Starting phenix.real_space_refine on Fri Aug 22 19:49:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bys_16332/08_2025/8bys_16332.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bys_16332/08_2025/8bys_16332.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8bys_16332/08_2025/8bys_16332.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bys_16332/08_2025/8bys_16332.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bys_16332/08_2025/8bys_16332.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bys_16332/08_2025/8bys_16332.map" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.029 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 9 5.16 5 C 4579 2.51 5 N 1325 2.21 5 O 1493 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7406 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2470 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 2, 'TRANS': 320} Chain: "B" Number of atoms: 2466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2466 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 2, 'TRANS': 319} Chain: "C" Number of atoms: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2470 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 2, 'TRANS': 320} Time building chain proxies: 1.67, per 1000 atoms: 0.23 Number of scatterers: 7406 At special positions: 0 Unit cell: (84.952, 94.136, 95.284, 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 9 16.00 O 1493 8.00 N 1325 7.00 C 4579 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 276.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1680 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 6 sheets defined 5.3% alpha, 56.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 100 through 113 Processing helix chain 'B' and resid 101 through 113 removed outlier: 3.581A pdb=" N ARG B 113 " --> pdb=" O ARG B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 244 removed outlier: 4.038A pdb=" N ALA B 243 " --> pdb=" O ASP B 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 114 removed outlier: 3.543A pdb=" N ASP C 112 " --> pdb=" O SER C 108 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG C 113 " --> pdb=" O ARG C 109 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 244 removed outlier: 4.020A pdb=" N ALA C 243 " --> pdb=" O ASP C 240 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 130 removed outlier: 6.866A pdb=" N THR A 160 " --> pdb=" O VAL A 156 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG A 185 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LYS A 167 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ILE A 183 " --> pdb=" O LYS A 167 " (cutoff:3.500A) removed outlier: 24.083A pdb=" N THR A 182 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 18.720A pdb=" N THR A 206 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 12.803A pdb=" N ASP A 184 " --> pdb=" O GLN A 204 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLN A 204 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL A 196 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TYR A 213 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER A 267 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LYS A 376 " --> pdb=" O SER A 400 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER A 400 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL A 390 " --> pdb=" O VAL A 386 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 279 through 283 Processing sheet with id=AA3, first strand: chain 'B' and resid 118 through 130 removed outlier: 6.575A pdb=" N THR B 160 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG B 185 " --> pdb=" O ARG B 165 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LYS B 167 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ILE B 183 " --> pdb=" O LYS B 167 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N ASN B 169 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ALA B 181 " --> pdb=" O ASN B 169 " (cutoff:3.500A) removed outlier: 23.957A pdb=" N THR B 182 " --> pdb=" O THR B 206 " (cutoff:3.500A) removed outlier: 18.730A pdb=" N THR B 206 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 12.867A pdb=" N ASP B 184 " --> pdb=" O GLN B 204 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLN B 204 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LYS B 376 " --> pdb=" O SER B 400 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER B 400 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL B 390 " --> pdb=" O VAL B 386 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 279 through 283 Processing sheet with id=AA5, first strand: chain 'C' and resid 118 through 130 removed outlier: 6.752A pdb=" N THR C 160 " --> pdb=" O VAL C 156 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG C 185 " --> pdb=" O ARG C 165 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LYS C 167 