Starting phenix.real_space_refine on Mon Apr 28 07:50:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n64_24193/04_2025/7n64_24193.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n64_24193/04_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_24193/04_2025/7n64_24193.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n64_24193/04_2025/7n64_24193.map" model { file = "/net/cci-nas-00/data/ceres_data/7n64_24193/04_2025/7n64_24193.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n64_24193/04_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 4.83, per 1000 atoms: 0.67 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: 2.29 Conformation dependent library (CDL) restraints added in 991.9 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: 1.27 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: 2.43 Time building geometry restraints manager: 2.40 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: 0.800 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.810 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.280 ------------------------------------------------------------------------------- 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 7392 Z= 0.430 Angle : 1.095 12.851 10076 Z= 0.594 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00939 ( 4) link_NAG-ASN : angle 6.06386 ( 12) link_BETA1-4 : bond 0.00687 ( 3) link_BETA1-4 : angle 4.96916 ( 9) hydrogen bonds : bond 0.13764 ( 181) hydrogen bonds : angle 9.33386 ( 444) SS BOND : bond 0.00803 ( 10) SS BOND : angle 2.67776 ( 20) covalent geometry : bond 0.00887 ( 7375) covalent geometry : angle 1.05984 (10035) *********************** 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 : 0.814 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: 0.2044 time to fit residues: 45.0083 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 : 0.815 ------------------------------------------------------------------------------- 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 = 37)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.108706 restraints weight = 17467.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.111373 restraints weight = 10111.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.113156 restraints weight = 6829.188| |-----------------------------------------------------------------------------| 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 7392 Z= 0.164 Angle : 0.837 13.699 10076 Z= 0.417 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00654 ( 4) link_NAG-ASN : angle 5.48064 ( 12) link_BETA1-4 : bond 0.00805 ( 3) link_BETA1-4 : angle 3.73145 ( 9) hydrogen bonds : bond 0.03985 ( 181) hydrogen bonds : angle 7.86809 ( 444) SS BOND : bond 0.00411 ( 10) SS BOND : angle 1.41953 ( 20) covalent geometry : bond 0.00364 ( 7375) covalent geometry : angle 0.80639 (10035) *********************** 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 : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 VAL cc_start: 0.7494 (p) cc_final: 0.6607 (p) REVERT: A 206 LYS cc_start: 0.7955 (ptmm) cc_final: 0.7709 (ptmm) REVERT: B 360 ASN cc_start: 0.8414 (t0) cc_final: 0.8196 (t0) REVERT: B 466 ARG cc_start: 0.7622 (ttp80) cc_final: 0.6652 (ttt-90) REVERT: H 87 GLU cc_start: 0.8443 (pm20) cc_final: 0.8166 (pm20) REVERT: H 166 PHE cc_start: 0.7572 (t80) cc_final: 0.7328 (t80) REVERT: L 4 MET cc_start: 0.6675 (tpt) cc_final: 0.6167 (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: 0.1902 time to fit residues: 41.3127 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 : 0.844 ------------------------------------------------------------------------------- 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: 6.9990 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: 4.9990 chunk 41 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 = 0.3838 r_free = 0.3838 target = 0.127995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.105364 restraints weight = 17892.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.107783 restraints weight = 10539.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.109499 restraints weight = 7293.559| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 7392 Z= 0.285 Angle : 0.906 14.661 10076 Z= 0.455 Chirality : 0.053 0.326 1116 Planarity : 0.006 0.062 1286 Dihedral : 8.107 53.316 1130 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 22.