 8.73e-01 1.24e+01 angle pdb=" N SER B 371 " pdb=" CA SER B 371 " pdb=" C SER B 371 " ideal model delta sigma weight residual 114.56 110.16 4.40 1.27e+00 6.20e-01 1.20e+01 ... (remaining 10030 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.86: 3946 18.86 - 37.72: 405 37.72 - 56.58: 61 56.58 - 75.44: 25 75.44 - 94.30: 8 Dihedral angle restraints: 4445 sinusoidal: 1815 harmonic: 2630 Sorted by residual: dihedral pdb=" CB CYS A 15 " pdb=" SG CYS A 15 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual 93.00 149.28 -56.28 1 1.00e+01 1.00e-02 4.27e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 40.22 52.78 1 1.00e+01 1.00e-02 3.79e+01 dihedral pdb=" CB CYS H 160 " pdb=" SG CYS H 160 " pdb=" SG CYS H 216 " pdb=" CB CYS H 216 " ideal model delta sinusoidal sigma weight residual 93.00 40.52 52.48 1 1.00e+01 1.00e-02 3.75e+01 ... (remaining 4442 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 981 0.091 - 0.181: 121 0.181 - 0.272: 11 0.272 - 0.362: 1 0.362 - 0.453: 2 Chirality restraints: 1116 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.12e+00 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" CB VAL A 130 " pdb=" CA VAL A 130 " pdb=" CG1 VAL A 130 " pdb=" CG2 VAL A 130 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 1113 not shown) Planarity restraints: 1290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE H 138 " 0.048 5.00e-02 4.00e+02 7.23e-02 8.36e+00 pdb=" N PRO H 139 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO H 139 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO H 139 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 368 " 0.013 2.00e-02 2.50e+03 2.72e-02 7.38e+00 pdb=" C LEU B 368 " -0.047 2.00e-02 2.50e+03 pdb=" O LEU B 368 " 0.018 2.00e-02 2.50e+03 pdb=" N TYR B 369 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 148 " 0.015 2.00e-02 2.50e+03 1.63e-02 6.64e+00 pdb=" CG TRP L 148 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP L 148 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP L 148 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP L 148 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP L 148 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP L 148 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 148 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 148 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP L 148 " -0.000 2.00e-02 2.50e+03 ... (remaining 1287 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 553 2.71 - 3.25: 7847 3.25 - 3.80: 11838 3.80 - 4.35: 14933 4.35 - 4.90: 24653 Nonbonded interactions: 59824 Sorted by model distance: nonbonded pdb=" O ASN H 53 " pdb=" OG SER H 54 " model vdw 2.157 3.040 nonbonded pdb=" CG2 ILE L 2 " pdb=" N GLN L 3 " model vdw 2.193 3.540 nonbonded pdb=" N GLY B 404 " pdb=" O GLN B 506 " model vdw 2.205 3.120 nonbonded pdb=" OD1 ASP A 53 " pdb=" N LEU A 54 " model vdw 2.211 3.120 nonbonded pdb=" N GLN H 191 " pdb=" O LEU H 195 " model vdw 2.216 3.120 ... (remaining 59819 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue 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: 0.480 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.490 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 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 : 0.009 0.093 7375 Z= 0.576 Angle : 1.060 11.208 10035 Z= 0.586 Chirality : 0.062 0.453 1116 Planarity : 0.006 0.072 1286 Dihedral : 15.983 94.299 2735 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 36.86 Ramachandran Plot: Outliers : 0.33 % Allowed : 20.76 % Favored : 78.91 % Rotamer: Outliers : 1.78 % Allowed : 1.40 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.80 (0.26), residues: 896 helix: -3.80 (0.50), residues: 40 sheet: -1.47 (0.32), residues: 269 loop : -3.15 (0.24), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP L 148 HIS 0.008 0.002 HIS L 189 PHE 0.036 0.004 PHE B 377 TYR 0.034 0.003 TYR H 93 ARG 0.010 0.001 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 LYS cc_start: 0.7737 (ptmm) cc_final: 0.7108 (ptmm) REVERT: A 224 GLU cc_start: 0.7898 (pm20) cc_final: 0.7504 (pm20) REVERT: B 517 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.6862 (tt) REVERT: L 138 ASN cc_start: 0.8587 (m110) cc_final: 0.7973 (m110) REVERT: L 192 TYR cc_start: 0.6668 (m-80) cc_final: 0.6394 (m-10) outliers start: 14 outliers final: 5 residues processed: 167 average time/residue: 0.2070 time to fit residues: 45.3909 Evaluate side-chains 127 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 121 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 35 optimal weight: 0.0050 chunk 68 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 370 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 124 GLN L 147 GLN L 166 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.131550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.108706 restraints weight = 17467.