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ILE C 183 " --> pdb=" O LYS C 167 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ASN C 169 " --> pdb=" O ALA C 181 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ALA C 181 " --> pdb=" O ASN C 169 " (cutoff:3.500A) removed outlier: 23.941A pdb=" N THR C 182 " --> pdb=" O THR C 206 " (cutoff:3.500A) removed outlier: 18.576A pdb=" N THR C 206 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 12.761A pdb=" N ASP C 184 " --> pdb=" O GLN C 204 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N GLN C 204 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LYS C 376 " --> pdb=" O SER C 400 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N SER C 400 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL C 390 " --> pdb=" O VAL C 386 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 279 through 283 465 hydrogen bonds defined for protein. 1311 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: 0.92 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2540 1.34 - 1.45: 1259 1.45 - 1.57: 3724 1.57 - 1.69: 0 1.69 - 1.80: 18 Bond restraints: 7541 Sorted by residual: bond pdb=" CG ASP C 218 " pdb=" OD1 ASP C 218 " ideal model delta sigma weight residual 1.249 1.230 0.019 1.90e-02 2.77e+03 1.03e+00 bond pdb=" CB ILE C 239 " pdb=" CG1 ILE C 239 " ideal model delta sigma weight residual 1.530 1.511 0.019 2.00e-02 2.50e+03 9.31e-01 bond pdb=" CA ASP C 214 " pdb=" C ASP C 214 " ideal model delta sigma weight residual 1.530 1.522 0.009 1.08e-02 8.57e+03 6.73e-01 bond pdb=" CB ASP C 218 " pdb=" CG ASP C 218 " ideal model delta sigma weight residual 1.516 1.496 0.020 2.50e-02 1.60e+03 6.43e-01 bond pdb=" N GLY A 261 " pdb=" CA GLY A 261 " ideal model delta sigma weight residual 1.456 1.447 0.009 1.16e-02 7.43e+03 5.70e-01 ... (remaining 7536 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 9946 1.55 - 3.10: 189 3.10 - 4.64: 21 4.64 - 6.19: 8 6.19 - 7.74: 1 Bond angle restraints: 10165 Sorted by residual: angle pdb=" N ASP B 215 " pdb=" CA ASP B 215 " pdb=" C ASP B 215 " ideal model delta sigma weight residual 107.73 113.36 -5.63 1.34e+00 5.57e-01 1.77e+01 angle pdb=" C ASP C 215 " pdb=" N THR C 216 " pdb=" CA THR C 216 " ideal model delta sigma weight residual 120.90 125.84 -4.94 1.41e+00 5.03e-01 1.23e+01 angle pdb=" CA PHE B 203 " pdb=" C PHE B 203 " pdb=" N GLN B 204 " ideal model delta sigma weight residual 115.54 120.09 -4.55 1.52e+00 4.33e-01 8.95e+00 angle pdb=" CA PHE B 203 " pdb=" C PHE B 203 " pdb=" O PHE B 203 " ideal model delta sigma weight residual 121.60 118.32 3.28 1.21e+00 6.83e-01 7.36e+00 angle pdb=" C ALA C 138 " pdb=" N ASN C 139 " pdb=" CA ASN C 139 " ideal model delta sigma weight residual 121.54 126.50 -4.96 1.91e+00 2.74e-01 6.75e+00 ... (remaining 10160 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4015 17.98 - 35.96: 284 35.96 - 53.94: 45 53.94 - 71.92: 16 71.92 - 89.90: 7 Dihedral angle restraints: 4367 sinusoidal: 1662 harmonic: 2705 Sorted by residual: dihedral pdb=" CA ASP C 214 " pdb=" CB ASP C 214 " pdb=" CG ASP C 214 " pdb=" OD1 ASP C 214 " ideal model delta sinusoidal sigma weight residual -30.00 -87.63 57.63 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA ASP A 367 " pdb=" C ASP A 367 " pdb=" N LEU A 368 " pdb=" CA LEU A 368 " ideal model delta harmonic sigma weight residual 180.00 163.63 16.37 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA TYR A 213 " pdb=" C TYR A 213 " pdb=" N ASP A 214 " pdb=" CA ASP A 214 " ideal model delta harmonic sigma weight residual 180.00 163.94 16.06 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 4364 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 444 0.026 - 0.052: 371 0.052 - 0.077: 139 0.077 - 0.103: 38 0.103 - 0.129: 40 Chirality restraints: 1032 Sorted by residual: chirality pdb=" CA VAL B 224 " pdb=" N VAL B 224 " pdb=" C VAL B 224 " pdb=" CB VAL B 224 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.15e-01 chirality pdb=" CA ASN B 321 " pdb=" N ASN B 321 " pdb=" C ASN B 321 " pdb=" CB ASN B 321 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA VAL C 163 " pdb=" N VAL C 163 " pdb=" C VAL C 163 " pdb=" CB VAL C 163 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 1029 not shown) Planarity restraints: 1367 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 214 " 0.006 2.00e-02 2.50e+03 1.19e-02 1.41e+00 pdb=" C ASP C 214 " -0.021 2.00e-02 2.50e+03 pdb=" O ASP C 214 " 0.008 2.00e-02 2.50e+03 pdb=" N ASP C 215 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 139 " 0.005 2.00e-02 2.50e+03 1.03e-02 1.07e+00 pdb=" C ASN C 139 " -0.018 2.00e-02 2.50e+03 pdb=" O ASN C 139 " 0.007 2.00e-02 2.50e+03 pdb=" N SER C 140 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 420 " -0.004 2.00e-02 2.50e+03 7.28e-03 9.27e-01 pdb=" CG PHE A 420 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE A 420 