Starting phenix.real_space_refine on Fri Dec 27 10:36:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k1b_36791/12_2024/8k1b_36791.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k1b_36791/12_2024/8k1b_36791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k1b_36791/12_2024/8k1b_36791.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k1b_36791/12_2024/8k1b_36791.map" model { file = "/net/cci-nas-00/data/ceres_data/8k1b_36791/12_2024/8k1b_36791.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k1b_36791/12_2024/8k1b_36791.cif" } resolution = 3.47 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= 0.007 sd= 0.121 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 16 5.16 5 C 2694 2.51 5 N 666 2.21 5 O 800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4176 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2046 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 239} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2046 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 239} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.03, per 1000 atoms: 0.73 Number of scatterers: 4176 At special positions: 0 Unit cell: (74.25, 81, 60.75, 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 16 16.00 O 800 8.00 N 666 7.00 C 2694 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS A 222 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 222 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 271 " 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 NAG-ASN " NAG A 401 " - " ASN A 67 " " NAG A 402 " - " ASN A 83 " " NAG A 403 " - " ASN A 136 " " NAG B 401 " - " ASN B 67 " " NAG B 402 " - " ASN B 83 " " NAG B 403 " - " ASN B 136 " Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 502.2 milliseconds 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 984 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 10 sheets defined 2.4% alpha, 40.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 115 through 117 No H-bonds generated for 'chain 'A' and resid 115 through 117' Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'B' and resid 115 through 117 No H-bonds generated for 'chain 'B' and resid 115 through 117' Processing helix chain 'B' and resid 251 through 253 No H-bonds generated for 'chain 'B' and resid 251 through 253' Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 56 removed outlier: 4.217A pdb=" N HIS A 50 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL A 163 " --> pdb=" O HIS A 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 70 removed outlier: 3.811A pdb=" N SER A 70 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU A 141 " --> pdb=" O SER A 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 113 removed outlier: 7.367A pdb=" N SER A 119 " --> pdb=" O GLN A 283 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 177 through 181 Processing sheet with id=AA5, first strand: chain 'A' and resid 187 through 192 Processing sheet with id=AA6, first strand: chain 'B' and resid 50 through 56 removed outlier: 4.216A pdb=" N HIS B 50 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL B 163 " --> pdb=" O HIS B 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 62 through 70 removed outlier: 3.812A pdb=" N SER B 70 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU B 141 " --> pdb=" O SER B 70 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 110 through 113 removed outlier: 7.367A pdb=" N SER B 119 " --> pdb=" O GLN B 283 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 177 through 181 Processing sheet with id=AB1, first strand: chain 'B' and resid 187 through 192 152 hydrogen bonds defined for protein. 402 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: 1.17 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 732 1.33 - 1.45: 1152 1.45 - 1.57: 2372 1.57 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 4280 Sorted by residual: bond pdb=" N MET B 152 " pdb=" CA MET B 152 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.08e-02 8.57e+03 7.17e+00 bond pdb=" N MET A 152 " pdb=" CA MET A 152 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.08e-02 8.57e+03 7.03e+00 bond pdb=" N ASN B 230 " pdb=" CA ASN B 230 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.29e-02 6.01e+03 6.66e+00 bond pdb=" C PRO B 183 " pdb=" O PRO B 183 " ideal model delta sigma weight residual 1.237 1.204 0.033 1.29e-02 6.01e+03 6.65e+00 bond pdb=" N ASN A 230 " pdb=" CA ASN A 230 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.29e-02 6.01e+03 6.62e+00 ... (remaining 4275 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.05: 5276 1.05 - 2.10: 399 2.10 - 3.16: 114 3.16 - 4.21: 35 4.21 - 5.26: 6 Bond angle restraints: 5830 Sorted by residual: angle pdb=" CA ARG A 127 " pdb=" C