Starting phenix.real_space_refine on Sun Apr 27 07:51:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ez8_28730/04_2025/8ez8_28730.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ez8_28730/04_2025/8ez8_28730.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ez8_28730/04_2025/8ez8_28730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ez8_28730/04_2025/8ez8_28730.map" model { file = "/net/cci-nas-00/data/ceres_data/8ez8_28730/04_2025/8ez8_28730.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ez8_28730/04_2025/8ez8_28730.cif" } resolution = 2.78 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= 0.002 sd= 0.068 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 28 5.16 5 C 2997 2.51 5 N 838 2.21 5 O 984 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 4847 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 951 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain: "L" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 786 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2996 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 13, 'TRANS': 371} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'MAN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.00, per 1000 atoms: 0.83 Number of scatterers: 4847 At special positions: 0 Unit cell: (76.32, 96.46, 92.22, 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 28 16.00 O 984 8.00 N 838 7.00 C 2997 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 175 " - pdb=" SG CYS A 193 " distance=2.03 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 337 " distance=2.04 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 447 " distance=2.03 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 ALPHA1-2 " MAN B 4 " - " MAN B 5 " ALPHA1-3 " BMA B 3 " - " MAN B 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG A 502 " - " ASN A 146 " " NAG A 503 " - " ASN A 234 " " NAG A 504 " - " ASN A 329 " " NAG B 1 " - " ASN A 200 " Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 554.1 milliseconds 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1106 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 11 sheets defined 4.2% alpha, 41.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 4.007A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.637A pdb=" N GLU L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 110 removed outlier: 3.664A pdb=" N ALA A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.573A pdb=" N SER A 145 " --> pdb=" O ASN A 142 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASN A 146 " --> pdb=" O GLY A 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 142 through 146' Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.252A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.884A pdb=" N SER L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.884A pdb=" N SER L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 16 through 24 removed outlier: 4.127A pdb=" N GLN L 17 " --> pdb=" O GLY L 77 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY L 77 " --> pdb=" O GLN L 17 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 96 through 102 removed outlier: 3.587A pdb=" N GLY A 96 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL A 445 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LYS A 102 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE A 443 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ARG A 420 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 115 through 125 removed outlier: 4.647A pdb=" N TRP A 115 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N THR A 138 " --> pdb=" O TRP A 115 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N THR A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLN A 136 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N CYS A 175 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N MET A 160 " --> pdb=" O GLN A 173 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N GLN A 173 " --> pdb=" O MET A 160 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 179 through 184 removed outlier: 3.566A pdb=" N SER A 179 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N TYR A 207 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LEU A 211 " --> pdb=" O TYR A 207 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 