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 420 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 420 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 420 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 420 " 0.001 2.00e-02 2.50e+03 ... (remaining 1364 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 524 2.74 - 3.28: 6826 3.28 - 3.82: 11482 3.82 - 4.36: 14516 4.36 - 4.90: 27290 Nonbonded interactions: 60638 Sorted by model distance: nonbonded pdb=" OD2 ASP B 215 " pdb=" OG SER B 359 " model vdw 2.195 3.040 nonbonded pdb=" OG1 THR C 206 " pdb=" OD2 ASP C 214 " model vdw 2.200 3.040 nonbonded pdb=" O VAL A 263 " pdb=" OG SER A 267 " model vdw 2.204 3.040 nonbonded pdb=" OG1 THR A 206 " pdb=" OD2 ASP A 214 " model vdw 2.204 3.040 nonbonded pdb=" OG1 THR B 206 " pdb=" OD1 ASP B 214 " model vdw 2.235 3.040 ... (remaining 60633 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' and resid 100 through 421) selection = chain 'B' selection = (chain 'C' and resid 100 through 421) } 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: 1.560 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: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.820 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 7541 Z= 0.176 Angle : 0.563 7.741 10165 Z= 0.325 Chirality : 0.044 0.129 1032 Planarity : 0.002 0.032 1367 Dihedral : 13.509 89.900 2687 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.29), residues: 962 helix: 1.49 (0.97), residues: 41 sheet: -0.36 (0.22), residues: 588 loop : -1.11 (0.36), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 303 TYR 0.013 0.002 TYR B 235 PHE 0.016 0.002 PHE A 420 TRP 0.014 0.001 TRP C 325 HIS 0.004 0.002 HIS C 283 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 7541) covalent geometry : angle 0.56308 (10165) hydrogen bonds : bond 0.08465 ( 465) hydrogen bonds : angle 6.08955 ( 1311) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.256 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.0762 time to fit residues: 5.4164 Evaluate side-chains 35 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 221 GLN A 223 ASN A 246 ASN A 305 ASN A 347 GLN A 417 ASN B 180 GLN B 190 HIS B 232 GLN ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.150966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.128981 restraints weight = 8117.873| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.91 r_work: 0.3447 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.0597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7541 Z= 0.162 Angle : 0.539 8.364 10165 Z= 0.308 Chirality : 0.045 0.135 1032 Planarity : 0.002 0.015 1367 Dihedral : 4.414 15.413 1064 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.13 % Allowed : 5.91 % Favored : 93.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.28), residues: 962 helix: 1.47 (0.93), residues: 41 sheet: -0.26 (0.22), residues: 577 loop : -1.33 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 106 TYR 0.011 0.001 TYR C 187 PHE 0.015 0.002 PHE A 217 TRP 0.014 0.001 TRP C 325 HIS 0.004 0.002 HIS A 190 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 7541) covalent geometry : angle 0.53917 (10165) hydrogen bonds : bond 0.03106 ( 465) hydrogen bonds : angle 5.42770 ( 1311) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.201 Fit side-chains REVERT: A 161 GLN cc_start: 0.8240 (pt0) cc_final: 0.8021 (pt0) outliers start: 1 outliers final: 1 residues processed: 43 average time/residue: 0.0567 time to fit residues: 3.6892 Evaluate side-chains 35 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 64 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 7 optimal weight: 0.0770 chunk 39 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 299 ASN A 347 GLN B 299 ASN ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.150513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.126535 restraints weight = 8582.661| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.20 r_work: 0.3349 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 7541 Z= 0.330 Angle : 0.654 8.411 10165 Z= 0.372 Chirality : 0.048 0.141 1032 Planarity : 0.003 0.035 1367 Dihedral : 4.938 18.028 1064 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 1.57 % Allowed : 9.84 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.28), residues: 962 helix: 1.62 (0.93), residues: 41 sheet: -0.41 (0.22), residues: 581 loop : -1.56 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 413 TYR 0.019 0.002 TYR A 348 PHE 0.023 0.003 PHE A 217 TRP 0.020 0.002 TRP C 325 HIS 0.007 0.002 HIS A 190 Details of bonding type rmsd covalent geometry : bond 0.00745 ( 7541) covalent geometry : angle 0.65378 (10165) hydrogen bonds : bond 0.03590 ( 465) hydrogen bonds : angle 5.76100 ( 1311) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.240 Fit side-chains REVERT: A 161 GLN cc_start: 0.8414 (pt0) cc_final: 