Starting phenix.real_space_refine on Tue Feb 3 16:54:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kzw_62677/02_2026/9kzw_62677.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kzw_62677/02_2026/9kzw_62677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kzw_62677/02_2026/9kzw_62677.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kzw_62677/02_2026/9kzw_62677.map" model { file = "/net/cci-nas-00/data/ceres_data/9kzw_62677/02_2026/9kzw_62677.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kzw_62677/02_2026/9kzw_62677.cif" } resolution = 3.0 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= 0.009 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 48 5.16 5 C 3378 2.51 5 N 884 2.21 5 O 916 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5226 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2613 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 12, 'TRANS': 321} Chain breaks: 1 Chain: "B" Number of atoms: 2613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2613 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 12, 'TRANS': 321} Chain breaks: 1 Time building chain proxies: 1.36, per 1000 atoms: 0.26 Number of scatterers: 5226 At special positions: 0 Unit cell: (75.15, 56.25, 122.85, 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 48 16.00 O 916 8.00 N 884 7.00 C 3378 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 276 " - pdb=" SG CYS A 282 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS B 291 " distance=1.87 Simple disulfide: pdb=" SG CYS B 276 " - pdb=" SG CYS B 282 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.44 Conformation dependent library (CDL) restraints added in 307.5 milliseconds 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1256 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 2 sheets defined 65.9% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 5 through 32 removed outlier: 3.755A pdb=" N ARG A 10 " --> pdb=" O ARG A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 63 removed outlier: 4.173A pdb=" N SER A 46 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP A 47 " --> pdb=" O HIS A 43 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG A 63 " --> pdb=" O ARG A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 106 removed outlier: 4.092A pdb=" N VAL A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 134 Processing helix chain 'A' and resid 232 through 272 removed outlier: 4.043A pdb=" N GLU A 236 " --> pdb=" O HIS A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 298 removed outlier: 3.642A pdb=" N GLU A 296 " --> pdb=" O LYS A 292 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE A 298 " --> pdb=" O PHE A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 344 removed outlier: 3.556A pdb=" N THR A 319 " --> pdb=" O TYR A 315 " (cutoff:3.500A) Proline residue: A 334 - end of helix Processing helix chain 'A' and resid 352 through 363 Processing helix chain 'A' and resid 395 through 411 removed outlier: 3.677A pdb=" N VAL A 399 " --> pdb=" O SER A 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 32 removed outlier: 3.755A pdb=" N ARG B 10 " --> pdb=" O ARG B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 63 removed outlier: 4.173A pdb=" N SER B 46 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP B 47 " --> pdb=" O HIS B 43 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG B 63 " --> pdb=" O ARG B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 106 removed outlier: 4.091A pdb=" N VAL B 79 " --> pdb=" O ILE B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 134 Processing helix chain 'B' and resid 232 through 272 removed outlier: 4.043A pdb=" N GLU B 236 " --> pdb=" O HIS B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 298 removed outlier: 3.905A pdb=" N ILE B 298 " --> pdb=" O PHE B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 344 removed outlier: 3.557A pdb=" N THR B 319 " --> pdb=" O TYR B 315 " (cutoff:3.500A) Proline residue: B 334 - end of helix Processing helix chain 'B' and resid 352 through 363 Processing helix chain 'B' and resid 395 through 411 removed outlier: 3.677A pdb=" N VAL B 399 " --> pdb=" O SER B 395 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 368 through 378 removed outlier: 6.211A pdb=" N VAL A 369 " --> pdb=" O LYS A 389 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N