231 through 233 removed outlier: 3.751A pdb=" N VAL A 231 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N THR A 252 " --> pdb=" O PRO A 267 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE A 254 " --> pdb=" O THR A 265 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR A 265 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N PHE A 256 " --> pdb=" O VAL A 263 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 279 through 283 Processing sheet with id=AB2, first strand: chain 'A' and resid 352 through 356 removed outlier: 4.703A pdb=" N TRP A 352 " --> pdb=" O GLY A 363 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY A 363 " --> pdb=" O TRP A 352 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N SER A 372 " --> pdb=" O ASP A 399 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ASP A 399 " --> pdb=" O SER A 372 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N TYR A 374 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS A 378 " --> pdb=" O ASN A 393 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ASN A 393 " --> pdb=" O LYS A 378 " (cutoff:3.500A) 156 hydrogen bonds defined for protein. 414 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: 1.74 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1593 1.35 - 1.47: 1277 1.47 - 1.59: 2051 1.59 - 1.71: 0 1.71 - 1.83: 34 Bond restraints: 4955 Sorted by residual: bond pdb=" C1 MAN B 4 " pdb=" C2 MAN B 4 " ideal model delta sigma weight residual 1.526 1.558 -0.032 2.00e-02 2.50e+03 2.56e+00 bond pdb=" C1 MAN B 4 " pdb=" O5 MAN B 4 " ideal model delta sigma weight residual 1.399 1.430 -0.031 2.00e-02 2.50e+03 2.33e+00 bond pdb=" C5 MAN B 4 " pdb=" O5 MAN B 4 " ideal model delta sigma weight residual 1.418 1.448 -0.030 2.00e-02 2.50e+03 2.31e+00 bond pdb=" C1 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.18e+00 bond pdb=" C5 MAN B 5 " pdb=" O5 MAN B 5 " ideal model delta sigma weight residual 1.418 1.446 -0.028 2.00e-02 2.50e+03 2.01e+00 ... (remaining 4950 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 6459 1.35 - 2.69: 207 2.69 - 4.04: 46 4.04 - 5.38: 11 5.38 - 6.73: 6 Bond angle restraints: 6729 Sorted by residual: angle pdb=" C ARG A 430 " pdb=" N LYS A 431 " pdb=" CA LYS A 431 " ideal model delta sigma weight residual 121.70 126.88 -5.18 1.80e+00 3.09e-01 8.29e+00 angle pdb=" CA CYS A 230 " pdb=" CB CYS A 230 " pdb=" SG CYS A 230 " ideal model delta sigma weight residual 114.40 120.11 -5.71 2.30e+00 1.89e-01 6.16e+00 angle pdb=" C HIS A 336 " pdb=" N CYS A 337 " pdb=" CA CYS A 337 " ideal model delta sigma weight residual 122.07 125.45 -3.38 1.43e+00 4.89e-01 5.59e+00 angle pdb=" C SER L 50 " pdb=" N ASN L 51 " pdb=" CA ASN L 51 " ideal model delta sigma weight residual 121.54 125.70 -4.16 1.91e+00 2.74e-01 4.75e+00 angle pdb=" C3 MAN B 4 " pdb=" C2 MAN B 4 " pdb=" O2 MAN B 4 " ideal model delta sigma weight residual 111.77 105.25 6.52 3.00e+00 1.11e-01 4.72e+00 ... (remaining 6724 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.55: 2711 21.55 - 43.09: 279 43.09 - 64.64: 43 64.64 - 86.19: 13 86.19 - 107.73: 6 Dihedral angle restraints: 3052 sinusoidal: 1307 harmonic: 1745 Sorted by residual: dihedral pdb=" CB CYS A 92 " pdb=" SG CYS A 92 " pdb=" SG CYS A 417 " pdb=" CB CYS A 417 " ideal model delta sinusoidal sigma weight residual 93.00 37.74 55.26 1 1.00e+01 1.00e-02 4.13e+01 dihedral pdb=" CA ALA A 177 " pdb=" C ALA A 177 " pdb=" N TRP A 178 " pdb=" CA TRP A 178 " ideal model delta harmonic sigma weight residual 180.00 158.60 21.40 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 58.52 34.48 1 1.00e+01 1.00e-02 1.69e+01 ... (remaining 3049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 592 0.053 - 0.105: 123 0.105 - 0.158: 35 0.158 - 0.210: 2 0.210 - 0.263: 1 Chirality restraints: 753 Sorted by residual: chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" C1 NAG A 504 " pdb=" ND2 ASN A 329 " pdb=" C2 NAG A 504 " pdb=" O5 NAG A 504 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 7.73e-01 chirality pdb=" C2 MAN B 4 " pdb=" C1 MAN B 4 " pdb=" C3 MAN B 4 " pdb=" O2 MAN B 4 " both_signs ideal model delta sigma weight residual False 2.52 2.67 -0.16 2.00e-01 2.50e+01 6.31e-01 ... (remaining 750 not shown) Planarity restraints: 866 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO L 7 " 0.032 5.00e-02 4.00e+02 4.96e-02 3.94e+00 pdb=" N PRO L 8 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 78 " -0.010 2.00e-02 2.50e+03 7.48e-03 9.80e-01 pdb=" CG PHE H 78 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 PHE H 78 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE H 78 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE H 78 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE H 78 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE H 78 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN H 39 " 0.005 2.00e-02 2.50e+03 9.72e-03 9.44e-01 pdb=" C GLN H 39 " -0.017 2.00e-02 2.50e+03 pdb=" O GLN H 39 " 0.006 2.00e-02 2.50e+03 pdb=" N PRO H 40 " 0.006 2.00e-02 2.50e+03 ... (remaining 863 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 50 2.53 - 3.13: 3649 3.13 - 3.72: 7634 3.72 - 4.31: 11502 4.31 - 4.90: 19416 Nonbonded interactions: 42251 Sorted by model distance: nonbonded pdb=" NE ARG A 403 " pdb=" OE1 GLN A 432 " model vdw 1.943 3.120 nonbonded pdb=" CZ ARG A 403 " pdb=" OE1 GLN A 432 " model vdw 2.202 3.270 nonbonded pdb=" O VAL A 317 " pdb=" OG SER A 335 " model vdw 2.245 3.040 nonbonded pdb=" OG SER A 279 " pdb=" O GLY A 351 " model vdw 2.249 3.040 nonbonded pdb=" OH TYR A 121 " pdb=" OG SER A 182 " model vdw 2.258 3.040 ... (remaining 42246 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.340 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.770 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 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 : 0.004 0.033 4974 Z= 0.168 Angle : 0.636 6.728 6775 Z= 0.321 Chirality : 0.048 0.263 753 Planarity : 0.003 0.050 862 Dihedral : 17.323 107.734 1913 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.07 % Favored : 95.77 % Rotamer: Outliers : 1.89 % Allowed : 26.65 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.35), residues: 615 helix: -1.81 (1.45), residues: 12 sheet: 0.00 (0.34), residues: 226 loop : -0.45 (0.34), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 34 HIS 0.004 0.001 HIS A 347 PHE 0.017 0.002 PHE H 78 TYR 0.013 0.001 TYR A 121 ARG 0.003 0.000 ARG H 43 Details of bonding type rmsd link_NAG-ASN : bond 0.00270 ( 4) link_NAG-ASN : angle 2.19548 ( 12) link_BETA1-4 : bond 0.00468 ( 2) link_BETA1-4 : angle 1.93335 ( 6) link_ALPHA1-2 : bond 0.00452 ( 1) link_ALPHA1-2 : angle 1.88553 ( 3) link_ALPHA1-3 : bond 0.00545 ( 1) link_ALPHA1-3 : angle 1.15005 ( 3) hydrogen bonds : bond 0.12395 ( 152) hydrogen bonds : angle 7.95801 ( 414) SS BOND : bond 0.00306 ( 11) SS BOND : angle 1.48614 ( 22) covalent geometry : bond 0.00351 ( 4955) covalent geometry : angle 0.62121 ( 6729) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.544 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 80 average time/residue: 0.9388 time to fit residues: 79.2676 Evaluate side-chains 79 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 28 optimal weight: 0.1980 chunk 35 optimal weight: 0.1980 chunk 54 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.115324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.093424 restraints weight = 6342.734| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.05 r_work: 0.3146 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.0616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4974 Z= 0.119 Angle : 0.541 7.389 6775 Z= 0.283 Chirality : 0.046 0.158 753 Planarity : 0.004 0.046 862 Dihedral : 9.274 68.763 863 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.58 % Favored : 96.26 % Rotamer: Outliers : 2.65 % Allowed : 25.90 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.35), residues: 615 helix: -1.69 (1.48), residues: 12 sheet: -0.13 (0.34), residues: 230 loop : -0.38 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 34 HIS 0.002 0.001 HIS A 336 PHE 0.015 0.002 PHE H 78 TYR 0.010 0.001 TYR H 50 ARG 0.003 0.000 ARG A 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00213 ( 4) link_NAG-ASN : angle 2.08865 ( 12) link_BETA1-4 : bond 0.00328 ( 2) link_BETA1-4 : angle 2.06916 ( 6) link_ALPHA1-2 : bond 0.00391 ( 1) link_ALPHA1-2 : angle 1.79805 ( 3) link_ALPHA1-3 : bond 0.00930 ( 1) link_ALPHA1-3 : angle 2.23244 ( 3) hydrogen bonds : bond 0.02905 ( 152) hydrogen bonds : angle 6.60959 ( 414) SS BOND : bond 0.00172 ( 11) SS BOND : angle 0.89521 ( 22) covalent geometry : bond 0.00261 ( 4955) covalent geometry : angle 0.52569 ( 6729) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.710 Fit side-chains revert: symmetry clash REVERT: A 431 LYS cc_start: 0.7952 (mmtt) cc_final: 0.7740 (tppt) outliers start: 14 outliers final: 5 residues processed: 88 average time/residue: 0.9854 time to fit residues: 91.6562 Evaluate side-chains 76 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 204 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 47 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 42 optimal weight: 0.0980 chunk 26 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 13 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82AASN L 37 GLN ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** 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 = 0.3548 r_free = 0.3548 target = 0.116126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.093920 restraints weight = 6357.735| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.06 r_work: 0.3154 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4974 Z= 0.113 Angle : 0.518 5.464 6775 Z= 0.271 Chirality : 0.046 0.154 753 Planarity : 0.003 0.042 862 Dihedral : 7.820 53.284 854 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.41 % Favored : 96.42 % Rotamer: Outliers : 2.46 % Allowed : 25.71 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.35), residues: 615 helix: -1.60 (1.48), residues: 12 sheet: -0.13 (0.33), residues: 237 loop : -0.27 (0.35), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 34 HIS 0.002 0.001 HIS A 336 PHE 0.017 0.002 PHE H 78 TYR 0.010 0.001 TYR H 50 ARG 0.003 0.000 ARG A 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00205 ( 4) link_NAG-ASN : angle 2.02715 ( 12) link_BETA1-4 : bond 0.00482 ( 2) link_BETA1-4 : angle 1.86051 ( 6) link_ALPHA1-2 : bond 0.00488 ( 1) link_ALPHA1-2 : angle 1.67676 ( 3) link_ALPHA1-3 : bond 0.01243 ( 1) link_ALPHA1-3 : angle 1.63523 ( 3) hydrogen bonds : bond 0.02728 ( 152) hydrogen bonds : angle 6.20749 ( 414) SS BOND : bond 0.00167 ( 11) SS BOND : angle 0.78208 ( 22) covalent geometry : bond 0.00250 ( 4955) covalent geometry : angle 0.50491 ( 6729) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: A 302 ILE cc_start: 0.8670 (mp) cc_final: 0.8462 (mp) outliers start: 13 outliers final: 9 residues processed: 88 average time/residue: 1.0016 time to fit residues: 93.1259 Evaluate side-chains 84 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 229 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 1 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 20 optimal weight: 9.9990 chunk 36 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82AASN L 37 GLN ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 GLN ** A 441 ASN ** 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 = 0.3518 r_free = 0.3518 target = 0.114070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.091400 restraints weight = 6412.980| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.07 r_work: 0.3107 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4974 Z= 0.183 Angle : 0.565 8.454 6775 Z= 0.291 Chirality : 0.047 0.181 753 Planarity : 0.004 0.038 862 Dihedral : 7.421 54.685 854 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.90 % Favored : 95.93 % Rotamer: Outliers : 4.16 % Allowed : 24.39 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.35), residues: 615 helix: -1.63 (1.48), residues: 12 sheet: -0.13 (0.33), residues: 235 loop : -0.32 (0.35), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 34 HIS 0.003 0.001 HIS A 336 PHE 0.015 0.002 PHE H 78 TYR 0.014 0.001 TYR A 121 ARG 0.003 0.000 ARG A 292 Details of bonding type rmsd link_NAG-ASN : bond 0.00306 ( 4) link_NAG-ASN : angle 2.32833 ( 12) link_BETA1-4 : bond 0.00396 ( 2) link_BETA1-4 : angle 2.15643 ( 6) link_ALPHA1-2 : bond 0.00315 ( 1) link_ALPHA1-2 : angle 1.94335 ( 3) link_ALPHA1-3 : bond 0.01007 ( 1) link_ALPHA1-3 : angle 2.08872 ( 3) hydrogen bonds : bond 0.02945 ( 152) hydrogen bonds : angle 6.25829 ( 414) SS BOND : bond 0.00280 ( 11) SS BOND : angle 0.82892 ( 22) covalent geometry : bond 0.00409 ( 4955) covalent geometry : angle 0.54894 ( 6729) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8568 (mp-120) outliers start: 22 outliers final: 