0.8187 (pt0) REVERT: A 420 PHE cc_start: 0.7654 (OUTLIER) cc_final: 0.6846 (m-10) REVERT: B 342 TRP cc_start: 0.9090 (p-90) cc_final: 0.8871 (p-90) outliers start: 12 outliers final: 8 residues processed: 51 average time/residue: 0.0718 time to fit residues: 5.2363 Evaluate side-chains 50 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 412 TYR Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 139 ASN Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 406 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 5 optimal weight: 0.9990 chunk 54 optimal weight: 0.0980 chunk 69 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 52 optimal weight: 0.0030 chunk 81 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 10 optimal weight: 0.4980 chunk 25 optimal weight: 0.3980 chunk 66 optimal weight: 0.9980 overall best weight: 0.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 305 ASN B 169 ASN B 299 ASN ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.153251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.134780 restraints weight = 8074.013| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.49 r_work: 0.3490 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7541 Z= 0.106 Angle : 0.496 9.060 10165 Z= 0.284 Chirality : 0.044 0.134 1032 Planarity : 0.002 0.024 1367 Dihedral : 4.311 15.438 1064 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.18 % Allowed : 10.24 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.28), residues: 962 helix: 1.72 (0.92), residues: 41 sheet: -0.29 (0.23), residues: 567 loop : -1.44 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 303 TYR 0.009 0.001 TYR C 187 PHE 0.013 0.001 PHE C 217 TRP 0.015 0.001 TRP C 325 HIS 0.003 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 7541) covalent geometry : angle 0.49613 (10165) hydrogen bonds : bond 0.02764 ( 465) hydrogen bonds : angle 5.28594 ( 1311) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.212 Fit side-chains REVERT: A 161 GLN cc_start: 0.8155 (pt0) cc_final: 0.7948 (pt0) REVERT: B 214 ASP cc_start: 0.8509 (t70) cc_final: 0.8280 (t0) outliers start: 9 outliers final: 6 residues processed: 58 average time/residue: 0.0678 time to fit residues: 5.7871 Evaluate side-chains 49 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 412 TYR Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain C residue 215 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 57 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 55 optimal weight: 0.4980 chunk 64 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 ASN ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.148269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.126146 restraints weight = 8191.760| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.92 r_work: 0.3407 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 7541 Z= 0.206 Angle : 0.545 8.991 10165 Z= 0.311 Chirality : 0.045 0.131 1032 Planarity : 0.002 0.024 1367 Dihedral : 4.461 16.672 1064 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.23 % Allowed : 11.02 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.28), residues: 962 helix: 1.79 (0.92), residues: 41 sheet: -0.33 (0.22), residues: 579 loop : -1.43 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 303 TYR 0.012 0.002 TYR A 348 PHE 0.016 0.002 PHE C 217 TRP 0.014 0.001 TRP C 325 HIS 0.004 0.002 HIS A 190 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 7541) covalent geometry : angle 0.54455 (10165) hydrogen bonds : bond 0.02980 ( 465) hydrogen bonds : angle 5.37591 ( 1311) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 43 time to evaluate : 0.189 Fit side-chains REVERT: A 161 GLN cc_start: 0.8230 (pt0) cc_final: 0.8007 (pt0) REVERT: A 420 PHE cc_start: 0.7274 (OUTLIER) cc_final: 0.6447 (m-10) outliers start: 17 outliers final: 10 residues processed: 56 average time/residue: 0.0768 time to fit residues: 6.3313 Evaluate side-chains 53 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 412 TYR Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 139 ASN Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 406 ASN Chi-restraints excluded: chain C residue 215 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 57 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 ASN ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.149928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.129299 restraints weight = 8108.076| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.77 r_work: 0.3405 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 7541 Z= 0.200 Angle : 0.546 9.150 10165 Z= 0.312 Chirality : 0.045 0.132 1032 Planarity : 0.002 0.021 1367 Dihedral : 4.503 16.673 1064 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.36 % Allowed : 12.07 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.28), residues: 962 helix: 1.84 (0.93), residues: 