LYS A 389 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N GLU A 371 " --> pdb=" O HIS A 387 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N HIS A 387 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ARG A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE A 382 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N THR A 416 " --> pdb=" O ILE A 382 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ALA A 384 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N GLN A 418 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA A 386 " --> pdb=" O GLN A 418 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 368 through 378 removed outlier: 6.212A pdb=" N VAL B 369 " --> pdb=" O LYS B 389 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N LYS B 389 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N GLU B 371 " --> pdb=" O HIS B 387 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N HIS B 387 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ARG B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE B 382 " --> pdb=" O ALA B 414 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N THR B 416 " --> pdb=" O ILE B 382 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ALA B 384 " --> pdb=" O THR B 416 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N GLN B 418 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA B 386 " --> pdb=" O GLN B 418 " (cutoff:3.500A) 353 hydrogen bonds defined for protein. 1059 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: 0.77 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 979 1.33 - 1.45: 1268 1.45 - 1.57: 3023 1.57 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 5342 Sorted by residual: bond pdb=" N PRO B 285 " pdb=" CA PRO B 285 " ideal model delta sigma weight residual 1.470 1.425 0.045 1.22e-02 6.72e+03 1.37e+01 bond pdb=" N LYS B 292 " pdb=" CA LYS B 292 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.29e-02 6.01e+03 7.99e+00 bond pdb=" C PRO B 288 " pdb=" O PRO B 288 " ideal model delta sigma weight residual 1.233 1.208 0.026 1.06e-02 8.90e+03 5.86e+00 bond pdb=" C ASP B 289 " pdb=" N PRO B 290 " ideal model delta sigma weight residual 1.336 1.365 -0.029 1.20e-02 6.94e+03 5.79e+00 bond pdb=" C PRO B 285 " pdb=" O PRO B 285 " ideal model delta sigma weight residual 1.236 1.206 0.031 1.36e-02 5.41e+03 5.03e+00 ... (remaining 5337 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 7182 2.03 - 4.06: 66 4.06 - 6.09: 12 6.09 - 8.12: 0 8.12 - 10.15: 2 Bond angle restraints: 7262 Sorted by residual: angle pdb=" N PHE B 287 " pdb=" CA PHE B 287 " pdb=" C PHE B 287 " ideal model delta sigma weight residual 110.50 100.35 10.15 1.52e+00 4.33e-01 4.46e+01 angle pdb=" N CYS B 286 " pdb=" CA CYS B 286 " pdb=" C CYS B 286 " ideal model delta sigma weight residual 111.56 120.90 -9.34 1.53e+00 4.27e-01 3.73e+01 angle pdb=" N PRO B 285 " pdb=" CA PRO B 285 " pdb=" C PRO B 285 " ideal model delta sigma weight residual 114.20 108.13 6.07 1.20e+00 6.94e-01 2.56e+01 angle pdb=" C PRO B 288 " pdb=" CA PRO B 288 " pdb=" CB PRO B 288 " ideal model delta sigma weight residual 111.11 105.66 5.45 1.17e+00 7.31e-01 2.17e+01 angle pdb=" CA PHE B 287 " pdb=" CB PHE B 287 " pdb=" CG PHE B 287 " ideal model delta sigma weight residual 113.80 118.23 -4.43 1.00e+00 1.00e+00 1.96e+01 ... (remaining 7257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 2666 17.28 - 34.57: 364 34.57 - 51.85: 108 51.85 - 69.13: 21 69.13 - 86.42: 6 Dihedral angle restraints: 3165 sinusoidal: 1233 harmonic: 1932 Sorted by residual: dihedral pdb=" CB CYS A 276 " pdb=" SG CYS A 276 " pdb=" SG CYS A 282 " pdb=" CB CYS A 282 " ideal model delta sinusoidal sigma weight residual -86.00 -152.56 66.56 1 1.00e+01 1.00e-02 5.78e+01 dihedral pdb=" CB CYS B 276 " pdb=" SG CYS B 276 " pdb=" SG CYS B 282 " pdb=" CB CYS B 282 " ideal model delta sinusoidal sigma weight residual -86.00 -152.55 66.55 1 1.00e+01 1.00e-02 5.78e+01 dihedral pdb=" CA PRO B 288 " pdb=" C PRO B 288 " pdb=" N ASP B 289 " pdb=" CA ASP B 289 " ideal model delta harmonic sigma weight residual -180.00 -156.35 -23.65 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 3162 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 754 0.060 - 0.120: 99 0.120 - 0.180: 6 0.180 - 0.240: 1 0.240 - 0.300: 2 Chirality restraints: 862 Sorted by residual: chirality pdb=" CA CYS B 286 " pdb=" N CYS B 286 " pdb=" C CYS B 286 " pdb=" CB CYS B 286 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CA CYS B 291 " pdb=" N CYS B 291 " pdb=" C CYS B 291 " pdb=" CB CYS B 291 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA LYS B 292 " pdb=" N LYS B 292 " pdb=" C LYS B 292 " pdb=" CB LYS B 292 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.62e-01 ... (remaining 859 not shown) Planarity restraints: 910 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 285 " -0.012 2.00e-02 2.50e+03 2.50e-02 6.24e+00 pdb=" C PRO B 285 " 0.043 2.00e-02 2.50e+03 pdb=" O PRO B 285 " -0.016 2.00e-02 2.50e+03 pdb=" N CYS B 286 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 283 " -0.010 2.00e-02 2.50e+03 1.94e-02 3.76e+00 pdb=" C VAL B 283 " 0.034 2.00e-02 2.50e+03 pdb=" O VAL B 283 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN B 284 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 86 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.15e+00 pdb=" C ALA A 86 " -0.025 2.00e-02 2.50e+03 pdb=" O ALA A 86 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE A 87 " 0.008 2.00e-02 2.50e+03 ... (remaining 907 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1232 2.79 - 3.32: 5230 3.32 - 3.85: 9005 3.85 - 4.37: 10049 4.37 - 4.90: 17494 Nonbonded interactions: 43010 Sorted by model distance: nonbonded pdb=" O HIS A 43 " pdb=" OG SER A 46 " model vdw 2.263 3.040 nonbonded pdb=" O HIS B 43 " pdb=" OG SER B 46 " model vdw 2.264 3.040 nonbonded pdb=" NE2 GLN A 376 " pdb=" O GLY A 379 " model vdw 2.304 3.120 nonbonded pdb=" NE2 GLN B 376 " pdb=" O GLY B 379 " model vdw 2.304 3.120 nonbonded pdb=" NH2 ARG B 76 " pdb=" OE1 GLN B 345 " model vdw 2.376 3.120 ... (remaining 43005 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: 0.01 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: 7.460 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: 0.230 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.870 Find NCS groups from input model: 0.070 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:7.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 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 0.157 5345 Z= 0.203 Angle : 0.640 22.201 7268 Z= 0.360 Chirality : 0.041 0.300 862 Planarity : 0.005 0.032 910 Dihedral : 17.214 86.415 1900 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.00 % Allowed : 24.83 % Favored : 75.17 % 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 are not related in a simple way. whole: -0.38 (0.34), residues: 660 helix: 0.53 (0.26), residues: 428 sheet: -1.37 (0.85), residues: 46 loop : -1.62 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 246 TYR 0.007 0.001 TYR B 333 PHE 0.022 0.001 PHE B 287 TRP 0.005 0.001 TRP B 375 HIS 0.003 0.001 HIS B 370 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 5342) covalent geometry : angle 0.52528 ( 7262) SS BOND : bond 0.09056 ( 3) SS BOND : angle 12.73327 ( 6) hydrogen bonds : bond 0.12086 ( 353) hydrogen bonds : angle 6.49095 ( 1059) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.208 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.5768 time to fit residues: 33.1586 Evaluate side-chains 51 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 HIS ** A 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 GLN ** B 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 HIS ** B 413 HIS ** 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 = 0.4141 r_free = 0.4141 target = 0.185814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.137323 restraints weight = 5460.908| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.63 r_work: 0.3472 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5345 Z= 0.141 Angle : 0.444 4.731 7268 Z= 0.232 Chirality : 0.039 0.130 862 Planarity : 0.004 0.033 910 Dihedral : 3.195 13.332 706 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.99 % Allowed : 19.79 % Favored : 76.22 % 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 are not related in a simple way. whole: 1.76 (0.35), residues: 660 helix: 2.42 (0.25), residues: 432 sheet: -1.28 (0.88), residues: 46 loop : -1.36 (0.47), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 62 TYR 0.009 0.001 TYR B 333 PHE 0.013 0.001 PHE B 287 TRP 0.006 0.001 TRP B 375 HIS 0.003 0.001 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 