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.63 % Favored : 83.37 % Rotamer: Outliers : 0.13 % Allowed : 5.84 % Favored : 94.04 % 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: -3.49 (0.27), residues: 896 helix: -3.24 (0.63), residues: 39 sheet: -1.57 (0.30), residues: 301 loop : -2.82 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP H 174 HIS 0.004 0.001 HIS H 220 PHE 0.026 0.003 PHE B 347 TYR 0.032 0.003 TYR L 192 ARG 0.005 0.001 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00822 ( 4) link_NAG-ASN : angle 6.01287 ( 12) link_BETA1-4 : bond 0.00630 ( 3) link_BETA1-4 : angle 3.28402 ( 9) hydrogen bonds : bond 0.04485 ( 181) hydrogen bonds : angle 8.00595 ( 444) SS BOND : bond 0.00547 ( 10) SS BOND : angle 1.50577 ( 20) covalent geometry : bond 0.00645 ( 7375) covalent geometry : angle 0.87548 (10035) *********************** 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 : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 LYS cc_start: 0.8229 (ptmm) cc_final: 0.7729 (ptmm) REVERT: A 224 GLU cc_start: 0.7740 (pm20) cc_final: 0.7428 (pm20) REVERT: B 466 ARG cc_start: 0.7709 (ttp80) cc_final: 0.6615 (ttt-90) REVERT: B 487 ASN cc_start: 0.6026 (t0) cc_final: 0.5820 (t0) REVERT: H 31 ASP cc_start: 0.6999 (m-30) cc_final: 0.6697 (m-30) REVERT: H 87 GLU cc_start: 0.8456 (pm20) cc_final: 0.8132 (pm20) REVERT: L 18 ARG cc_start: 0.8408 (tpt90) cc_final: 0.8165 (tpt90) REVERT: L 82 ASP cc_start: 0.8125 (m-30) cc_final: 0.7309 (m-30) REVERT: L 138 ASN cc_start: 0.8804 (m110) cc_final: 0.8091 (m110) outliers start: 1 outliers final: 0 residues processed: 152 average time/residue: 0.2079 time to fit residues: 41.5361 Evaluate side-chains 122 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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: 2.9990 chunk 71 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 38 optimal weight: 0.0670 chunk 52 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 overall best weight: 1.1922 ------------------------------------------------------------------------------- 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 82 ASN H 191 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 = 0.3919 r_free = 0.3919 target = 0.134184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.111120 restraints weight = 17424.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.113888 restraints weight = 9953.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.115729 restraints weight = 6671.870| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7392 Z= 0.151 Angle : 0.795 14.507 10076 Z= 0.398 Chirality : 0.050 0.281 1116 Planarity : 0.005 0.050 1286 Dihedral : 7.280 47.948 1130 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.16 % Favored : 89.84 % Rotamer: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % 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: -3.12 (0.27), residues: 896 helix: -3.89 (0.67), residues: 27 sheet: -1.29 (0.30), residues: 301 loop : -2.56 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 148 HIS 0.004 0.001 HIS H 35 PHE 0.018 0.002 PHE B 497 TYR 0.016 0.002 TYR L 192 ARG 0.007 0.001 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00689 ( 4) link_NAG-ASN : angle 5.50584 ( 12) link_BETA1-4 : bond 0.00716 ( 3) link_BETA1-4 : angle 3.21109 ( 9) hydrogen bonds : bond 0.03713 ( 181) hydrogen bonds : angle 7.52893 ( 444) SS BOND : bond 0.00727 ( 10) SS BOND : angle 1.17729 ( 20) covalent geometry : bond 0.00337 ( 7375) covalent geometry : angle 0.76569 (10035) *********************** 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 171 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 405 ASP cc_start: 0.8066 (p0) cc_final: 0.7568 (p0) REVERT: B 487 ASN cc_start: 0.5591 (t0) cc_final: 0.5330 (t0) REVERT: H 19 ARG cc_start: 0.8450 (ttp80) cc_final: 0.8113 (ttp80) REVERT: H 31 ASP cc_start: 0.6993 (m-30) cc_final: 0.6466 (m-30) REVERT: H 87 GLU cc_start: 0.8507 (pm20) cc_final: 0.8136 (pm20) REVERT: H 181 SER cc_start: 0.7662 (t) cc_final: 0.7270 (m) REVERT: L 138 ASN cc_start: 0.8646 (m110) cc_final: 0.8134 (m110) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.1960 time to fit residues: 44.6941 Evaluate side-chains 134 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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: 7.9990 chunk 54 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 62 optimal weight: 20.0000 chunk 8 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 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 = 0.3884 r_free = 0.3884 target = 0.131412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.108577 restraints weight = 17304.