Starting phenix.real_space_refine on Sat May 2 10:52:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ui6_64185/05_2026/9ui6_64185.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ui6_64185/05_2026/9ui6_64185.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ui6_64185/05_2026/9ui6_64185.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ui6_64185/05_2026/9ui6_64185.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ui6_64185/05_2026/9ui6_64185.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ui6_64185/05_2026/9ui6_64185.map" } resolution = 3.22 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= -0.001 sd= 0.031 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 24 5.16 5 C 3029 2.51 5 N 684 2.21 5 O 755 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4492 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4240 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 22, 'TRANS': 524} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 252 Unusual residues: {'CLR': 4, 'POV': 10} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 380 Unresolved non-hydrogen angles: 461 Unresolved non-hydrogen dihedrals: 339 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'POV:plan-1': 10, 'POV:plan-2': 10, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 81 Time building chain proxies: 0.87, per 1000 atoms: 0.19 Number of scatterers: 4492 At special positions: 0 Unit cell: (90.1, 82.45, 75.65, 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 24 16.00 O 755 8.00 N 684 7.00 C 3029 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 170 " 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: 0.21 Conformation dependent library (CDL) restraints added in 89.6 milliseconds 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1008 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 1 sheets defined 77.0% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 63 through 66 removed outlier: 3.858A pdb=" N LYS A 66 " --> pdb=" O ARG A 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 63 through 66' Processing helix chain 'A' and resid 67 through 88 removed outlier: 3.715A pdb=" N ASN A 74 " --> pdb=" O PHE A 70 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ASN A 88 " --> pdb=" O GLY A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 97 removed outlier: 3.629A pdb=" N THR A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 129 removed outlier: 3.576A pdb=" N ALA A 104 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR A 106 " --> pdb=" O TYR A 102 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 156 removed outlier: 3.669A pdb=" N ALA A 154 " --> pdb=" O ILE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 160 removed outlier: 3.931A pdb=" N HIS A 160 " --> pdb=" O PRO A 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 157 through 160' Processing helix chain 'A' and resid 174 through 205 removed outlier: 3.700A pdb=" N ILE A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 179 " --> pdb=" O VAL A 175 " (cutoff:3.500A) Proline residue: A 197 - end of helix removed outlier: 4.996A pdb=" N LEU A 200 " --> pdb=" O ARG A 196 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA A 201 " --> pdb=" O PRO A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 247 removed outlier: 3.892A pdb=" N LYS A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS A 216 " --> pdb=" O GLU A 212 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 270 removed outlier: 3.792A pdb=" N ILE A 255 " --> pdb=" O ILE A 251 " (cutoff:3.500A) Proline residue: A 256 - end of helix removed outlier: 4.017A pdb=" N GLY A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 297 removed outlier: 3.575A pdb=" N ILE A 287 " --> pdb=" O PRO A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.618A pdb=" N LEU A 310 " --> pdb=" O PRO A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 334 removed outlier: 3.802A pdb=" N ASP A 333 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS A 334 " --> pdb=" O ARG A 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 329 through 334' Processing helix chain 'A' and resid 335 through 337 No H-bonds generated for 'chain 'A' and resid 335 through 337' Processing helix chain 'A' and resid 345 through 349 removed outlier: 3.680A pdb=" N GLY A 348 " --> pdb=" O ASN