5342) covalent geometry : angle 0.44346 ( 7262) SS BOND : bond 0.00277 ( 3) SS BOND : angle 1.06438 ( 6) hydrogen bonds : bond 0.04509 ( 353) hydrogen bonds : angle 3.86931 ( 1059) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 60 time to evaluate : 0.197 Fit side-chains REVERT: A 25 GLU cc_start: 0.6607 (tt0) cc_final: 0.6321 (tt0) REVERT: A 71 THR cc_start: 0.8838 (OUTLIER) cc_final: 0.8617 (p) REVERT: A 102 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6374 (mp0) REVERT: A 108 HIS cc_start: 0.6645 (OUTLIER) cc_final: 0.5974 (m-70) REVERT: B 25 GLU cc_start: 0.6574 (tt0) cc_final: 0.6296 (tt0) REVERT: B 71 THR cc_start: 0.8833 (OUTLIER) cc_final: 0.8615 (p) REVERT: B 108 HIS cc_start: 0.6604 (OUTLIER) cc_final: 0.5971 (m-70) outliers start: 23 outliers final: 7 residues processed: 71 average time/residue: 0.5394 time to fit residues: 40.0462 Evaluate side-chains 72 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 282 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 385 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 56 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 GLN ** B 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 HIS ** 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 = 0.4131 r_free = 0.4131 target = 0.185674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.136576 restraints weight = 5433.853| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.62 r_work: 0.3441 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5345 Z= 0.152 Angle : 0.453 5.037 7268 Z= 0.234 Chirality : 0.039 0.133 862 Planarity : 0.003 0.034 910 Dihedral : 3.290 13.839 706 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 3.82 % Allowed : 18.92 % Favored : 77.26 % 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 are not related in a simple way. whole: 2.03 (0.35), residues: 660 helix: 2.62 (0.26), residues: 432 sheet: -1.25 (0.90), residues: 46 loop : -1.20 (0.46), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 76 TYR 0.010 0.001 TYR B 333 PHE 0.008 0.001 PHE B 287 TRP 0.010 0.001 TRP A 375 HIS 0.004 0.001 HIS A 370 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 5342) covalent geometry : angle 0.45249 ( 7262) SS BOND : bond 0.00208 ( 3) SS BOND : angle 0.53856 ( 6) hydrogen bonds : bond 0.04530 ( 353) hydrogen bonds : angle 3.77735 ( 1059) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 0.210 Fit side-chains REVERT: A 25 GLU cc_start: 0.6627 (tt0) cc_final: 0.6318 (tt0) REVERT: A 102 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6318 (mp0) REVERT: A 108 HIS cc_start: 0.6828 (OUTLIER) cc_final: 0.6097 (m-70) REVERT: B 25 GLU cc_start: 0.6588 (tt0) cc_final: 0.6279 (tt0) REVERT: B 108 HIS cc_start: 0.6814 (OUTLIER) cc_final: 0.6053 (m-70) REVERT: B 228 ARG cc_start: 0.4411 (tpm170) cc_final: 0.4150 (tpm170) outliers start: 22 outliers final: 6 residues processed: 80 average time/residue: 0.5674 time to fit residues: 47.4267 Evaluate side-chains 76 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 385 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 61 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 51 optimal weight: 0.0970 chunk 34 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 22 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 108 HIS ** A 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 GLN ** B 413 HIS ** 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 = 0.4144 r_free = 0.4144 target = 0.187065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.137632 restraints weight = 5447.383| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.68 r_work: 0.3451 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5345 Z= 0.127 Angle : 0.431 4.921 7268 Z= 0.221 Chirality : 0.038 0.133 862 Planarity : 0.003 0.033 910 Dihedral : 3.207 13.840 706 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.65 % Allowed : 19.79 % Favored : 76.56 % 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 are not related in a simple way. whole: 2.14 (0.35), residues: 660 helix: 2.65 (0.25), residues: 432 sheet: -1.12 (0.91), residues: 46 loop : -1.00 (0.47), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 103 TYR 0.007 0.001 TYR B 333 PHE 0.006 0.001 PHE A 60 TRP 0.007 0.001 TRP A 375 HIS 0.008 0.001 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 5342) covalent geometry : angle 