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.111120 restraints weight = 10254.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.112801 restraints weight = 7018.751| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 7392 Z= 0.208 Angle : 0.826 14.290 10076 Z= 0.412 Chirality : 0.050 0.281 1116 Planarity : 0.006 0.050 1286 Dihedral : 7.345 45.970 1130 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 19.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.96 % Favored : 85.04 % Rotamer: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % 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: -3.30 (0.71), residues: 33 sheet: -1.17 (0.32), residues: 267 loop : -2.62 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP H 174 HIS 0.004 0.001 HIS L 189 PHE 0.028 0.002 PHE A 58 TYR 0.017 0.002 TYR L 91 ARG 0.003 0.000 ARG H 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00651 ( 4) link_NAG-ASN : angle 5.67520 ( 12) link_BETA1-4 : bond 0.00540 ( 3) link_BETA1-4 : angle 2.99857 ( 9) hydrogen bonds : bond 0.03849 ( 181) hydrogen bonds : angle 7.54778 ( 444) SS BOND : bond 0.00673 ( 10) SS BOND : angle 1.54015 ( 20) covalent geometry : bond 0.00474 ( 7375) covalent geometry : angle 0.79583 (10035) *********************** 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 155 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 466 ARG cc_start: 0.7797 (ttp80) cc_final: 0.6742 (ttt180) REVERT: B 487 ASN cc_start: 0.6080 (t0) cc_final: 0.5803 (t0) REVERT: H 19 ARG cc_start: 0.8450 (ttp80) cc_final: 0.7872 (ttp80) REVERT: H 31 ASP cc_start: 0.7011 (m-30) cc_final: 0.6572 (m-30) REVERT: H 87 GLU cc_start: 0.8514 (pm20) cc_final: 0.8139 (pm20) REVERT: H 181 SER cc_start: 0.7718 (t) cc_final: 0.7328 (m) REVERT: L 82 ASP cc_start: 0.7905 (m-30) cc_final: 0.7508 (m-30) REVERT: L 138 ASN cc_start: 0.8674 (m110) cc_final: 0.7931 (m110) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.1907 time to fit residues: 39.3816 Evaluate side-chains 123 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.788 ------------------------------------------------------------------------------- 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: 6.9990 chunk 86 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 360 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.129780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.106826 restraints weight = 17497.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.109167 restraints weight = 10325.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.110894 restraints weight = 7185.445| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 7392 Z= 0.260 Angle : 0.884 14.189 10076 Z= 0.445 Chirality : 0.053 0.331 1116 Planarity : 0.006 0.056 1286 Dihedral : 7.710 45.861 1130 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 21.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.07 % Favored : 84.93 % Rotamer: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % 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: -3.31 (0.27), residues: 896 helix: -3.37 (0.58), residues: 45 sheet: -1.35 (0.32), residues: 273 loop : -2.68 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 148 HIS 0.005 0.001 HIS L 189 PHE 0.019 0.003 PHE B 497 TYR 0.022 0.003 TYR L 91 ARG 0.003 0.001 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00710 ( 4) link_NAG-ASN : angle 5.84385 ( 12) link_BETA1-4 : bond 0.00474 ( 3) link_BETA1-4 : angle 2.94976 ( 9) hydrogen bonds : bond 0.04017 ( 181) hydrogen bonds : angle 7.73946 ( 444) SS BOND : bond 0.00525 ( 10) SS BOND : angle 2.05610 ( 20) covalent geometry : bond 0.00592 ( 7375) covalent geometry : angle 0.85315 (10035) *********************** 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 151 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLU cc_start: 0.7804 (pm20) cc_final: 0.7597 (pm20) REVERT: B 466 ARG cc_start: 0.7530 (ttp80) cc_final: 0.6601 (ttt180) REVERT: B 487 ASN cc_start: 0.5975 (t0) cc_final: 0.5572 (t0) REVERT: H 19 ARG cc_start: 0.8478 (ttp80) cc_final: 0.7967 (ttp80) REVERT: H 31 ASP cc_start: 0.7084 (m-30) cc_final: 0.6705 (m-30) REVERT: H 87 GLU cc_start: 0.8540 (pm20) cc_final: 0.8187 (pm20) REVERT: L 21 ILE cc_start: 0.6458 (tp) cc_final: 0.5932 (mp) REVERT: L 91 TYR cc_start: 0.6749 (p90) cc_final: 0.6497 (p90) REVERT: L 132 VAL cc_start: 0.8422 (t) cc_final: 0.8095 (m) REVERT: L 138 ASN cc_start: 0.8761 (m110) cc_final: 0.8043 (m110) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.2032 time to fit residues: 40.7592 Evaluate side-chains 127 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.753 ------------------------------------------------------------------------------- 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: 4.9990 chunk 20 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 62 optimal weight: 0.0170 chunk 11 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 47 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 overall best weight: 2.4026 ------------------------------------------------------------------------------- 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** L 79 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 = 0.3906 r_free = 0.3906 target = 0.132750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.109538 restraints weight = 17371.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.112148 restraints weight = 10140.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.113938 restraints weight = 6896.892| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7392 Z= 0.172 Angle : 0.828 13.861 10076 Z= 0.411 Chirality : 0.050 0.296 1116 Planarity : 0.006 0.048 1286 Dihedral : 7.206 47.117 1130 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.17 % Favored : 86.83 % Rotamer: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % 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: -3.04 (0.28), residues: 896 helix: -3.19 (0.65), residues: 39 sheet: -1.10 (0.32), residues: 283 loop : -2.56 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP H 174 HIS 0.004 0.001 HIS H 35 PHE 0.023 0.002 PHE B 347 TYR 0.029 0.002 TYR B 365 ARG 0.007 0.001 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00670 ( 4) link_NAG-ASN : angle 5.44268 ( 12) link_BETA1-4 : bond 0.00751 ( 3) link_BETA1-4 : angle 2.96105 ( 9) hydrogen bonds : bond 0.03700 ( 181) hydrogen bonds : angle 7.42916 ( 444) SS BOND : bond 0.00396 ( 10) SS BOND : angle 1.78497 ( 20) covalent geometry : bond 0.00391 ( 7375) covalent geometry : angle 0.79901 (10035) *********************** 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 160 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLU cc_start: 0.7787 (pm20) cc_final: 0.7406 (pm20) REVERT: B 402 ILE cc_start: 0.8790 (pt) cc_final: 0.8449 (pt) REVERT: B 403 ARG cc_start: 0.8121 (ptm-80) cc_final: 0.7488 (ptm160) REVERT: B 406 GLU cc_start: 0.8141 (pm20) cc_final: 0.7832 (pm20) REVERT: B 466 ARG cc_start: 0.7339 (ttp80) cc_final: 0.6926 (ptm160) REVERT: B 487 ASN cc_start: 0.5757 (t0) cc_final: 0.5370 (t0) REVERT: H 87 GLU cc_start: 0.8558 (pm20) cc_final: 0.8188 (pm20) REVERT: H 181 SER cc_start: 0.7636 (t) cc_final: 0.7291 (m) REVERT: L 21 ILE cc_start: 0.6546 (tp) cc_final: 0.5886 (mp) REVERT: L 91 TYR cc_start: 0.6773 (p90) cc_final: 0.6465 (p90) REVERT: L 132 VAL cc_start: 0.8404 (t) cc_final: 0.8042 (m) REVERT: L 138 ASN cc_start: 0.8687 (m110) cc_final: 0.7927 (m110) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.2034 time to fit residues: 43.8251 Evaluate side-chains 133 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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: 6.9990 chunk 71 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 6 optimal weight: 0.1980 chunk 5 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 67 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3948 r_free = 0.3948 target = 0.136260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.112564 restraints weight = 17034.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.115198 restraints weight = 9734.