Starting phenix.real_space_refine on Tue Feb 11 09:14:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ez8_28730/02_2025/8ez8_28730.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ez8_28730/02_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_28730/02_2025/8ez8_28730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ez8_28730/02_2025/8ez8_28730.map" model { file = "/net/cci-nas-00/data/ceres_data/8ez8_28730/02_2025/8ez8_28730.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ez8_28730/02_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-5592/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: 4.17, per 1000 atoms: 0.86 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: 1.39 Conformation dependent library (CDL) restraints added in 565.6 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: 0.66 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: 1.45 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: 1.910 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.590 Find NCS groups from input model: 0.050 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:13.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.910 ------------------------------------------------------------------------------- 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 4955 Z= 0.243 Angle : 0.621 6.728 6729 Z= 0.317 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 *********************** 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 : 0.572 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 80 average time/residue: 0.9223 time to fit residues: 77.9921 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: 0.6980 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: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3542 r_free = 0.3542 target = 0.115575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.093752 restraints weight = 6336.765| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.03 r_work: 0.3154 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.0604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4955 Z= 0.178 Angle : 0.525 7.403 6729 Z= 0.279 Chirality : 0.046 0.158 753 Planarity : 0.004 0.047 862 Dihedral : 9.338 69.745 863 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.74 % Favored : 96.10 % Rotamer: Outliers : 2.65 % Allowed : 26.09 % Favored : 71.27 % 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: -1.68 (1.48), residues: 12 sheet: -0.12 (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 0.000 HIS A 336 PHE 0.015 0.002 PHE H 78 TYR 0.010 0.001 TYR H 50 ARG 0.003 0.001 ARG A 85 *********************** 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 : 0.600 Fit side-chains revert: symmetry clash REVERT: A 431 LYS cc_start: 0.7959 (mmtt) cc_final: 0.7746 (tppt) outliers start: 14 outliers final: 5 residues processed: 88 average time/residue: 0.9278 time to fit residues: 86.6058 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 : 0.530 ------------------------------------------------------------------------------- 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: 8.9990 chunk 32 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 59 optimal weight: 0.0570 chunk 15 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.3904 ------------------------------------------------------------------------------- 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 = 0.3504 r_free = 0.3504 target = 0.113086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.090574 restraints weight = 6400.306| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.07 r_work: 0.3107 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.0825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4955 Z= 0.290 Angle : 0.553 6.125 6729 Z= 0.293 Chirality : 0.047 0.163 753 Planarity : 0.004 0.042 862 Dihedral : 8.298 56.869 854 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.23 % Favored : 95.61 % Rotamer: Outliers : 2.84 % Allowed : 25.14 % Favored : 72.02 % 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: -0.55 (0.35), residues: 615 helix: -1.61 (1.51), residues: 12 sheet: -0.21 (0.33), residues: 237 loop : -0.34 (0.35), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 34 HIS 0.003 0.001 HIS A 336 PHE 0.019 0.002 PHE H 78 TYR 0.013 0.001 TYR A 121 ARG 0.003 0.001 ARG A 85 *********************** 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 92 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.506 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 87 average time/residue: 1.0721 time to fit residues: 98.6339 Evaluate side-chains 81 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.571 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 13 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3503 r_free = 0.3503 target = 0.113092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.090493 restraints weight = 6428.579| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.07 r_work: 0.3106 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4955 Z= 0.277 Angle : 0.556 7.947 6729 Z= 0.293 Chirality : 0.047 0.182 753 Planarity : 0.004 0.040 862 Dihedral : 7.742 54.509 854 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.25 % Favored : 96.59 % Rotamer: Outliers : 3.78 % Allowed : 24.95 % Favored : 71.27 % 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: -0.54 (0.35), residues: 615 helix: -1.68 (1.48), residues: 12 sheet: -0.21 (0.33), residues: 234 loop : -0.32 (0.35), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 