ARG A 127 " pdb=" O ARG A 127 " ideal model delta sigma weight residual 121.23 117.74 3.49 1.07e+00 8.73e-01 1.06e+01 angle pdb=" CA ARG B 127 " pdb=" C ARG B 127 " pdb=" O ARG B 127 " ideal model delta sigma weight residual 121.23 117.88 3.35 1.07e+00 8.73e-01 9.78e+00 angle pdb=" N GLN A 100 " pdb=" CA GLN A 100 " pdb=" C GLN A 100 " ideal model delta sigma weight residual 112.54 108.92 3.62 1.22e+00 6.72e-01 8.79e+00 angle pdb=" CA ASN B 219 " pdb=" C ASN B 219 " pdb=" O ASN B 219 " ideal model delta sigma weight residual 121.94 118.54 3.40 1.15e+00 7.56e-01 8.74e+00 angle pdb=" CA ASN A 219 " pdb=" C ASN A 219 " pdb=" O ASN A 219 " ideal model delta sigma weight residual 121.94 118.54 3.40 1.15e+00 7.56e-01 8.73e+00 ... (remaining 5825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 2216 16.82 - 33.65: 336 33.65 - 50.47: 66 50.47 - 67.30: 22 67.30 - 84.12: 6 Dihedral angle restraints: 2646 sinusoidal: 1126 harmonic: 1520 Sorted by residual: dihedral pdb=" CB CYS B 212 " pdb=" SG CYS B 212 " pdb=" SG CYS B 271 " pdb=" CB CYS B 271 " ideal model delta sinusoidal sigma weight residual 93.00 54.29 38.71 1 1.00e+01 1.00e-02 2.11e+01 dihedral pdb=" CB CYS A 212 " pdb=" SG CYS A 212 " pdb=" SG CYS A 271 " pdb=" CB CYS A 271 " ideal model delta sinusoidal sigma weight residual 93.00 54.30 38.70 1 1.00e+01 1.00e-02 2.11e+01 dihedral pdb=" CA ASN B 136 " pdb=" C ASN B 136 " pdb=" N GLU B 137 " pdb=" CA GLU B 137 " ideal model delta harmonic sigma weight residual 180.00 162.88 17.12 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 2643 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 356 0.031 - 0.062: 168 0.062 - 0.092: 64 0.092 - 0.123: 71 0.123 - 0.154: 13 Chirality restraints: 672 Sorted by residual: chirality pdb=" CA MET A 152 " pdb=" N MET A 152 " pdb=" C MET A 152 " pdb=" CB MET A 152 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.91e-01 chirality pdb=" CA MET B 152 " pdb=" N MET B 152 " pdb=" C MET B 152 " pdb=" CB MET B 152 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.82e-01 chirality pdb=" CA LEU A 94 " pdb=" N LEU A 94 " pdb=" C LEU A 94 " pdb=" CB LEU A 94 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.36e-01 ... (remaining 669 not shown) Planarity restraints: 748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 91 " -0.012 2.00e-02 2.50e+03 1.52e-02 4.60e+00 pdb=" CG TYR A 91 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR A 91 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR A 91 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR A 91 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 91 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 91 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 91 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 91 " 0.012 2.00e-02 2.50e+03 1.51e-02 4.59e+00 pdb=" CG TYR B 91 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR B 91 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 91 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR B 91 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 91 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 91 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 91 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS B 222 " -0.031 5.00e-02 4.00e+02 4.66e-02 3.47e+00 pdb=" N PRO B 223 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 223 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 223 " -0.023 5.00e-02 4.00e+02 ... (remaining 745 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 1558 2.87 - 3.37: 3514 3.37 - 3.88: 6502 3.88 - 4.39: 6905 4.39 - 4.90: 12590 Nonbonded interactions: 31069 Sorted by model distance: nonbonded pdb=" NH2 ARG B 79 " pdb=" OE1 GLN B 187 " model vdw 2.357 3.120 nonbonded pdb=" NH2 ARG A 79 " pdb=" OE1 GLN A 187 " model vdw 2.358 3.120 nonbonded pdb=" NH2 ARG A 79 " pdb=" O PRO A 186 " model vdw 2.380 3.120 nonbonded pdb=" NH2 ARG B 79 " pdb=" O PRO B 186 " model vdw 2.381 3.120 nonbonded pdb=" O PRO A 266 " pdb=" NH2 ARG A 289 " model vdw 2.389 3.120 ... (remaining 31064 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 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.280 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.890 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 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 : 0.005 0.043 4280 Z= 0.297 Angle : 0.710 5.260 5830 Z= 0.409 Chirality : 0.052 0.154 672 Planarity : 0.005 0.056 742 Dihedral : 16.501 84.119 1650 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.85 % Allowed : 28.42 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: -1.31 (0.36), residues: 504 helix: None (None), residues: 0 sheet: -0.04 (0.29), residues: 278 loop : -1.97 (0.39), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 