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.117146 restraints weight = 6579.580| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7392 Z= 0.144 Angle : 0.789 13.701 10076 Z= 0.394 Chirality : 0.050 0.266 1116 Planarity : 0.006 0.049 1286 Dihedral : 6.758 47.527 1130 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.50 % Favored : 88.50 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % 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 (0.28), residues: 896 helix: -3.36 (0.60), residues: 39 sheet: -0.90 (0.32), residues: 281 loop : -2.48 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 148 HIS 0.006 0.001 HIS L 189 PHE 0.027 0.002 PHE B 497 TYR 0.020 0.002 TYR H 78 ARG 0.007 0.001 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00721 ( 4) link_NAG-ASN : angle 5.17113 ( 12) link_BETA1-4 : bond 0.00551 ( 3) link_BETA1-4 : angle 2.87761 ( 9) hydrogen bonds : bond 0.03565 ( 181) hydrogen bonds : angle 7.14699 ( 444) SS BOND : bond 0.00477 ( 10) SS BOND : angle 1.48267 ( 20) covalent geometry : bond 0.00327 ( 7375) covalent geometry : angle 0.76206 (10035) *********************** 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 168 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 406 GLU cc_start: 0.8144 (pm20) cc_final: 0.7341 (pm20) REVERT: B 466 ARG cc_start: 0.7411 (ttp80) cc_final: 0.7008 (ptm160) REVERT: B 487 ASN cc_start: 0.5716 (t0) cc_final: 0.5452 (t0) REVERT: H 87 GLU cc_start: 0.8533 (pm20) cc_final: 0.8181 (pm20) REVERT: H 224 ASN cc_start: 0.8218 (m-40) cc_final: 0.7323 (p0) REVERT: L 91 TYR cc_start: 0.6688 (p90) cc_final: 0.6314 (p90) REVERT: L 124 GLN cc_start: 0.6764 (tp40) cc_final: 0.6515 (tp-100) REVERT: L 132 VAL cc_start: 0.8297 (t) cc_final: 0.8034 (m) REVERT: L 138 ASN cc_start: 0.8648 (m110) cc_final: 0.7962 (m110) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1998 time to fit residues: 45.0535 Evaluate side-chains 140 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.815 ------------------------------------------------------------------------------- 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: 0.9980 chunk 5 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 46 optimal weight: 0.0970 chunk 73 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 L 189 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.138156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.114271 restraints weight = 17110.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.117138 restraints weight = 9717.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.119020 restraints weight = 6479.508| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7392 Z= 0.143 Angle : 0.803 13.335 10076 Z= 0.399 Chirality : 0.051 0.270 1116 Planarity : 0.005 0.049 1286 Dihedral : 6.585 47.750 1130 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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: -2.83 (0.28), residues: 896 helix: -3.20 (0.63), residues: 39 sheet: -0.98 (0.31), residues: 291 loop : -2.39 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP H 174 HIS 0.005 0.001 HIS L 189 PHE 0.033 0.002 PHE B 497 TYR 0.021 0.002 TYR L 140 ARG 0.007 0.001 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00676 ( 4) link_NAG-ASN : angle 5.03450 ( 12) link_BETA1-4 : bond 0.00674 ( 3) link_BETA1-4 : angle 2.90734 ( 9) hydrogen bonds : bond 0.03721 ( 181) hydrogen bonds : angle 7.02450 ( 444) SS BOND : bond 0.00309 ( 10) SS BOND : angle 1.96540 ( 20) covalent geometry : bond 0.00324 ( 7375) covalent geometry : angle 0.77580 (10035) *********************** 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 172 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 402 ILE cc_start: 0.8717 (pt) cc_final: 0.8368 (pt) REVERT: B 403 ARG cc_start: 0.7926 (ptm-80) cc_final: 0.7504 (ptm-80) REVERT: B 406 GLU cc_start: 0.7944 (pm20) cc_final: 0.6660 (pm20) REVERT: B 466 ARG cc_start: 0.7416 (ttp80) cc_final: 0.6961 (ptm160) REVERT: B 487 ASN cc_start: 0.6044 (t0) cc_final: 0.5763 (t0) REVERT: B 505 TYR cc_start: 0.7096 (m-80) cc_final: 0.6495 (m-80) REVERT: B 516 GLU cc_start: 0.7266 (tm-30) cc_final: 0.6927 (tm-30) REVERT: H 87 GLU cc_start: 0.8530 (pm20) cc_final: 0.8182 (pm20) REVERT: H 190 LEU cc_start: 0.8205 (tp) cc_final: 0.7661 (mp) REVERT: H 224 ASN cc_start: 0.8129 (m-40) cc_final: 0.7292 (p0) REVERT: L 91 TYR cc_start: 0.6674 (p90) cc_final: 0.6256 (p90) REVERT: L 132 VAL cc_start: 0.8402 (t) cc_final: 0.8106 (m) REVERT: L 138 ASN cc_start: 0.8637 (m110) cc_final: 0.7979 (m110) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.2160 time to fit residues: 48.8801 Evaluate side-chains 130 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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: 6.9990 chunk 19 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 2 optimal weight: 0.4980 chunk 68 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- 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** L 189 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.135435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.111250 restraints weight = 17780.