0.43143 ( 7262) SS BOND : bond 0.00157 ( 3) SS BOND : angle 0.28386 ( 6) hydrogen bonds : bond 0.04291 ( 353) hydrogen bonds : angle 3.69533 ( 1059) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.211 Fit side-chains REVERT: A 102 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6371 (mp0) REVERT: A 125 LEU cc_start: 0.6789 (OUTLIER) cc_final: 0.6574 (mp) REVERT: B 25 GLU cc_start: 0.6544 (tt0) cc_final: 0.6238 (tt0) REVERT: B 125 LEU cc_start: 0.6779 (OUTLIER) cc_final: 0.6564 (mp) REVERT: B 228 ARG cc_start: 0.4396 (tpm170) cc_final: 0.4091 (tpm170) outliers start: 21 outliers final: 10 residues processed: 73 average time/residue: 0.5497 time to fit residues: 41.9200 Evaluate side-chains 74 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 385 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 12 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 47 optimal weight: 9.9990 chunk 59 optimal weight: 0.3980 chunk 33 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 GLN ** B 413 HIS ** 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 = 0.4138 r_free = 0.4138 target = 0.186161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.136257 restraints weight = 5569.742| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.70 r_work: 0.3437 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5345 Z= 0.135 Angle : 0.443 5.219 7268 Z= 0.228 Chirality : 0.039 0.132 862 Planarity : 0.003 0.033 910 Dihedral : 3.206 14.092 706 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 4.17 % Allowed : 19.10 % Favored : 76.74 % 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 are not related in a simple way. whole: 2.11 (0.34), residues: 660 helix: 2.59 (0.25), residues: 432 sheet: -1.03 (0.92), residues: 46 loop : -0.96 (0.47), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 103 TYR 0.007 0.001 TYR B 333 PHE 0.007 0.001 PHE A 60 TRP 0.008 0.001 TRP A 375 HIS 0.003 0.001 HIS A 370 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 5342) covalent geometry : angle 0.44353 ( 7262) SS BOND : bond 0.00149 ( 3) SS BOND : angle 0.26418 ( 6) hydrogen bonds : bond 0.04309 ( 353) hydrogen bonds : angle 3.65247 ( 1059) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.126 Fit side-chains REVERT: A 102 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6382 (mp0) REVERT: B 25 GLU cc_start: 0.6577 (tt0) cc_final: 0.6377 (tt0) REVERT: B 125 LEU cc_start: 0.6779 (OUTLIER) cc_final: 0.6579 (mp) REVERT: B 228 ARG cc_start: 0.4405 (tpm170) cc_final: 0.4085 (tpm170) outliers start: 24 outliers final: 10 residues processed: 82 average time/residue: 0.5248 time to fit residues: 44.9861 Evaluate side-chains 79 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 385 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 64 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 47 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 20 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 18 optimal weight: 0.0000 chunk 1 optimal weight: 0.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 GLN ** B 413 HIS ** 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 = 0.4165 r_free = 0.4165 target = 0.188749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.138202 restraints weight = 5539.783| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.69 r_work: 0.3459 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5345 Z= 0.111 Angle : 0.423 5.489 7268 Z= 0.215 Chirality : 0.038 0.133 862 Planarity : 0.003 0.035 910 Dihedral : 3.121 13.868 706 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.74 % Allowed : 21.53 % Favored : 76.74 % 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 are not related in a simple way. whole: 2.31 (0.35), residues: 660 helix: 2.73 (0.25), residues: 432 sheet: -0.90 (0.95), residues: 46 loop : -0.84 (0.49), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 103 TYR 0.006 0.001 TYR A 333 PHE 0.005 0.001 PHE A 60 TRP 0.006 0.001 TRP A 375 HIS 0.002 0.001 HIS A 370 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 5342) covalent geometry : angle 0.42283 ( 7262) SS BOND : bond 0.00125 ( 3) SS BOND : angle 0.15411 ( 6) hydrogen bonds : bond 0.04103 ( 353) hydrogen bonds : angle 3.52158 ( 1059) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.208 Fit side-chains REVERT: B 25 GLU cc_start: 0.6545 (tt0) cc_final: 0.6301 (tt0) REVERT: B 125 LEU cc_start: 0.6771 (OUTLIER) cc_final: 0.6553 (mp) REVERT: B 228 ARG cc_start: 0.4410 (tpm170) cc_final: 0.4098 (tpm170) outliers start: 10 outliers final: 5 residues processed: 67 average time/residue: 0.5860 time to fit residues: 40.9920 Evaluate side-chains 69 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 125 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 18 optimal weight: 0.0270 chunk 14 optimal weight: 7.9990 chunk 30 optimal weight: 0.0020 chunk 29 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 overall best weight: 0.5248 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 GLN ** B 413 HIS ** 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 = 0.4133 r_free = 0.4133 target = 0.185140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.136831 restraints weight = 5509.408| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.62 r_work: 0.3468 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5345 Z= 0.113 Angle : 0.426 5.648 7268 Z= 0.216 Chirality : 0.038 0.132 862 Planarity : 0.003 0.034 910 Dihedral : 3.103 13.676 706 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.95 % Allowed : 21.18 % Favored : 75.87 % 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 are not related in a simple way. whole: 2.38 (0.35), residues: 660 helix: 2.76 (0.25), residues: 432 sheet: -0.75 (0.96), residues: 46 loop : -0.79 (0.49), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 103 TYR 0.006 0.001 TYR B 333 PHE 0.005 0.001 PHE B 60 TRP 0.007 0.001 TRP A 375 HIS 0.002 0.001 HIS A 370 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 5342) covalent geometry : angle 0.42607 ( 7262) SS BOND : bond 0.00126 ( 3) SS BOND : angle 0.16155 ( 6) hydrogen bonds : bond 0.04088 ( 353) hydrogen bonds : angle 3.49082 ( 1059) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.191 Fit side-chains REVERT: B 25 GLU cc_start: 0.6546 (tt0) cc_final: 0.6213 (tt0) REVERT: B 102 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6450 (mp0) outliers start: 17 outliers final: 8 residues processed: 77 average time/residue: 0.4835 time to fit residues: 38.9697 Evaluate side-chains 74 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 385 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 35 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 53 optimal weight: 20.0000 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 GLN ** B 413 HIS ** 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 = 0.4137 r_free = 0.4137 target = 0.185838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.135097 restraints weight = 5506.735| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.70 r_work: 0.3423 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5345 Z= 0.143 Angle : 0.459 5.815 7268 Z= 0.230 Chirality : 0.039 0.133 862 Planarity : 0.003 0.033 910 Dihedral : 3.222 13.898 706 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.43 % Allowed : 22.22 % Favored : 75.35 % 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 are not related in a simple way. whole: 2.28 (0.35), residues: 660 helix: 2.66 (0.25), residues: 432 sheet: -0.63 (0.98), residues: 46 loop : -0.79 (0.49), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 103 TYR 0.007 0.001 TYR B 333 PHE 0.007 0.001 PHE A 60 TRP 0.009 0.001 TRP B 375 HIS 0.003 0.001 HIS A 370 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 5342) covalent geometry : angle 0.45937 ( 7262) SS BOND : bond 0.00145 ( 3) SS BOND : angle 0.36549 ( 6) hydrogen bonds : bond 0.04270 ( 353) hydrogen bonds : angle 3.56983 ( 1059) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.198 Fit side-chains REVERT: B 102 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6445 (mp0) outliers start: 14 outliers final: 9 residues processed: 79 average time/residue: 0.4629 time to fit residues: 38.2844 Evaluate side-chains 83 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 385 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 42 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 GLN ** B 413 HIS ** 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 = 0.4119 r_free = 0.4119 target = 0.183485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.134084 restraints weight = 5507.103| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.66 r_work: 0.3435 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5345 