106 HIS 0.001 0.000 HIS A 229 PHE 0.007 0.001 PHE A 193 TYR 0.038 0.002 TYR A 91 ARG 0.002 0.001 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 132 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 132 average time/residue: 0.2041 time to fit residues: 32.3395 Evaluate side-chains 75 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.7980 chunk 37 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 20 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 30.0000 chunk 29 optimal weight: 0.2980 chunk 45 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN B 178 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4280 Z= 0.197 Angle : 0.621 7.492 5830 Z= 0.325 Chirality : 0.050 0.173 672 Planarity : 0.004 0.032 742 Dihedral : 7.049 57.264 672 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.63 % Allowed : 28.21 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: -0.90 (0.35), residues: 504 helix: None (None), residues: 0 sheet: 0.17 (0.29), residues: 268 loop : -1.52 (0.38), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 106 HIS 0.004 0.001 HIS B 178 PHE 0.010 0.001 PHE B 177 TYR 0.017 0.001 TYR A 188 ARG 0.001 0.000 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 PHE cc_start: 0.6229 (m-80) cc_final: 0.5786 (m-80) REVERT: B 48 PHE cc_start: 0.6204 (m-80) cc_final: 0.5726 (m-80) REVERT: B 208 MET cc_start: 0.6656 (mmm) cc_final: 0.6331 (mmm) outliers start: 17 outliers final: 9 residues processed: 98 average time/residue: 0.1539 time to fit residues: 19.2105 Evaluate side-chains 87 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 297 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 45 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 44 optimal weight: 0.3980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS B 158 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4280 Z= 0.192 Angle : 0.634 7.605 5830 Z= 0.316 Chirality : 0.049 0.172 672 Planarity : 0.004 0.032 742 Dihedral : 6.364 59.273 672 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 5.98 % Allowed : 26.71 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: -0.76 (0.35), residues: 504 helix: None (None), residues: 0 sheet: 0.25 (0.31), residues: 248 loop : -1.29 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 106 HIS 0.006 0.002 HIS B 168 PHE 0.008 0.001 PHE A 253 TYR 0.017 0.001 TYR B 91 ARG 0.001 0.000 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 80 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 PHE cc_start: 0.6240 (m-80) cc_final: 0.5930 (m-80) REVERT: A 100 GLN cc_start: 0.7303 (pp30) cc_final: 0.7061 (tt0) REVERT: B 48 PHE cc_start: 0.6258 (m-80) cc_final: 0.5998 (m-80) REVERT: B 265 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7905 (mmtp) outliers start: 28 outliers final: 16 residues processed: 106 average time/residue: 0.1676 time to fit residues: 22.3141 Evaluate side-chains 89 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 297 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 0.9990 chunk 23 optimal weight: 0.0030 chunk 5 optimal weight: 5.9990 chunk 21 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 48 optimal weight: 20.0000 chunk 43 optimal weight: 0.0870 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 overall best weight: 0.5370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4280 Z= 0.175 Angle : 0.637 7.536 5830 Z= 0.315 Chirality : 0.049 0.165 672 Planarity : 0.003 0.031 742 Dihedral : 6.154 59.807 672 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.49 % Allowed : 27.78 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: -0.50 (0.35), residues: 504 helix: None (None), residues: 0 sheet: 0.52 (0.32), residues: 244 loop : -1.20 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 106 HIS 0.005 0.001 HIS B 178 PHE 0.007 0.001 PHE B 66 TYR 0.016 0.001 TYR B 188 ARG 0.001 0.000 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 PHE cc_start: 0.6141 (m-80) cc_final: 0.5855 (m-80) REVERT: B 208 MET cc_start: 0.5948 (mmm) cc_final: 0.5702 (mtm) REVERT: B 265 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7824 (mmtp) outliers start: 21 outliers final: 16 residues processed: 99 average time/residue: 0.1675 time to fit residues: 21.0459 Evaluate side-chains 83 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 249 GLN Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 297 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 41 optimal weight: 0.0010 chunk 33 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 16 optimal weight: 0.0030 chunk 9 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4280 Z= 0.191 Angle : 0.643 8.035 5830 Z= 0.318 Chirality : 0.049 0.220 672 Planarity : 0.003 0.029 742 Dihedral : 5.869 56.484 672 