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.111407 restraints weight = 10111.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.113142 restraints weight = 6785.265| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7375 Z= 0.234 Angle : 0.806 9.290 10035 Z= 0.410 Chirality : 0.051 0.241 1116 Planarity : 0.006 0.050 1286 Dihedral : 8.093 58.842 1130 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.05 % Favored : 88.95 % Rotamer: Outliers : 0.13 % Allowed : 8.12 % Favored : 91.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.27), residues: 896 helix: -3.71 (0.48), residues: 39 sheet: -1.31 (0.31), residues: 286 loop : -2.75 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 148 HIS 0.004 0.001 HIS H 35 PHE 0.014 0.002 PHE B 497 TYR 0.040 0.002 TYR L 91 ARG 0.006 0.001 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 VAL cc_start: 0.7493 (p) cc_final: 0.6604 (p) REVERT: A 206 LYS cc_start: 0.7955 (ptmm) cc_final: 0.7709 (ptmm) REVERT: B 360 ASN cc_start: 0.8416 (t0) cc_final: 0.8197 (t0) REVERT: B 466 ARG cc_start: 0.7622 (ttp80) cc_final: 0.6651 (ttt-90) REVERT: H 87 GLU cc_start: 0.8445 (pm20) cc_final: 0.8168 (pm20) REVERT: H 166 PHE cc_start: 0.7568 (t80) cc_final: 0.7324 (t80) REVERT: L 4 MET cc_start: 0.6669 (tpt) cc_final: 0.6163 (tpt) REVERT: L 138 ASN cc_start: 0.8707 (m110) cc_final: 0.8291 (m110) outliers start: 1 outliers final: 0 residues processed: 162 average time/residue: 0.1982 time to fit residues: 42.7610 Evaluate side-chains 131 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 85 optimal weight: 9.9990 chunk 66 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 75 ASN ** H 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 124 GLN ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.128257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.105678 restraints weight = 17909.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.108135 restraints weight = 10522.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.109788 restraints weight = 7253.039| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 7375 Z= 0.414 Angle : 0.868 9.120 10035 Z= 0.444 Chirality : 0.052 0.323 1116 Planarity : 0.006 0.061 1286 Dihedral : 8.055 53.373 1130 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 22.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.74 % Favored : 83.26 % Rotamer: Outliers : 0.13 % Allowed : 5.58 % Favored : 94.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.27), residues: 896 helix: -3.26 (0.62), residues: 39 sheet: -1.55 (0.30), residues: 301 loop : -2.81 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP H 174 HIS 0.004 0.001 HIS H 220 PHE 0.027 0.003 PHE B 347 TYR 0.032 0.003 TYR L 192 ARG 0.005 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 151 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.5935 (mm-30) cc_final: 0.5414 (mm-30) REVERT: A 206 LYS cc_start: 0.8220 (ptmm) cc_final: 0.7710 (ptmm) REVERT: A 224 GLU cc_start: 0.7731 (pm20) cc_final: 0.7422 (pm20) REVERT: B 466 ARG cc_start: 0.7705 (ttp80) cc_final: 0.6655 (ttt-90) REVERT: B 487 ASN cc_start: 0.5972 (t0) cc_final: 0.5767 (t0) REVERT: H 31 ASP cc_start: 0.6989 (m-30) cc_final: 0.6689 (m-30) REVERT: H 87 GLU cc_start: 0.8454 (pm20) cc_final: 0.8133 (pm20) REVERT: L 82 ASP cc_start: 0.8151 (m-30) cc_final: 0.7394 (m-30) REVERT: L 138 ASN cc_start: 0.8803 (m110) cc_final: 0.8098 (m110) outliers start: 1 outliers final: 0 residues processed: 152 average time/residue: 0.2169 time to fit residues: 43.0684 Evaluate side-chains 124 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 72 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 66 optimal weight: 8.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 ASN H 191 GLN ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.135539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.112225 restraints weight = 17384.