Starting phenix.real_space_refine on Fri Dec 27 12:04:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v2c_42905/12_2024/8v2c_42905.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v2c_42905/12_2024/8v2c_42905.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v2c_42905/12_2024/8v2c_42905.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v2c_42905/12_2024/8v2c_42905.map" model { file = "/net/cci-nas-00/data/ceres_data/8v2c_42905/12_2024/8v2c_42905.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v2c_42905/12_2024/8v2c_42905.cif" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.016 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 23 5.16 5 C 2886 2.51 5 N 767 2.21 5 O 924 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4600 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1343 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 8, 'TRANS': 160} Chain breaks: 1 Chain: "B" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1583 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 13, 'TRANS': 184} Chain: "C" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1492 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 177} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.88, per 1000 atoms: 0.84 Number of scatterers: 4600 At special positions: 0 Unit cell: (87.72, 102.34, 105.78, 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 23 16.00 O 924 8.00 N 767 7.00 C 2886 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 71 " - pdb=" SG CYS A 177 " distance=2.03 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 144 " distance=2.03 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 180 " distance=2.03 Simple disulfide: pdb=" SG CYS C 178 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 242 " - pdb=" SG CYS C 252 " distance=2.03 Simple disulfide: pdb=" SG CYS C 275 " - pdb=" SG CYS C 282 " 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG B 701 " - " ASN B 225 " " NAG B 702 " - " ASN B 157 " " NAG C 801 " - " ASN C 239 " " NAG D 1 " - " ASN B 131 " " NAG E 1 " - " ASN C 162 " " NAG F 1 " - " ASN C 271 " " NAG G 1 " - " ASN C 304 " " NAG H 1 " - " ASN C 323 " Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 866.3 milliseconds 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1048 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 9 sheets defined 26.5% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 32 through 47 Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 64 through 74 Processing helix chain 'A' and resid 80 through 87 Processing helix chain 'A' and resid 88 through 115 removed outlier: 3.517A pdb=" N LEU A 115 " --> pdb=" O ARG A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 144 removed outlier: 4.475A pdb=" N ASP A 124 " --> pdb=" O PHE A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 201 Processing helix chain 'B' and resid 213 through 216 Processing helix chain 'B' and resid 245 through 250 removed outlier: 3.705A pdb=" N GLY B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 276 removed outlier: 3.809A pdb=" N MET B 276 " --> pdb=" O GLU B 273 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 180 through 181 removed outlier: 3.631A pdb=" N CYS B 180 " --> pdb=" O CYS B 144 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N CYS B 144 " --> pdb=" O CYS B 180 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ASP B 147 " --> pdb=" O ASN B 131 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ASN B 131 " --> pdb=" O ASP B 147 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N LYS B 219 " --> pdb=" O CYS B 134 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL B 136 " --> pdb=" O LYS B 219 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 172 through 173 Processing sheet with id=AA3, first strand: chain 'B' and resid 172 through 173 Processing sheet with id=AA4, first strand: chain 'B' and resid 224 through 229 removed outlier: 5.746A pdb=" N ASN B 225 " --> pdb=" O VAL B 243 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL B 243 " --> pdb=" O ASN B 225 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE B 282 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 268 through 269 Processing sheet with id=AA6, first strand: chain 'C' and resid 148 through 151 Processing sheet with id=AA7, first strand: chain 'C' and resid 155 through 158 removed outlier: 3.933A pdb=" N LYS C 155 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR C 226 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER C 177 " --> pdb=" O GLN C 215 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 238 through 241 removed outlier: 6.707A pdb=" N ASN C 239 " --> pdb=" O GLU C 255 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N GLU C 255 " --> pdb=" O ASN C 239 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 271 through 274 removed outlier: 3.886A pdb=" N TYR C 303 " --> pdb=" O PHE C 322 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE C 322 " --> pdb=" O TYR C 303 " (cutoff:3.500A) 190 hydrogen bonds defined for protein. 