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.113995 restraints weight = 10171.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.115825 restraints weight = 6844.443| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7392 Z= 0.171 Angle : 0.801 13.484 10076 Z= 0.400 Chirality : 0.051 0.274 1116 Planarity : 0.005 0.061 1286 Dihedral : 6.794 47.285 1130 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.39 % Favored : 87.61 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: -2.83 (0.28), residues: 896 helix: -3.53 (0.56), residues: 39 sheet: -0.91 (0.32), residues: 287 loop : -2.40 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP L 35 HIS 0.006 0.001 HIS L 189 PHE 0.034 0.002 PHE B 497 TYR 0.029 0.002 TYR H 78 ARG 0.010 0.001 ARG H 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00661 ( 4) link_NAG-ASN : angle 5.20801 ( 12) link_BETA1-4 : bond 0.00548 ( 3) link_BETA1-4 : angle 2.82423 ( 9) hydrogen bonds : bond 0.03694 ( 181) hydrogen bonds : angle 6.95343 ( 444) SS BOND : bond 0.00353 ( 10) SS BOND : angle 1.79244 ( 20) covalent geometry : bond 0.00396 ( 7375) covalent geometry : angle 0.77376 (10035) ********************** 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 165 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 402 ILE cc_start: 0.8723 (pt) cc_final: 0.8445 (pt) REVERT: B 403 ARG cc_start: 0.7734 (ptm-80) cc_final: 0.7357 (ptm160) REVERT: B 466 ARG cc_start: 0.7650 (ttp80) cc_final: 0.6861 (ptm160) REVERT: B 487 ASN cc_start: 0.5930 (t0) cc_final: 0.5575 (t0) REVERT: B 505 TYR cc_start: 0.7121 (m-80) cc_final: 0.6032 (m-80) REVERT: B 516 GLU cc_start: 0.7275 (tm-30) cc_final: 0.6920 (tm-30) REVERT: H 87 GLU cc_start: 0.8523 (pm20) cc_final: 0.8175 (pm20) REVERT: H 186 PHE cc_start: 0.8087 (m-80) cc_final: 0.7635 (m-10) REVERT: H 190 LEU cc_start: 0.8343 (tp) cc_final: 0.7840 (mp) REVERT: H 224 ASN cc_start: 0.8201 (m-40) cc_final: 0.7398 (p0) REVERT: L 91 TYR cc_start: 0.6699 (p90) cc_final: 0.6479 (p90) REVERT: L 132 VAL cc_start: 0.8418 (t) cc_final: 0.8129 (m) REVERT: L 138 ASN cc_start: 0.8774 (m110) cc_final: 0.8041 (m110) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.1898 time to fit residues: 42.0735 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 : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.253 > 50: distance: 3 - 7: 22.726 distance: 7 - 8: 24.456 distance: 8 - 9: 24.320 distance: 8 - 11: 40.818 distance: 9 - 10: 9.862 distance: 9 - 15: 31.858 distance: 11 - 12: 19.565 distance: 12 - 13: 39.192 distance: 12 - 14: 47.039 distance: 15 - 16: 44.340 distance: 16 - 17: 19.441 distance: 16 - 19: 5.720 distance: 17 - 18: 26.704 distance: 17 - 21: 34.209 distance: 19 - 20: 26.812 distance: 21 - 22: 45.165 distance: 22 - 25: 8.551 distance: 23 - 26: 40.484 distance: 26 - 27: 22.977 distance: 27 - 28: 29.770 distance: 27 - 30: 18.210 distance: 28 - 29: 26.126 distance: 28 - 32: 25.223 distance: 30 - 31: 30.244 distance: 32 - 33: 8.654 distance: 33 - 34: 28.392 distance: 33 - 36: 13.219 distance: 34 - 35: 40.073 distance: 34 - 39: 11.691 distance: 36 - 37: 41.007 distance: 36 - 38: 48.291 distance: 39 - 40: 15.598 distance: 40 - 41: 30.089 distance: 41 - 42: 11.318 distance: 41 - 43: 18.291 distance: 43 - 44: 21.845 distance: 44 - 45: 10.132 distance: 44 - 47: 26.301 distance: 45 - 46: 7.389 distance: 45 - 51: 4.939 distance: 47 - 48: 11.153 distance: 48 - 49: 17.585 distance: 48 - 50: 8.458 distance: 51 - 52: 14.733 distance: 52 - 53: 11.846 distance: 52 - 55: 12.076 distance: 53 - 54: 29.066 distance: 53 - 62: 13.392 distance: 55 - 56: 10.278 distance: 56 - 57: 23.158 distance: 57 - 58: 11.684 distance: 58 - 59: 10.713 distance: 59 - 60: 3.539 distance: 59 - 61: 11.525 distance: 62 - 63: 35.835 distance: 62 - 99: 16.764 distance: 63 - 64: 5.125 distance: 63 - 66: 17.171 distance: 64 - 65: 18.695 distance: 64 - 69: 13.584 distance: 65 - 96: 5.138 distance: 66 - 67: 8.727 distance: 66 - 68: 17.418 distance: 69 - 70: 38.259 distance: 70 - 71: 20.841 distance: 70 - 73: 38.515 distance: 71 - 72: 18.095 distance: 71 - 76: 11.531 distance: 73 - 74: 40.056 distance: 73 - 75: 10.125