12 residues processed: 87 average time/residue: 1.1661 time to fit residues: 107.6210 Evaluate side-chains 84 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 294 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 9 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.115066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.092483 restraints weight = 6390.764| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.08 r_work: 0.3129 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4974 Z= 0.141 Angle : 0.543 5.888 6775 Z= 0.282 Chirality : 0.046 0.172 753 Planarity : 0.003 0.037 862 Dihedral : 7.123 53.834 854 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.90 % Favored : 95.93 % Rotamer: Outliers : 3.21 % Allowed : 25.90 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.35), residues: 615 helix: 0.18 (2.51), residues: 6 sheet: -0.16 (0.33), residues: 236 loop : -0.32 (0.35), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 178 HIS 0.002 0.001 HIS A 336 PHE 0.019 0.002 PHE H 78 TYR 0.012 0.001 TYR A 121 ARG 0.003 0.000 ARG H 43 Details of bonding type rmsd link_NAG-ASN : bond 0.00224 ( 4) link_NAG-ASN : angle 2.16844 ( 12) link_BETA1-4 : bond 0.00479 ( 2) link_BETA1-4 : angle 2.01857 ( 6) link_ALPHA1-2 : bond 0.00381 ( 1) link_ALPHA1-2 : angle 1.88922 ( 3) link_ALPHA1-3 : bond 0.01201 ( 1) link_ALPHA1-3 : angle 1.83351 ( 3) hydrogen bonds : bond 0.02805 ( 152) hydrogen bonds : angle 6.13225 ( 414) SS BOND : bond 0.00235 ( 11) SS BOND : angle 0.78080 ( 22) covalent geometry : bond 0.00313 ( 4955) covalent geometry : angle 0.52889 ( 6729) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 13 residues processed: 84 average time/residue: 1.0107 time to fit residues: 89.9302 Evaluate side-chains 82 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 55 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 35 optimal weight: 0.0040 chunk 24 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 20 optimal weight: 9.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN H 105 GLN L 37 GLN ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.116794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.094447 restraints weight = 6327.439| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.06 r_work: 0.3159 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 4974 Z= 0.108 Angle : 0.521 8.556 6775 Z= 0.269 Chirality : 0.045 0.164 753 Planarity : 0.003 0.036 862 Dihedral : 6.633 53.286 854 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.25 % Favored : 96.59 % Rotamer: Outliers : 3.59 % Allowed : 25.90 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.35), residues: 615 helix: 0.30 (2.46), residues: 6 sheet: -0.09 (0.33), residues: 236 loop : -0.31 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 115 HIS 0.002 0.001 HIS A 336 PHE 0.017 0.002 PHE H 78 TYR 0.011 0.001 TYR A 121 ARG 0.003 0.000 ARG H 43 Details of bonding type rmsd link_NAG-ASN : bond 0.00193 ( 4) link_NAG-ASN : angle 1.95249 ( 12) link_BETA1-4 : bond 0.00538 ( 2) link_BETA1-4 : angle 1.85883 ( 6) link_ALPHA1-2 : bond 0.00462 ( 1) link_ALPHA1-2 : angle 1.80728 ( 3) link_ALPHA1-3 : bond 0.01299 ( 1) link_ALPHA1-3 : angle 1.54849 ( 3) hydrogen bonds : bond 0.02647 ( 152) hydrogen bonds : angle 5.98163 ( 414) SS BOND : bond 0.00210 ( 11) SS BOND : angle 0.75354 ( 22) covalent geometry : bond 0.00241 ( 4955) covalent geometry : angle 0.50911 ( 6729) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 SER cc_start: 0.8651 (p) cc_final: 0.8162 (t) outliers start: 19 outliers final: 10 residues processed: 92 average time/residue: 1.0008 time to fit residues: 97.5419 Evaluate side-chains 81 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 57 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 GLN A 294 ASN ** A 441 ASN ** 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 = 0.3524 r_free = 0.3524 target = 0.114492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.091764 restraints weight = 6322.260| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.07 r_work: 0.3111 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4974 Z= 0.183 Angle : 0.569 6.324 6775 Z= 0.295 Chirality : 0.047 0.177 753 Planarity : 0.003 0.034 862 Dihedral : 6.751 54.664 853 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.74 % Favored : 96.10 % Rotamer: Outliers : 3.02 % Allowed : 27.22 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.35), residues: 615 helix: -0.03 (2.39), residues: 6 sheet: -0.07 (0.33), residues: 233 loop : -0.35 (0.35), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 34 HIS 0.003 0.001 HIS A 336 PHE 0.016 0.002 PHE H 78 TYR 0.014 0.002 TYR A 121 ARG 0.007 0.001 ARG H 43 Details of bonding type rmsd link_NAG-ASN : bond 0.00274 ( 4) link_NAG-ASN : angle 2.24222 ( 12) link_BETA1-4 : bond 0.00395 ( 2) link_BETA1-4 : angle 2.21034 ( 6) link_ALPHA1-2 : bond 0.00300 ( 1) link_ALPHA1-2 : angle 2.00793 ( 3) link_ALPHA1-3 : bond 0.01064 ( 1) link_ALPHA1-3 : angle 1.90350 ( 3) hydrogen bonds : bond 0.02922 ( 152) hydrogen bonds : angle 6.11057 ( 414) SS BOND : bond 0.00257 ( 11) SS BOND : angle 0.90547 ( 22) covalent geometry : bond 0.00414 ( 4955) covalent geometry : angle 0.55347 ( 6729) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8694 (tt) REVERT: A 180 SER cc_start: 0.8794 (p) cc_final: 0.8359 (t) outliers start: 16 outliers final: 10 residues processed: 82 average time/residue: 1.1683 time to fit residues: 102.6154 Evaluate side-chains 80 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 57 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN L 37 GLN ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** 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 = 0.3533 r_free = 0.3533 target = 0.115167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.092568 restraints weight = 6332.026| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.06 r_work: 0.3128 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4974 Z= 0.141 Angle : 0.551 9.005 6775 Z= 0.284 Chirality : 0.046 0.166 753 Planarity : 0.003 0.034 862 Dihedral : 6.547 53.445 853 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.74 % Favored : 96.10 % Rotamer: Outliers : 2.84 % Allowed : 28.17 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.35), residues: 615 helix: 0.17 (2.46), residues: 6 sheet: -0.13 (0.32), residues: 235 loop : -0.34 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.002 0.001 HIS A 336 PHE 0.016 0.002 PHE H 78 TYR 0.012 0.001 TYR A 121 ARG 0.007 0.000 ARG H 43 Details of bonding type rmsd link_NAG-ASN : bond 0.00234 ( 4) link_NAG-ASN : angle 2.09897 ( 12) link_BETA1-4 : bond 0.00489 ( 2) link_BETA1-4 : angle 2.03174 ( 6) link_ALPHA1-2 : bond 0.00377 ( 1) link_ALPHA1-2 : angle 1.95571 ( 3) link_ALPHA1-3 : bond 0.01221 ( 1) link_ALPHA1-3 : angle 1.64271 ( 3) hydrogen bonds : bond 0.02810 ( 152) hydrogen bonds : angle 6.05023 ( 414) SS BOND : bond 0.00191 ( 11) SS BOND : angle 0.84643 ( 22) covalent geometry : bond 0.00316 ( 4955) covalent geometry : angle 0.53729 ( 6729) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8671 (tt) REVERT: A 180 SER cc_start: 0.8716 (p) cc_final: 0.8233 (t) outliers start: 15 outliers final: 11 residues processed: 77 average time/residue: 0.8481 time to fit residues: 69.5038 Evaluate side-chains 78 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 3 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 21 optimal weight: 0.0370 chunk 6 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 overall best weight: 1.5464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82AASN H 105 GLN ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** 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 = 0.3516 r_free = 0.3516 target = 0.113815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.091258 restraints weight = 6274.543| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.04 r_work: 0.3108 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 4974 Z= 0.204 Angle : 0.585 7.136 6775 Z= 0.303 Chirality : 0.047 0.177 753 Planarity : 0.003 0.033 862 Dihedral : 6.791 54.557 853 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.90 % Favored : 95.93 % Rotamer: Outliers : 2.65 % Allowed : 28.36 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.34), residues: 615 helix: -0.11 (2.42), residues: 6 sheet: -0.12 (0.32), residues: 234 loop : -0.44 (0.34), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 47 HIS 0.003 0.001 HIS A 336 PHE 0.015 0.002 PHE H 78 TYR 0.016 0.002 TYR L 36 ARG 0.007 0.001 ARG H 43 Details of bonding type rmsd link_NAG-ASN : bond 0.00328 ( 4) link_NAG-ASN : angle 2.34502 ( 12) link_BETA1-4 : bond 0.00410 ( 2) link_BETA1-4 : angle 2.31395 ( 6) link_ALPHA1-2 : bond 0.00250 ( 1) link_ALPHA1-2 : angle 2.10530 ( 3) link_ALPHA1-3 : bond 0.01026 ( 1) link_ALPHA1-3 : angle 1.94787 ( 3) hydrogen bonds : bond 0.03029 ( 152) hydrogen bonds : angle 6.18502 ( 414) SS BOND : bond 0.00264 ( 11) SS BOND : angle 0.97363 ( 22) covalent geometry : bond 0.00459 ( 4955) covalent geometry : angle 0.56901 ( 6729) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8711 (tt) REVERT: A 180 SER cc_start: 0.8823 (p) cc_final: 0.8377 (t) outliers start: 14 outliers final: 12 residues processed: 80 average time/residue: 0.8996 time to fit residues: 76.2719 Evaluate side-chains 81 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 57 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 13 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 59 optimal weight: 0.0050 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.115847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.093223 restraints weight = 6285.458| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.06 r_work: 0.3140 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4974 Z= 0.121 Angle : 0.543 7.316 6775 Z= 0.282 Chirality : 0.046 0.161 753 Planarity : 0.003 0.034 862 Dihedral : 6.444 52.712 853 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.58 % Favored : 96.26 % Rotamer: Outliers : 2.65 % Allowed : 28.17 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.34), residues: 615 helix: 0.09 (2.43), residues: 6 sheet: -0.16 (0.32), residues: 235 loop : -0.33 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 34 HIS 0.002 0.001 HIS A 336 PHE 0.016 0.002 PHE H 78 TYR 0.012 0.001 TYR A 121 ARG 0.007 0.000 ARG H 43 Details of bonding type rmsd link_NAG-ASN : bond 0.00178 ( 4) link_NAG-ASN : angle 1.98365 ( 12) link_BETA1-4 : bond 0.00525 ( 2) link_BETA1-4 : angle 1.95665 ( 6) link_ALPHA1-2 : bond 0.00397 ( 1) link_ALPHA1-2 : angle 1.94389 ( 3) link_ALPHA1-3 : bond 0.01281 ( 1) link_ALPHA1-3 : angle 1.45370 ( 3) hydrogen bonds : bond 0.02732 ( 152) hydrogen bonds : angle 6.01612 ( 414) SS BOND : bond 0.00152 ( 11) SS BOND : angle 0.80731 ( 22) covalent geometry : bond 0.00270 ( 4955) covalent geometry : angle 0.53035 ( 6729) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 95 ASP cc_start: 0.8045 (t0) cc_final: 0.7638 (t0) REVERT: A 140 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8687 (tt) REVERT: A 180 SER cc_start: 0.8686 (p) cc_final: 0.8200 (t) outliers start: 14 outliers final: 12 residues processed: 79 average time/residue: 0.8740 time to fit residues: 73.2894 Evaluate side-chains 77 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 58 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 47 optimal weight: 0.0770 chunk 17 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.116346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.093691 restraints weight = 6353.928| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.06 r_work: 0.3141 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4974 Z= 0.126 Angle : 0.546 7.768 6775 Z= 0.284 Chirality : 0.046 0.160 753 Planarity : 0.003 0.034 862 Dihedral : 6.370 53.207 853 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.74 % Favored : 96.10 % Rotamer: Outliers : 2.46 % Allowed : 28.54 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.35), residues: 615 helix: 0.15 (2.43), residues: 6 sheet: -0.11 (0.33), residues: 234 loop : -0.32 (0.34), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 34 HIS 0.002 0.001 HIS A 336 PHE 0.016 0.002 PHE H 78 TYR 0.012 0.001 TYR L 36 ARG 0.007 0.001 ARG H 43 Details of bonding type rmsd link_NAG-ASN : bond 0.00188 ( 4) link_NAG-ASN : angle 1.97776 ( 12) link_BETA1-4 : bond 0.00528 ( 2) link_BETA1-4 : angle 1.99509 ( 6) link_ALPHA1-2 : bond 0.00423 ( 1) link_ALPHA1-2 : angle 1.94080 ( 3) link_ALPHA1-3 : bond 0.01117 ( 1) link_ALPHA1-3 : angle 1.42233 ( 3) hydrogen bonds : bond 0.02688 ( 152) hydrogen bonds : angle 5.97366 ( 414) SS BOND : bond 0.00205 ( 11) SS BOND : angle 0.81175 ( 22) covalent geometry : bond 0.00285 ( 4955) covalent geometry : angle 0.53385 ( 6729) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7450.52 seconds wall clock time: 132 minutes 43.13 seconds (7963.13 seconds total)