525 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: 1.09 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1469 1.34 - 1.46: 1142 1.46 - 1.58: 2058 1.58 - 1.70: 0 1.70 - 1.82: 31 Bond restraints: 4700 Sorted by residual: bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.57e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.15e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.00e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.96e+00 bond pdb=" C1 NAG B 702 " pdb=" O5 NAG B 702 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.87e+00 ... (remaining 4695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 6148 1.26 - 2.53: 186 2.53 - 3.79: 40 3.79 - 5.06: 2 5.06 - 6.32: 3 Bond angle restraints: 6379 Sorted by residual: angle pdb=" N GLY B 177 " pdb=" CA GLY B 177 " pdb=" C GLY B 177 " ideal model delta sigma weight residual 110.95 114.28 -3.33 1.70e+00 3.46e-01 3.84e+00 angle pdb=" CA GLU A 54 " pdb=" C GLU A 54 " pdb=" N PRO A 55 " ideal model delta sigma weight residual 118.44 121.50 -3.06 1.59e+00 3.96e-01 3.71e+00 angle pdb=" CA LYS A 89 " pdb=" C LYS A 89 " pdb=" N PRO A 90 " ideal model delta sigma weight residual 118.44 121.28 -2.84 1.59e+00 3.96e-01 3.20e+00 angle pdb=" N THR A 117 " pdb=" CA THR A 117 " pdb=" C THR A 117 " ideal model delta sigma weight residual 109.81 113.57 -3.76 2.21e+00 2.05e-01 2.89e+00 angle pdb=" N GLU A 54 " pdb=" CA GLU A 54 " pdb=" C GLU A 54 " ideal model delta sigma weight residual 109.81 113.41 -3.60 2.21e+00 2.05e-01 2.66e+00 ... (remaining 6374 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.72: 2735 21.72 - 43.44: 146 43.44 - 65.15: 63 65.15 - 86.87: 12 86.87 - 108.59: 56 Dihedral angle restraints: 3012 sinusoidal: 1397 harmonic: 1615 Sorted by residual: dihedral pdb=" CB CYS B 172 " pdb=" SG CYS B 172 " pdb=" SG CYS B 180 " pdb=" CB CYS B 180 " ideal model delta sinusoidal sigma weight residual 93.00 144.13 -51.13 1 1.00e+01 1.00e-02 3.58e+01 dihedral pdb=" CB CYS C 275 " pdb=" SG CYS C 275 " pdb=" SG CYS C 282 " pdb=" CB CYS C 282 " ideal model delta sinusoidal sigma weight residual -86.00 -40.75 -45.25 1 1.00e+01 1.00e-02 2.84e+01 dihedral pdb=" C1 NAG E 1 " pdb=" C2 NAG E 1 " pdb=" C3 NAG E 1 " pdb=" O3 NAG E 1 " ideal model delta sinusoidal sigma weight residual -175.09 -66.50 -108.59 1 3.00e+01 1.11e-03 1.41e+01 ... (remaining 3009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 664 0.072 - 0.143: 81 0.143 - 0.214: 0 0.214 - 0.286: 0 0.286 - 0.357: 1 Chirality restraints: 746 Sorted by residual: chirality pdb=" C1 NAG C 801 " pdb=" ND2 ASN C 239 " pdb=" C2 NAG C 801 " pdb=" O5 NAG C 801 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CA ILE A 150 " pdb=" N ILE A 150 " pdb=" C ILE A 150 " pdb=" CB ILE A 150 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.66e-01 chirality pdb=" C1 NAG B 701 " pdb=" ND2 ASN B 225 " pdb=" C2 NAG B 701 " pdb=" O5 NAG B 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 4.64e-01 ... (remaining 743 not shown) Planarity restraints: 810 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 64 " -0.018 5.00e-02 4.00e+02 2.75e-02 1.21e+00 pdb=" N PRO A 65 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 65 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 65 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 213 " 0.017 5.00e-02 4.00e+02 2.55e-02 1.04e+00 pdb=" N PRO B 214 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO B 214 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 214 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 183 " -0.017 5.00e-02 4.00e+02 2.54e-02 1.03e+00 pdb=" N PRO C 184 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO C 184 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 184 " -0.014 5.00e-02 4.00e+02 ... (remaining 807 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 1525 2.85 - 3.36: 3796 3.36 - 3.87: 6931 3.87 - 4.39: 7285 4.39 - 4.90: 13310 Nonbonded interactions: 32847 Sorted by model distance: nonbonded pdb=" NE2 GLN A 38 " pdb=" OD2 ASP B 213 " model vdw 2.336 3.120 nonbonded pdb=" OG1 THR C 306 " pdb=" O6 NAG G 1 " model vdw 2.375 3.040 nonbonded pdb=" OE1 GLN C 270 " pdb=" NH2 ARG C 288 " model vdw 2.393 3.120 nonbonded pdb=" OD1 ASP C 146 " pdb=" ND2 ASN C 172 " model vdw 2.425 3.120 nonbonded pdb=" N ASP C 251 " pdb=" OD1 ASP C 251 " model vdw 2.428 3.120 ... (remaining 32842 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 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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=0.99 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: 2.