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.115053 restraints weight = 9952.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.116933 restraints weight = 6670.756| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7375 Z= 0.206 Angle : 0.761 9.046 10035 Z= 0.389 Chirality : 0.050 0.269 1116 Planarity : 0.006 0.051 1286 Dihedral : 7.087 48.502 1130 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.27), residues: 896 helix: -3.65 (0.63), residues: 33 sheet: -1.28 (0.31), residues: 295 loop : -2.57 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 148 HIS 0.005 0.001 HIS H 35 PHE 0.019 0.002 PHE B 497 TYR 0.017 0.002 TYR B 365 ARG 0.004 0.001 ARG H 104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 405 ASP cc_start: 0.7972 (p0) cc_final: 0.7318 (p0) REVERT: B 487 ASN cc_start: 0.5599 (t0) cc_final: 0.5338 (t0) REVERT: H 19 ARG cc_start: 0.8411 (ttp80) cc_final: 0.8159 (ttp80) REVERT: H 31 ASP cc_start: 0.6971 (m-30) cc_final: 0.6422 (m-30) REVERT: H 87 GLU cc_start: 0.8526 (pm20) cc_final: 0.8152 (pm20) REVERT: H 181 SER cc_start: 0.7582 (t) cc_final: 0.7238 (m) REVERT: L 138 ASN cc_start: 0.8594 (m110) cc_final: 0.8083 (m110) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.2020 time to fit residues: 47.4348 Evaluate side-chains 137 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 84 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 16 optimal weight: 0.0040 chunk 62 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 191 GLN ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.135229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.112089 restraints weight = 17072.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.114783 restraints weight = 9844.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.116526 restraints weight = 6692.404| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7375 Z= 0.214 Angle : 0.749 9.800 10035 Z= 0.378 Chirality : 0.049 0.259 1116 Planarity : 0.005 0.053 1286 Dihedral : 6.858 47.376 1130 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.72 % Favored : 87.28 % Rotamer: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.27), residues: 896 helix: -3.63 (0.64), residues: 33 sheet: -1.14 (0.31), residues: 282 loop : -2.46 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 174 HIS 0.004 0.001 HIS H 35 PHE 0.031 0.002 PHE A 58 TYR 0.014 0.002 TYR B 451 ARG 0.003 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 487 ASN cc_start: 0.5925 (t0) cc_final: 0.5638 (t0) REVERT: H 19 ARG cc_start: 0.8379 (ttp80) cc_final: 0.8152 (ttp80) REVERT: H 31 ASP cc_start: 0.6986 (m-30) cc_final: 0.6396 (m-30) REVERT: H 87 GLU cc_start: 0.8523 (pm20) cc_final: 0.8130 (pm20) REVERT: H 181 SER cc_start: 0.7591 (t) cc_final: 0.7202 (m) REVERT: H 224 ASN cc_start: 0.8262 (m-40) cc_final: 0.7412 (p0) REVERT: L 138 ASN cc_start: 0.8601 (m110) cc_final: 0.8050 (m110) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1989 time to fit residues: 44.8224 Evaluate side-chains 132 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 57 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 84 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 69 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.131232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.107972 restraints weight = 17348.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.110514 restraints weight = 10349.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.112142 restraints weight = 7082.108| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 7375 Z= 0.355 Angle : 0.829 8.011 10035 Z= 0.424 Chirality : 0.052 0.317 1116 Planarity : 0.006 0.053 1286 Dihedral : 7.379 46.043 1130 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.73 % Favored : 85.27 % Rotamer: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.27), residues: 896 helix: -3.25 (0.60), residues: 45 sheet: -1.20 (0.33), residues: 262 loop : -2.50 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 148 HIS 0.005 0.001 HIS L 189 PHE 0.024 0.002 PHE B 497 TYR 0.023 0.003 TYR L 140 ARG 0.005 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 466 ARG cc_start: 0.7416 (ttp80) cc_final: 0.6750 (ttt180) REVERT: B 487 ASN cc_start: 0.6082 (t0) cc_final: 0.5722 (t0) REVERT: H 19 ARG cc_start: 0.8450 (ttp80) cc_final: 0.7867 (ttp80) REVERT: H 31 ASP cc_start: 0.7049 (m-30) cc_final: 0.6662 (m-30) REVERT: H 72 ASN cc_start: 0.7384 (m-40) cc_final: 0.7022 (m-40) REVERT: H 87 GLU cc_start: 0.8543 (pm20) cc_final: 0.8181 (pm20) REVERT: H 181 SER cc_start: 0.7720 (t) cc_final: 0.7350 (m) REVERT: L 91 TYR cc_start: 0.6781 (p90) cc_final: 0.6519 (p90) REVERT: L 138 ASN cc_start: 0.8683 (m110) cc_final: 0.7908 (m110) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.2047 time to fit residues: 44.3464 Evaluate side-chains 131 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 34 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.134457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.111369 restraints weight = 17065.