34 HIS 0.002 0.001 HIS A 336 PHE 0.017 0.002 PHE H 78 TYR 0.013 0.001 TYR L 36 ARG 0.003 0.000 ARG H 43 *********************** 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 91 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 15 residues processed: 84 average time/residue: 0.9553 time to fit residues: 84.7887 Evaluate side-chains 82 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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 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 400 ARG Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 9 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 136 GLN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.114291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.091788 restraints weight = 6417.976| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.06 r_work: 0.3121 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4955 Z= 0.214 Angle : 0.529 6.532 6729 Z= 0.279 Chirality : 0.046 0.174 753 Planarity : 0.003 0.039 862 Dihedral : 7.297 53.838 854 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.90 % Favored : 95.93 % Rotamer: Outliers : 3.97 % Allowed : 25.14 % 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: -0.54 (0.35), residues: 615 helix: -1.71 (1.45), residues: 12 sheet: -0.21 (0.33), residues: 235 loop : -0.33 (0.35), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 178 HIS 0.003 0.001 HIS A 336 PHE 0.018 0.002 PHE H 78 TYR 0.011 0.001 TYR L 36 ARG 0.003 0.000 ARG H 43 *********************** 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 98 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8587 (mp-120) outliers start: 21 outliers final: 13 residues processed: 88 average time/residue: 0.9775 time to fit residues: 90.9581 Evaluate side-chains 85 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 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 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: 0.8980 chunk 35 optimal weight: 0.0000 chunk 24 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 20 optimal weight: 10.0000 chunk 42 optimal weight: 0.6980 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** 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 = 0.116176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.093875 restraints weight = 6360.003| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.06 r_work: 0.3151 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 4955 Z= 0.171 Angle : 0.514 8.162 6729 Z= 0.271 Chirality : 0.045 0.168 753 Planarity : 0.003 0.038 862 Dihedral : 6.893 53.163 854 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.58 % Favored : 96.26 % Rotamer: Outliers : 3.21 % Allowed : 26.65 % Favored : 70.13 % 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: -0.47 (0.35), residues: 615 helix: 0.07 (2.44), residues: 6 sheet: -0.20 (0.33), residues: 238 loop : -0.31 (0.35), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 178 HIS 0.002 0.001 HIS A 336 PHE 0.017 0.002 PHE H 78 TYR 0.010 0.001 TYR L 49 ARG 0.003 0.000 ARG H 43 *********************** 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 94 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 12 residues processed: 89 average time/residue: 0.8954 time to fit residues: 84.1754 Evaluate side-chains 83 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 107 THR Chi-restraints excluded: chain L residue 42 THR 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 57 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 0.3980 chunk 19 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- 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 82AASN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.113039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.090555 restraints weight = 6338.830| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.04 r_work: 0.3087 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 4955 Z= 0.474 Angle : 0.640 7.605 6729 Z= 0.335 Chirality : 0.050 0.196 753 Planarity : 0.004 0.034 862 Dihedral : 7.698 56.940 854 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.55 % Favored : 95.28 % Rotamer: Outliers : 3.59 % Allowed : 26.28 % Favored : 70.13 % 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: -0.68 (0.34), residues: 615 helix: -0.27 (2.41), residues: 6 sheet: -0.22 (0.32), residues: 238 loop : -0.55 (0.35), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 47 HIS 0.003 0.001 HIS A 336 PHE 0.019 0.003 PHE A 354 TYR 0.021 0.002 TYR L 36 ARG 0.004 0.001 ARG A 420 *********************** 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 93 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 102 ILE cc_start: 0.8455 (mm) cc_final: 0.8199 (tp) outliers start: 19 outliers final: 15 residues processed: 88 average time/residue: 1.0146 time to fit residues: 94.0488 Evaluate side-chains 84 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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 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 210 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 57 optimal weight: 0.2980 chunk 58 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 82AASN 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.114354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.091841 restraints weight = 6366.757| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.08 r_work: 0.3118 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4955 Z= 0.204 Angle : 0.547 6.891 6729 Z= 0.289 Chirality : 0.046 0.169 