41 sheet: -0.35 (0.22), residues: 579 loop : -1.46 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 303 TYR 0.012 0.002 TYR A 348 PHE 0.017 0.002 PHE C 217 TRP 0.016 0.002 TRP C 325 HIS 0.004 0.002 HIS A 190 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 7541) covalent geometry : angle 0.54602 (10165) hydrogen bonds : bond 0.02992 ( 465) hydrogen bonds : angle 5.39575 ( 1311) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 45 time to evaluate : 0.274 Fit side-chains REVERT: A 161 GLN cc_start: 0.8229 (pt0) cc_final: 0.8002 (pt0) REVERT: A 420 PHE cc_start: 0.7316 (OUTLIER) cc_final: 0.6517 (m-10) outliers start: 18 outliers final: 15 residues processed: 60 average time/residue: 0.0808 time to fit residues: 7.0330 Evaluate side-chains 56 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 412 TYR Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 139 ASN Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 406 ASN Chi-restraints excluded: chain B residue 413 ARG Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 326 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 54 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 94 optimal weight: 0.0010 chunk 86 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 GLN A 305 ASN ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 ASN ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.145915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.122197 restraints weight = 8725.284| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.20 r_work: 0.3341 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 7541 Z= 0.249 Angle : 0.579 9.358 10165 Z= 0.329 Chirality : 0.046 0.135 1032 Planarity : 0.003 0.022 1367 Dihedral : 4.628 17.012 1064 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.76 % Allowed : 12.47 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.28), residues: 962 helix: 1.93 (0.94), residues: 41 sheet: -0.40 (0.22), residues: 579 loop : -1.48 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 303 TYR 0.014 0.002 TYR A 348 PHE 0.018 0.002 PHE C 217 TRP 0.017 0.002 TRP C 325 HIS 0.005 0.002 HIS A 190 Details of bonding type rmsd covalent geometry : bond 0.00558 ( 7541) covalent geometry : angle 0.57891 (10165) hydrogen bonds : bond 0.03154 ( 465) hydrogen bonds : angle 5.50703 ( 1311) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 40 time to evaluate : 0.175 Fit side-chains REVERT: A 161 GLN cc_start: 0.8289 (pt0) cc_final: 0.8052 (pt0) REVERT: A 420 PHE cc_start: 0.7408 (OUTLIER) cc_final: 0.6577 (m-10) outliers start: 21 outliers final: 16 residues processed: 58 average time/residue: 0.0847 time to fit residues: 6.9513 Evaluate side-chains 57 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 412 TYR Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 139 ASN Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 406 ASN Chi-restraints excluded: chain B residue 413 ARG Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 326 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 18 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 ASN ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.146837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.122260 restraints weight = 8582.818| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.25 r_work: 0.3360 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 7541 Z= 0.162 Angle : 0.526 9.527 10165 Z= 0.300 Chirality : 0.044 0.133 1032 Planarity : 0.002 0.019 1367 Dihedral : 4.447 16.307 1064 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 2.36 % Allowed : 12.86 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.28), residues: 962 helix: 1.85 (0.94), residues: 41 sheet: -0.33 (0.22), residues: 579 loop : -1.43 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 303 TYR 0.010 0.001 TYR C 187 PHE 0.014 0.002 PHE C 217 TRP 0.017 0.001 TRP C 325 HIS 0.004 0.002 HIS C 283 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 7541) covalent geometry : angle 0.52594 (10165) hydrogen bonds : bond 0.02862 ( 465) hydrogen bonds : angle 5.35226 ( 1311) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 42 time to evaluate : 0.277 Fit side-chains REVERT: A 161 GLN cc_start: 0.8251 (pt0) cc_final: 0.8023 (pt0) REVERT: A 420 PHE cc_start: 0.7400 (OUTLIER) cc_final: 0.6603 (m-10) outliers start: 18 outliers final: 14 residues processed: 57 average time/residue: 0.0794 time to fit residues: 6.5384 Evaluate side-chains 57 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 412 TYR Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 406 ASN Chi-restraints excluded: chain B residue 413 ARG Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 326 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 0.4980 chunk 30 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 ASN A 305 ASN ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 