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.113905 restraints weight = 10003.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.115669 restraints weight = 6856.355| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7375 Z= 0.218 Angle : 0.775 12.153 10035 Z= 0.390 Chirality : 0.050 0.285 1116 Planarity : 0.005 0.052 1286 Dihedral : 6.911 47.976 1130 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.50 % Favored : 88.50 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.27), residues: 896 helix: -3.06 (0.66), residues: 39 sheet: -1.02 (0.32), residues: 286 loop : -2.43 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP H 174 HIS 0.007 0.001 HIS L 189 PHE 0.026 0.002 PHE B 347 TYR 0.018 0.002 TYR L 186 ARG 0.008 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 402 ILE cc_start: 0.8755 (pt) cc_final: 0.8372 (pt) REVERT: B 406 GLU cc_start: 0.8021 (pm20) cc_final: 0.6997 (pm20) REVERT: B 466 ARG cc_start: 0.7751 (ttp80) cc_final: 0.7033 (ptm160) REVERT: B 487 ASN cc_start: 0.5833 (t0) cc_final: 0.5453 (t0) REVERT: H 87 GLU cc_start: 0.8546 (pm20) cc_final: 0.8192 (pm20) REVERT: L 4 MET cc_start: 0.6472 (tpt) cc_final: 0.6071 (tpt) REVERT: L 91 TYR cc_start: 0.6841 (p90) cc_final: 0.6525 (p90) REVERT: L 138 ASN cc_start: 0.8596 (m110) cc_final: 0.7830 (m110) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.2012 time to fit residues: 45.4499 Evaluate side-chains 132 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 82 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 6 optimal weight: 0.0470 chunk 5 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 67 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 overall best weight: 0.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.136856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.113240 restraints weight = 17059.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.116014 restraints weight = 9786.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.117755 restraints weight = 6572.559| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7375 Z= 0.208 Angle : 0.758 10.699 10035 Z= 0.381 Chirality : 0.049 0.266 1116 Planarity : 0.006 0.053 1286 Dihedral : 6.591 48.306 1130 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.94 % Favored : 88.06 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.28), residues: 896 helix: -2.92 (0.70), residues: 39 sheet: -0.86 (0.32), residues: 290 loop : -2.37 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP L 148 HIS 0.007 0.001 HIS L 189 PHE 0.023 0.002 PHE B 497 TYR 0.017 0.002 TYR H 78 ARG 0.008 0.001 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 402 ILE cc_start: 0.8709 (pt) cc_final: 0.8326 (pt) REVERT: B 406 GLU cc_start: 0.8027 (pm20) cc_final: 0.7146 (pm20) REVERT: B 466 ARG cc_start: 0.7726 (ttp80) cc_final: 0.6952 (ptm160) REVERT: B 487 ASN cc_start: 0.5814 (t0) cc_final: 0.5435 (t0) REVERT: B 516 GLU cc_start: 0.7298 (tm-30) cc_final: 0.6933 (tm-30) REVERT: H 87 GLU cc_start: 0.8543 (pm20) cc_final: 0.8167 (pm20) REVERT: H 121 GLN cc_start: 0.8287 (tp-100) cc_final: 0.8082 (tp-100) REVERT: H 224 ASN cc_start: 0.8188 (m-40) cc_final: 0.7375 (p0) REVERT: L 4 MET cc_start: 0.6486 (tpt) cc_final: 0.6167 (tpt) REVERT: L 21 ILE cc_start: 0.6323 (tp) cc_final: 0.5600 (mp) REVERT: L 91 TYR cc_start: 0.6682 (p90) cc_final: 0.6323 (p90) REVERT: L 138 ASN cc_start: 0.8544 (m110) cc_final: 0.7912 (m110) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.2003 time to fit residues: 45.7670 Evaluate side-chains 144 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 chunk 53 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 57 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.133376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.109624 restraints weight = 17387.