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.870 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 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 : 0.003 0.032 4700 Z= 0.192 Angle : 0.511 6.325 6379 Z= 0.258 Chirality : 0.042 0.357 746 Planarity : 0.003 0.027 802 Dihedral : 22.682 108.587 1943 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.20 % Allowed : 5.71 % Favored : 94.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.33), residues: 543 helix: 2.07 (0.45), residues: 130 sheet: -1.48 (0.37), residues: 170 loop : -2.82 (0.28), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 293 HIS 0.003 0.001 HIS B 176 PHE 0.005 0.001 PHE A 120 TYR 0.006 0.001 TYR A 183 ARG 0.001 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8279 (tm-30) cc_final: 0.8007 (tm-30) REVERT: A 149 GLU cc_start: 0.5790 (mm-30) cc_final: 0.5463 (mp0) REVERT: C 245 ARG cc_start: 0.8189 (tpp80) cc_final: 0.7468 (tpm170) outliers start: 1 outliers final: 1 residues processed: 90 average time/residue: 0.2123 time to fit residues: 23.5664 Evaluate side-chains 57 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 282 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.0040 chunk 40 optimal weight: 0.0870 chunk 22 optimal weight: 0.2980 chunk 13 optimal weight: 0.1980 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 0.4980 chunk 41 optimal weight: 0.0980 chunk 16 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 overall best weight: 0.1370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 61 ASN B 176 HIS C 171 GLN C 286 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 4700 Z= 0.139 Angle : 0.631 9.245 6379 Z= 0.277 Chirality : 0.047 0.317 746 Planarity : 0.004 0.041 802 Dihedral : 24.451 113.755 868 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.57 % Allowed : 10.63 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.36), residues: 543 helix: 3.09 (0.45), residues: 130 sheet: -0.96 (0.37), residues: 174 loop : -2.29 (0.34), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 293 HIS 0.003 0.001 HIS A 74 PHE 0.007 0.001 PHE C 305 TYR 0.015 0.001 TYR A 105 ARG 0.002 0.000 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7968 (tm-30) REVERT: A 149 GLU cc_start: 0.5793 (mm-30) cc_final: 0.5488 (mp0) REVERT: C 245 ARG cc_start: 0.8186 (tpp80) cc_final: 0.7464 (tpm170) REVERT: C 276 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7627 (tm-30) REVERT: C 294 GLN cc_start: 0.7046 (mm-40) cc_final: 0.6844 (mm-40) outliers start: 8 outliers final: 3 residues processed: 72 average time/residue: 0.1367 time to fit residues: 13.3743 Evaluate side-chains 54 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 282 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 40 optimal weight: 0.0870 chunk 32 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 47 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 38 optimal weight: 0.4980 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4700 Z= 0.224 Angle : 0.704 11.290 6379 Z= 0.310 Chirality : 0.048 0.245 746 Planarity : 0.004 0.035 802 Dihedral : 18.561 115.074 868 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.36 % Allowed : 12.40 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.37), residues: 543 helix: 3.45 (0.45), residues: 130 sheet: -0.76 (0.38), residues: 178 loop : -2.10 (0.36), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 293 HIS 0.003 0.001 HIS C 193 PHE 0.013 0.002 PHE A 114 TYR 0.014 0.002 TYR A 183 ARG 0.002 0.000 ARG C 265 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7215 (tp) REVERT: A 149 GLU cc_start: 0.5820 (mm-30) cc_final: 0.5566 (mp0) REVERT: C 245 ARG cc_start: 0.8311 (tpp80) cc_final: 0.7467 (tpm170) outliers start: 12 outliers final: 7 residues processed: 66 average time/residue: 0.1296 time to fit residues: 11.9559 Evaluate side-chains 56 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 282 CYS Chi-restraints excluded: chain C residue 318 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 0.3980 chunk 36 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4700 Z= 0.199 Angle : 0.681 10.696 6379 Z= 0.297 Chirality : 0.047 0.267 746 Planarity : 0.004 0.038 802 Dihedral : 15.413 98.926 868 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.77 % Allowed : 14.76 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.37), residues: 543 helix: 3.63 (0.45), residues: 130 sheet: -0.54 (0.38), residues: 176 loop : -1.94 (0.36), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 293 HIS 0.002 0.001 HIS C 193 PHE 0.010 0.001 PHE A 114 TYR 0.014 0.001 TYR A 105 ARG 0.003 0.000 ARG C 327 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8399 (tp30) cc_final: 0.8013 (tm-30) REVERT: A 144 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7254 (tp) REVERT: A 149 GLU cc_start: 0.5814 (mm-30) cc_final: 0.5614 (mp0) REVERT: A 196 GLU cc_start: 0.7524 (tp30) cc_final: 0.7269 (tp30) REVERT: C 245 ARG cc_start: 0.8322 (tpp80) cc_final: 0.7411 (tpm170) outliers start: 9 outliers final: 7 residues processed: 59 average time/residue: 0.1294 time to fit residues: 10.7494 Evaluate side-chains 54 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 282 CYS Chi-restraints excluded: chain C residue 319 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 45 optimal weight: 0.0970 chunk 12 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4700 Z= 0.185 Angle : 0.665 11.920 6379 Z= 0.291 Chirality : 0.045 0.246 746 Planarity : 0.004 0.035 802 Dihedral : 13.446 98.302 868 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.17 % Allowed : 14.96 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.37), residues: 543 helix: 3.74 (0.45), residues: 130 sheet: -0.46 (0.38), residues: 180 loop : -1.77 (0.38), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 293 HIS 0.001 0.001 HIS C 193 PHE 0.011 0.001 PHE A 114 TYR 0.010 0.001 TYR A 183 ARG 0.003 0.000 ARG C 222 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7299 (tp) REVERT: C 245 ARG cc_start: 0.8382 (tpp80) cc_final: 0.7390 (tpm170) REVERT: C 327 ARG cc_start: 0.7127 (mtt-85) cc_final: 0.5619 (mmp-170) outliers start: 11 outliers final: 10 residues processed: 55 average time/residue: 0.1514 time to fit residues: 11.3885 Evaluate side-chains 55 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 282 CYS Chi-restraints excluded: chain C residue 319 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 0.0870 chunk 51 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4700 Z= 0.194 Angle : 0.654 12.938 6379 Z= 0.291 Chirality : 0.044 0.222 746 Planarity : 0.004 0.034 802 Dihedral : 11.514 91.612 868 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.36 % Allowed : 16.14 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.38), residues: 543 helix: 3.83 (0.45), residues: 130 sheet: -0.41 (0.39), residues: 176 loop : -1.59 (0.38), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 293 HIS 0.002 0.001 HIS A 146 PHE 0.011 0.001 PHE A 114 TYR 0.011 0.001 TYR A 183 ARG 0.004 0.000 ARG C 327 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7372 (tp) REVERT: C 327 ARG cc_start: 0.6781 (mtt-85) cc_final: 0.5509 (mmp-170) outliers start: 12 outliers final: 10 residues processed: 55 average time/residue: 0.1245 time to fit residues: 9.7880 Evaluate side-chains 55 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 282 CYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 319 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 43 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4700 Z= 0.184 Angle : 0.640 13.970 6379 Z= 0.287 Chirality : 0.043 0.221 746 Planarity : 0.003 0.034 802 Dihedral : 10.576 89.632 868 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.56 % Allowed : 16.14 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.38), residues: 543 helix: 3.90 (0.45), residues: 130 sheet: -0.36 (0.39), residues: 176 loop : -1.49 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 293 HIS 0.002 0.000 HIS A 146 PHE 0.011 0.001 PHE A 114 TYR 0.010 0.001 TYR A 183 ARG 0.003 0.000 ARG C 327 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7344 (tp) REVERT: C 327 ARG cc_start: 0.6260 (mtt-85) cc_final: 0.5324 (mmp-170) outliers start: 13 outliers final: 9 residues processed: 57 average time/residue: 0.1329 time to fit residues: 10.7529 Evaluate side-chains 54 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 282 CYS Chi-restraints excluded: chain C residue 319 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 0.0570 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 25 optimal weight: 0.0980 chunk 4 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4700 Z= 0.163 Angle : 0.625 13.973 6379 Z= 0.281 Chirality : 0.043 0.217 746 Planarity : 0.003 0.034 802 Dihedral : 10.106 