ASN ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.146176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.121583 restraints weight = 8547.938| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.26 r_work: 0.3346 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 7541 Z= 0.204 Angle : 0.553 9.545 10165 Z= 0.315 Chirality : 0.045 0.141 1032 Planarity : 0.002 0.022 1367 Dihedral : 4.527 16.800 1064 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.49 % Allowed : 13.12 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.28), residues: 962 helix: 1.88 (0.94), residues: 41 sheet: -0.37 (0.22), residues: 579 loop : -1.44 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 303 TYR 0.012 0.002 TYR C 256 PHE 0.018 0.002 PHE C 217 TRP 0.016 0.002 TRP C 325 HIS 0.004 0.002 HIS A 190 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 7541) covalent geometry : angle 0.55272 (10165) hydrogen bonds : bond 0.02984 ( 465) hydrogen bonds : angle 5.40792 ( 1311) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 42 time to evaluate : 0.165 Fit side-chains REVERT: A 161 GLN cc_start: 0.8264 (pt0) cc_final: 0.8027 (pt0) REVERT: A 420 PHE cc_start: 0.7301 (OUTLIER) cc_final: 0.6521 (m-10) outliers start: 19 outliers final: 18 residues processed: 56 average time/residue: 0.0684 time to fit residues: 5.5314 Evaluate side-chains 61 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 42 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 412 TYR Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 406 ASN Chi-restraints excluded: chain B residue 413 ARG Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 326 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 61 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 ASN A 305 ASN ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 ASN ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.145217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.120867 restraints weight = 8616.560| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.23 r_work: 0.3340 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 7541 Z= 0.243 Angle : 0.578 9.563 10165 Z= 0.329 Chirality : 0.046 0.141 1032 Planarity : 0.003 0.025 1367 Dihedral : 4.619 16.897 1064 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.62 % Allowed : 12.99 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.28), residues: 962 helix: 1.88 (0.94), residues: 41 sheet: -0.44 (0.23), residues: 569 loop : -1.49 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 303 TYR 0.013 0.002 TYR C 256 PHE 0.018 0.002 PHE C 217 TRP 0.016 0.002 TRP C 325 HIS 0.005 0.002 HIS A 190 Details of bonding type rmsd covalent geometry : bond 0.00544 ( 7541) covalent geometry : angle 0.57845 (10165) hydrogen bonds : bond 0.03111 ( 465) hydrogen bonds : angle 5.49314 ( 1311) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 41 time to evaluate : 0.263 Fit side-chains REVERT: A 161 GLN cc_start: 0.8285 (pt0) cc_final: 0.8050 (pt0) REVERT: A 420 PHE cc_start: 0.7365 (OUTLIER) cc_final: 0.6569 (m-10) outliers start: 20 outliers final: 19 residues processed: 57 average time/residue: 0.0798 time to fit residues: 6.6067 Evaluate side-chains 61 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 41 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 412 TYR Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 406 ASN Chi-restraints excluded: chain B residue 413 ARG Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 326 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 9 optimal weight: 1.9990 chunk 62 optimal weight: 0.0010 chunk 54 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 ASN A 305 ASN ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 ASN ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.146835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.122497 restraints weight = 8467.769| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.22 r_work: 0.3361 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7541 Z= 0.152 Angle : 0.530 9.667 10165 Z= 0.302 Chirality : 0.044 0.139 1032 Planarity : 0.002 0.024 1367 Dihedral : 4.468 16.179 1064 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 2.62 % Allowed : 12.99 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.28), residues: 962 helix: 1.82 (0.93), residues: 41 sheet: -0.34 (0.22), residues: 579 loop : -1.42 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 303 TYR 0.010 0.001 TYR C 187 PHE 0.015 0.002 PHE C 217 TRP 0.017 0.001 TRP C 325 HIS 0.003 0.002 HIS C 283 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 7541) covalent geometry : angle 0.53033 (10165) hydrogen bonds : bond 0.02857 ( 465) hydrogen bonds : angle 5.39307 ( 1311) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1710.52 seconds wall clock time: 30 minutes 3.80 seconds (1803.80 seconds total)