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.112114 restraints weight = 10264.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.113945 restraints weight = 7082.281| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 7375 Z= 0.306 Angle : 0.810 9.753 10035 Z= 0.411 Chirality : 0.051 0.295 1116 Planarity : 0.006 0.049 1286 Dihedral : 6.978 47.564 1130 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.84 % Favored : 86.16 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.27), residues: 896 helix: -3.16 (0.64), residues: 39 sheet: -0.95 (0.32), residues: 286 loop : -2.43 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP H 174 HIS 0.008 0.001 HIS L 189 PHE 0.032 0.002 PHE B 497 TYR 0.025 0.002 TYR B 451 ARG 0.007 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 466 ARG cc_start: 0.7777 (ttp80) cc_final: 0.7103 (ptm160) REVERT: B 487 ASN cc_start: 0.6057 (t0) cc_final: 0.5674 (t0) REVERT: H 72 ASN cc_start: 0.7287 (m-40) cc_final: 0.7069 (m-40) REVERT: H 87 GLU cc_start: 0.8523 (pm20) cc_final: 0.8168 (pm20) REVERT: L 21 ILE cc_start: 0.6402 (tp) cc_final: 0.6091 (tp) REVERT: L 138 ASN cc_start: 0.8748 (m110) cc_final: 0.8046 (m110) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.2094 time to fit residues: 47.0264 Evaluate side-chains 128 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 71 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 3 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 68 optimal weight: 0.0570 chunk 15 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 overall best weight: 2.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.134845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.110897 restraints weight = 17727.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.113614 restraints weight = 10239.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.115464 restraints weight = 6883.984| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7375 Z= 0.253 Angle : 0.792 10.534 10035 Z= 0.402 Chirality : 0.051 0.300 1116 Planarity : 0.006 0.068 1286 Dihedral : 6.911 48.478 1130 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.27), residues: 896 helix: -3.28 (0.63), residues: 39 sheet: -0.89 (0.32), residues: 286 loop : -2.42 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP L 35 HIS 0.008 0.002 HIS L 189 PHE 0.037 0.002 PHE B 497 TYR 0.033 0.002 TYR H 78 ARG 0.009 0.001 ARG H 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 403 ARG cc_start: 0.7954 (ptm-80) cc_final: 0.7677 (ptm-80) REVERT: B 466 ARG cc_start: 0.7793 (ttp80) cc_final: 0.6984 (ptm160) REVERT: B 487 ASN cc_start: 0.5956 (t0) cc_final: 0.5592 (t0) REVERT: B 516 GLU cc_start: 0.7048 (tm-30) cc_final: 0.6683 (tm-30) REVERT: H 19 ARG cc_start: 0.8133 (ttp80) cc_final: 0.7881 (ttp80) REVERT: H 87 GLU cc_start: 0.8542 (pm20) cc_final: 0.8192 (pm20) REVERT: H 224 ASN cc_start: 0.8250 (m-40) cc_final: 0.7394 (p0) REVERT: L 138 ASN cc_start: 0.8778 (m110) cc_final: 0.8038 (m-40) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.1986 time to fit residues: 43.6841 Evaluate side-chains 132 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 30 optimal weight: 0.4980 chunk 66 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 3 optimal weight: 0.2980 chunk 14 optimal weight: 0.3980 chunk 85 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.137212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.113678 restraints weight = 17119.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.116303 restraints weight = 9998.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.118102 restraints weight = 6809.662| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7375 Z= 0.209 Angle : 0.766 9.188 10035 Z= 0.386 Chirality : 0.050 0.279 1116 Planarity : 0.005 0.048 1286 Dihedral : 6.592 48.709 1130 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.72 % Favored : 87.28 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.27), residues: 896 helix: -3.28 (0.64), residues: 39 sheet: -0.94 (0.31), residues: 291 loop : -2.36 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP H 174 HIS 0.008 0.001 HIS L 189 PHE 0.024 0.002 PHE A 106 TYR 0.023 0.002 TYR L 140 ARG 0.007 0.000 ARG H 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2302.38 seconds wall clock time: 42 minutes 27.69 seconds (2547.69 seconds total)