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 5.56 % Allowed : 27.99 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: -0.51 (0.35), residues: 504 helix: None (None), residues: 0 sheet: 0.49 (0.31), residues: 244 loop : -1.18 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 106 HIS 0.006 0.002 HIS B 178 PHE 0.008 0.001 PHE B 112 TYR 0.016 0.001 TYR A 188 ARG 0.002 0.000 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 74 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 PHE cc_start: 0.6127 (m-80) cc_final: 0.5873 (m-80) REVERT: B 190 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7056 (tp) REVERT: B 265 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7811 (mmtp) outliers start: 26 outliers final: 18 residues processed: 97 average time/residue: 0.1577 time to fit residues: 19.6230 Evaluate side-chains 91 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 297 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 6.9990 chunk 48 optimal weight: 20.0000 chunk 40 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 9.9990 chunk 46 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 35 optimal weight: 0.6980 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN B 100 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 4280 Z= 0.390 Angle : 0.746 9.489 5830 Z= 0.372 Chirality : 0.052 0.186 672 Planarity : 0.004 0.032 742 Dihedral : 6.497 46.705 672 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 6.62 % Allowed : 27.56 % Favored : 65.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: -0.95 (0.35), residues: 504 helix: None (None), residues: 0 sheet: -0.05 (0.29), residues: 262 loop : -1.26 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 106 HIS 0.007 0.002 HIS A 178 PHE 0.016 0.002 PHE B 253 TYR 0.025 0.002 TYR B 188 ARG 0.002 0.001 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 74 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.6983 (pt0) REVERT: A 190 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7148 (tp) REVERT: A 267 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7661 (mt-10) REVERT: B 190 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7035 (tp) outliers start: 31 outliers final: 19 residues processed: 100 average time/residue: 0.1489 time to fit residues: 19.1513 Evaluate side-chains 90 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 100 GLN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 297 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 48 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 9 optimal weight: 9.9990 chunk 32 optimal weight: 0.6980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4280 Z= 0.251 Angle : 0.692 9.445 5830 Z= 0.342 Chirality : 0.050 0.173 672 Planarity : 0.004 0.030 742 Dihedral : 5.722 35.508 672 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 5.34 % Allowed : 30.34 % Favored : 64.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: -0.78 (0.36), residues: 504 helix: None (None), residues: 0 sheet: 0.10 (0.30), residues: 258 loop : -1.17 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 106 HIS 0.006 0.002 HIS A 178 PHE 0.017 0.001 PHE A 146 TYR 0.020 0.001 TYR B 188 ARG 0.003 0.000 ARG B 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 0.899 Fit side-chains revert: symmetry clash REVERT: A 100 GLN cc_start: 0.7398 (pp30) cc_final: 0.7014 (pt0) REVERT: A 267 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7541 (mt-10) REVERT: B 187 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7495 (mm-40) REVERT: B 208 MET cc_start: 0.6465 (mmm) cc_final: 0.6173 (mtm) outliers start: 25 outliers final: 19 residues processed: 92 average time/residue: 0.1635 time to fit residues: 19.0612 Evaluate side-chains 85 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 100 GLN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 187 GLN Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 297 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 chunk 42 optimal weight: 0.3980 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 19 optimal weight: 0.2980 chunk 35 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 GLN B 158 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 4280 Z= 0.282 Angle : 0.721 11.393 5830 Z= 0.353 Chirality : 0.051 0.204 672 Planarity : 0.004 0.032 742 Dihedral : 5.432 38.459 672 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.91 % Allowed : 31.62 % Favored : 63.