86.463 868 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.76 % Allowed : 16.34 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.38), residues: 543 helix: 3.96 (0.45), residues: 130 sheet: -0.30 (0.39), residues: 176 loop : -1.38 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 293 HIS 0.001 0.000 HIS A 146 PHE 0.009 0.001 PHE A 114 TYR 0.009 0.001 TYR A 183 ARG 0.002 0.000 ARG C 327 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7340 (tp) REVERT: C 327 ARG cc_start: 0.6318 (mtt-85) cc_final: 0.5285 (mmp-170) outliers start: 14 outliers final: 12 residues processed: 56 average time/residue: 0.1256 time to fit residues: 10.1982 Evaluate side-chains 57 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 282 CYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 319 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 0.3980 chunk 37 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 45 optimal weight: 0.6980 chunk 47 optimal weight: 0.3980 chunk 31 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 189 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4700 Z= 0.158 Angle : 0.619 14.487 6379 Z= 0.280 Chirality : 0.043 0.214 746 Planarity : 0.003 0.034 802 Dihedral : 9.874 84.442 868 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.56 % Allowed : 16.54 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.38), residues: 543 helix: 4.02 (0.45), residues: 130 sheet: -0.29 (0.39), residues: 176 loop : -1.32 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 293 HIS 0.001 0.000 HIS A 146 PHE 0.010 0.001 PHE A 114 TYR 0.009 0.001 TYR A 183 ARG 0.003 0.000 ARG C 265 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7334 (tp) REVERT: C 276 GLU cc_start: 0.8319 (tm-30) cc_final: 0.7797 (tm-30) REVERT: C 327 ARG cc_start: 0.6290 (mtt-85) cc_final: 0.5301 (mmp-170) outliers start: 13 outliers final: 12 residues processed: 53 average time/residue: 0.1332 time to fit residues: 10.0695 Evaluate side-chains 56 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 282 CYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 319 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 0.0970 chunk 48 optimal weight: 0.9990 chunk 42 optimal weight: 0.4980 chunk 4 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 0.2980 chunk 6 optimal weight: 2.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4700 Z= 0.153 Angle : 0.612 15.131 6379 Z= 0.277 Chirality : 0.043 0.210 746 Planarity : 0.003 0.034 802 Dihedral : 9.643 81.766 868 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.56 % Allowed : 16.54 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.38), residues: 543 helix: 4.07 (0.44), residues: 130 sheet: -0.32 (0.38), residues: 182 loop : -1.26 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 293 HIS 0.001 0.000 HIS A 146 PHE 0.008 0.001 PHE A 114 TYR 0.009 0.001 TYR A 183 ARG 0.002 0.000 ARG C 327 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7319 (tp) REVERT: C 276 GLU cc_start: 0.8291 (tm-30) cc_final: 0.7803 (tm-30) REVERT: C 327 ARG cc_start: 0.6315 (mtt-85) cc_final: 0.5281 (mmp-170) outliers start: 13 outliers final: 11 residues processed: 54 average time/residue: 0.1228 time to fit residues: 9.4224 Evaluate side-chains 55 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 282 CYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 319 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 1.9990 chunk 42 optimal weight: 0.0970 chunk 17 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 5 optimal weight: 0.0040 chunk 7 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 2 optimal weight: 0.3980 chunk 30 optimal weight: 0.4980 chunk 48 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.116993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.097696 restraints weight = 7530.348| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.64 r_work: 0.3118 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4700 Z= 0.146 Angle : 0.605 14.712 6379 Z= 0.275 Chirality : 0.042 0.202 746 Planarity : 0.003 0.034 802 Dihedral : 9.388 77.388 868 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.97 % Allowed : 17.32 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.38), residues: 543 helix: 4.12 (0.44), residues: 130 sheet: -0.23 (0.38), residues: 176 loop : -1.24 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 181 HIS 0.001 0.000 HIS A 146 PHE 0.010 0.001 PHE A 114 TYR 0.009 0.001 TYR A 183 ARG 0.003 0.000 ARG C 265 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1500.33 seconds wall clock time: 27 minutes 51.20 seconds (1671.20 seconds total)