Z= 0.132 Angle : 0.462 6.015 7268 Z= 0.230 Chirality : 0.038 0.133 862 Planarity : 0.003 0.034 910 Dihedral : 3.202 13.871 706 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.26 % Allowed : 22.05 % Favored : 75.69 % 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 are not related in a simple way. whole: 2.31 (0.35), residues: 660 helix: 2.66 (0.24), residues: 432 sheet: -0.59 (0.99), residues: 46 loop : -0.76 (0.49), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 103 TYR 0.007 0.001 TYR B 333 PHE 0.006 0.001 PHE B 42 TRP 0.008 0.001 TRP B 375 HIS 0.003 0.001 HIS A 370 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 5342) covalent geometry : angle 0.46248 ( 7262) SS BOND : bond 0.00134 ( 3) SS BOND : angle 0.32595 ( 6) hydrogen bonds : bond 0.04182 ( 353) hydrogen bonds : angle 3.55789 ( 1059) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.210 Fit side-chains REVERT: B 102 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6447 (mp0) outliers start: 13 outliers final: 9 residues processed: 77 average time/residue: 0.4404 time to fit residues: 35.5331 Evaluate side-chains 80 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 385 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 16 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 55 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 GLN ** B 413 HIS ** 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 = 0.4148 r_free = 0.4148 target = 0.186757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.135924 restraints weight = 5550.742| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.71 r_work: 0.3437 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5345 Z= 0.126 Angle : 0.467 6.444 7268 Z= 0.231 Chirality : 0.038 0.133 862 Planarity : 0.003 0.034 910 Dihedral : 3.193 13.829 706 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.43 % Allowed : 22.57 % Favored : 75.00 % 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 are not related in a simple way. whole: 2.31 (0.34), residues: 660 helix: 2.67 (0.24), residues: 432 sheet: -0.59 (0.99), residues: 46 loop : -0.75 (0.49), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 103 TYR 0.007 0.001 TYR A 333 PHE 0.006 0.001 PHE A 42 TRP 0.007 0.001 TRP A 375 HIS 0.003 0.001 HIS A 370 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 5342) covalent geometry : angle 0.46713 ( 7262) SS BOND : bond 0.00134 ( 3) SS BOND : angle 0.32408 ( 6) hydrogen bonds : bond 0.04160 ( 353) hydrogen bonds : angle 3.55218 ( 1059) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.200 Fit side-chains REVERT: B 102 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6417 (mp0) outliers start: 14 outliers final: 9 residues processed: 75 average time/residue: 0.5272 time to fit residues: 41.4352 Evaluate side-chains 77 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain B residue 385 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 57 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 20 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 GLN ** B 413 HIS ** 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 = 0.4131 r_free = 0.4131 target = 0.185175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.137958 restraints weight = 5577.231| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.47 r_work: 0.3446 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5345 Z= 0.134 Angle : 0.480 7.281 7268 Z= 0.237 Chirality : 0.038 0.133 862 Planarity : 0.003 0.034 910 Dihedral : 3.218 13.845 706 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.43 % Allowed : 22.40 % Favored : 75.17 % 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 are not related in a simple way. whole: 2.28 (0.34), residues: 660 helix: 2.63 (0.24), residues: 432 sheet: -0.59 (0.99), residues: 46 loop : -0.74 (0.49), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 103 TYR 0.007 0.001 TYR A 333 PHE 0.006 0.001 PHE B 60 TRP 0.008 0.001 TRP B 375 HIS 0.003 0.001 HIS A 370 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 5342) covalent geometry : angle 0.48054 ( 7262) SS BOND : bond 0.00144 ( 3) SS BOND : angle 0.36344 ( 6) hydrogen bonds : bond 0.04203 ( 353) hydrogen bonds : angle 3.58030 ( 1059) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1848.13 seconds wall clock time: 32 minutes 17.75 seconds (1937.75 seconds total)