753 Planarity : 0.003 0.037 862 Dihedral : 7.078 53.032 854 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.25 % Favored : 96.59 % Rotamer: Outliers : 4.16 % Allowed : 26.65 % 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: -0.60 (0.35), residues: 615 helix: 0.02 (2.40), residues: 6 sheet: -0.21 (0.33), residues: 238 loop : -0.46 (0.35), residues: 371 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 0.018 0.002 PHE H 78 TYR 0.011 0.001 TYR A 121 ARG 0.004 0.000 ARG H 43 *********************** 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 95 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 102 ILE cc_start: 0.8415 (mm) cc_final: 0.8209 (tp) outliers start: 22 outliers final: 16 residues processed: 85 average time/residue: 0.9277 time to fit residues: 83.5493 Evaluate side-chains 82 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL 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 42 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 160 MET 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 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: 2.9990 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 6 GLN ** 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 402 ASN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.112743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.090198 restraints weight = 6325.419| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.06 r_work: 0.3088 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 4955 Z= 0.322 Angle : 0.586 8.785 6729 Z= 0.307 Chirality : 0.048 0.183 753 Planarity : 0.003 0.035 862 Dihedral : 7.205 54.687 854 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.39 % Favored : 95.45 % Rotamer: Outliers : 3.02 % Allowed : 27.03 % Favored : 69.94 % 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: -0.69 (0.34), residues: 615 helix: -0.17 (2.37), residues: 6 sheet: -0.25 (0.32), residues: 240 loop : -0.54 (0.34), residues: 369 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 0.016 0.002 PHE H 78 TYR 0.015 0.002 TYR L 36 ARG 0.005 0.001 ARG L 103 *********************** 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 87 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 95 ASP cc_start: 0.8127 (t0) cc_final: 0.7640 (t0) REVERT: H 102 ILE cc_start: 0.8438 (mm) cc_final: 0.8207 (tp) outliers start: 16 outliers final: 14 residues processed: 84 average time/residue: 1.0160 time to fit residues: 89.7455 Evaluate side-chains 84 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL 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 42 THR 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 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: 6.9990 chunk 33 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 22 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 6 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.113885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.091300 restraints weight = 6352.783| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.07 r_work: 0.3107 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4955 Z= 0.248 Angle : 0.562 7.176 6729 Z= 0.296 Chirality : 0.047 0.176 753 Planarity : 0.003 0.037 862 Dihedral : 7.008 53.753 854 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.07 % Favored : 95.77 % Rotamer: Outliers : 3.59 % Allowed : 26.84 % Favored : 69.57 % 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: -0.61 (0.34), residues: 615 helix: -0.09 (2.39), residues: 6 sheet: -0.19 (0.33), residues: 236 loop : -0.49 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.002 0.001 HIS A 336 PHE 0.017 0.002 PHE H 78 TYR 0.012 0.001 TYR L 36 ARG 0.006 0.001 ARG H 43 ********************** 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 85 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 95 ASP cc_start: 0.8118 (t0) cc_final: 0.7665 (t0) REVERT: H 102 ILE cc_start: 0.8436 (mm) cc_final: 0.8219 (tp) outliers start: 19 outliers final: 16 residues processed: 81 average time/residue: 0.8517 time to fit residues: 73.1942 Evaluate side-chains 81 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL 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 42 THR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 95 THR 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 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: 2.9990 chunk 50 optimal weight: 0.0570 chunk 24 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 47 optimal weight: 0.0970 chunk 17 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.116207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.093862 restraints weight = 6385.482| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.07 r_work: 0.3147 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4955 Z= 0.174 Angle : 0.532 7.803 6729 Z= 0.280 Chirality : 0.046 0.162 753 Planarity : 0.003 0.037 862 Dihedral : 6.525 52.493 854 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.74 % Favored : 96.10 % Rotamer: Outliers : 2.84 % Allowed : 27.60 % Favored : 69.57 % 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: -0.55 (0.35), residues: 615 helix: 0.10 (2.40), residues: 6 sheet: -0.21 (0.33), residues: 239 loop : -0.40 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 34 HIS 0.002 0.001 HIS A 274 PHE 0.017 0.002 PHE H 78 TYR 0.010 0.001 TYR L 49 ARG 0.007 0.000 ARG H 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6293.83 seconds wall clock time: 111 minutes 20.21 seconds (6680.21 seconds total)