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: -0.73 (0.36), residues: 504 helix: None (None), residues: 0 sheet: 0.14 (0.30), residues: 258 loop : -1.14 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 106 HIS 0.006 0.002 HIS A 178 PHE 0.018 0.002 PHE A 177 TYR 0.020 0.001 TYR B 188 ARG 0.002 0.000 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLN cc_start: 0.7399 (pp30) cc_final: 0.6946 (pt0) REVERT: A 208 MET cc_start: 0.6783 (mmm) cc_final: 0.6406 (mtm) REVERT: A 267 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7562 (mt-10) REVERT: B 187 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7450 (mm-40) REVERT: B 208 MET cc_start: 0.6543 (mmm) cc_final: 0.6105 (mtm) outliers start: 23 outliers final: 21 residues processed: 87 average time/residue: 0.1506 time to fit residues: 16.7127 Evaluate side-chains 89 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 100 GLN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 187 GLN Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 297 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 22 optimal weight: 0.0170 chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 overall best weight: 0.8820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 HIS B 100 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4280 Z= 0.221 Angle : 0.720 11.692 5830 Z= 0.352 Chirality : 0.051 0.200 672 Planarity : 0.004 0.032 742 Dihedral : 4.953 34.677 672 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 5.77 % Allowed : 31.41 % Favored : 62.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: -0.62 (0.36), residues: 504 helix: None (None), residues: 0 sheet: 0.31 (0.32), residues: 246 loop : -1.14 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 106 HIS 0.007 0.002 HIS A 178 PHE 0.029 0.002 PHE A 177 TYR 0.017 0.001 TYR B 188 ARG 0.002 0.000 ARG B 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 72 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLN cc_start: 0.7356 (pp30) cc_final: 0.6866 (pt0) REVERT: A 267 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7564 (mt-10) REVERT: B 187 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7422 (mm-40) outliers start: 27 outliers final: 20 residues processed: 94 average time/residue: 0.1792 time to fit residues: 20.8336 Evaluate side-chains 85 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 100 GLN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 187 GLN Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 297 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 31 optimal weight: 0.0980 chunk 42 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 16 optimal weight: 0.2980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN A 185 GLN ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4280 Z= 0.216 Angle : 0.704 11.275 5830 Z= 0.348 Chirality : 0.051 0.191 672 Planarity : 0.004 0.033 742 Dihedral : 4.736 31.144 672 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.91 % Allowed : 31.41 % Favored : 63.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: -0.59 (0.36), residues: 504 helix: None (None), residues: 0 sheet: 0.34 (0.32), residues: 246 loop : -1.13 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 106 HIS 0.006 0.002 HIS A 178 PHE 0.015 0.001 PHE A 177 TYR 0.018 0.001 TYR A 91 ARG 0.002 0.000 ARG B 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1008 Ramachandran restraints generated. 504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 187 GLN cc_start: 0.7618 (OUTLIER) cc_final: 0.7333 (mm-40) REVERT: B 236 VAL cc_start: 0.8580 (OUTLIER) cc_final: 0.8366 (p) outliers start: 23 outliers final: 16 residues processed: 87 average time/residue: 0.1597 time to fit residues: 17.4733 Evaluate side-chains 84 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 187 GLN Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain B residue 290 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 297 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 7 optimal weight: 0.0010 chunk 34 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 26 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN B 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.184693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.132627 restraints weight = 5644.294| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 4.44 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4280 Z= 0.202 Angle : 0.703 10.958 5830 Z= 0.347 Chirality : 0.051 0.190 672 Planarity : 0.004 0.034 742 Dihedral : 4.493 23.785 672 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.27 % Allowed : 32.05 % Favored : 63.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: -0.60 (0.36), residues: 504 helix: None (None), residues: 0 sheet: 0.31 (0.31), residues: 246 loop : -1.11 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 106 HIS 0.006 0.002 HIS B 168 PHE 0.014 0.001 PHE B 146 TYR 0.016 0.001 TYR A 188 ARG 0.002 0.000 ARG B 127 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1271.72 seconds wall clock time: 23 minutes 56.14 seconds (1436.14 seconds total)