A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 370 removed outlier: 3.704A pdb=" N ILE A 368 " --> pdb=" O GLU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 388 removed outlier: 4.083A pdb=" N LEU A 383 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ALA A 384 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 398 removed outlier: 3.924A pdb=" N PHE A 394 " --> pdb=" O THR A 390 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN A 398 " --> pdb=" O PHE A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 414 Processing helix chain 'A' and resid 415 through 443 removed outlier: 4.082A pdb=" N LEU A 419 " --> pdb=" O TYR A 415 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VAL A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Proline residue: A 436 - end of helix removed outlier: 3.806A pdb=" N VAL A 441 " --> pdb=" O SER A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 482 removed outlier: 3.521A pdb=" N PHE A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A 473 " --> pdb=" O GLY A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 501 removed outlier: 3.508A pdb=" N TRP A 501 " --> pdb=" O SER A 498 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 498 through 501' Processing helix chain 'A' and resid 502 through 528 removed outlier: 3.552A pdb=" N LEU A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ILE A 518 " --> pdb=" O ALA A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 531 No H-bonds generated for 'chain 'A' and resid 529 through 531' Processing helix chain 'A' and resid 532 through 562 removed outlier: 3.943A pdb=" N PHE A 540 " --> pdb=" O ALA A 536 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR A 541 " --> pdb=" O GLY A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 605 removed outlier: 4.119A pdb=" N PHE A 583 " --> pdb=" O LYS A 579 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 600 " --> pdb=" O ALA A 596 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 487 through 488 removed outlier: 3.691A pdb=" N GLY A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) 279 hydrogen bonds defined for protein. 831 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: 0.41 Time building geometry restraints manager: 0.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 680 1.33 - 1.45: 1237 1.45 - 1.57: 2647 1.57 - 1.69: 0 1.69 - 1.81: 40 Bond restraints: 4604 Sorted by residual: bond pdb=" C31 POV A 705 " pdb=" O31 POV A 705 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.97e+01 bond pdb=" N PRO A 302 " pdb=" CD PRO A 302 " ideal model delta sigma weight residual 1.473 1.502 -0.029 1.40e-02 5.10e+03 4.22e+00 bond pdb=" C MET A 68 " pdb=" O MET A 68 " ideal model delta sigma weight residual 1.243 1.229 0.014 9.90e-03 1.02e+04 1.92e+00 bond pdb=" C CYS A 367 " pdb=" O CYS A 367 " ideal model delta sigma weight residual 1.237 1.224 0.013 1.17e-02 7.31e+03 1.27e+00 bond pdb=" C ALA A 192 " pdb=" O ALA A 192 " ideal model delta sigma weight residual 1.237 1.224 0.012 1.17e-02 7.31e+03 1.13e+00 ... (remaining 4599 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 6109 1.84 - 3.68: 104 3.68 - 5.52: 19 5.52 - 7.36: 2 7.36 - 9.20: 2 Bond angle restraints: 6236 Sorted by residual: angle pdb=" N ASN A 199 " pdb=" CA ASN A 199 " pdb=" C ASN A 199 " ideal model delta sigma weight residual 111.28 117.97 -6.69 1.09e+00 8.42e-01 3.77e+01 angle pdb=" N CYS A 198 " pdb=" CA CYS A 198 " pdb=" C CYS A 198 " ideal model delta sigma weight residual 111.33 116.25 -4.92 1.21e+00 6.83e-01 1.65e+01 angle pdb=" N ARG A 196 " pdb=" CA ARG A 196 " pdb=" C ARG A 196 " ideal model delta sigma weight residual 109.81 118.33 -8.52 2.21e+00 2.05e-01 1.49e+01 angle pdb=" N ILE A 195 " pdb=" CA ILE A 195 " pdb=" C ILE A 195 " ideal model delta sigma weight residual 110.62 114.07 -3.45 1.02e+00 9.61e-01 1.15e+01 angle pdb=" C LEU A 502 " pdb=" N ILE A 503 " pdb=" CA ILE A 503 " ideal model delta sigma weight residual 120.33 123.04 -2.71 8.00e-01 1.56e+00 1.14e+01 ... (remaining 6231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 2516 17.38 - 34.77: 304 34.77 - 52.15: 50 52.15 - 69.53: 12 69.53 - 86.91: 2 Dihedral angle restraints: 2884 sinusoidal: 1306 harmonic: 1578 Sorted by residual: dihedral pdb=" CA TYR A 129 " pdb=" C TYR A 129 " pdb=" N PHE A 130 " pdb=" CA PHE A 130 " ideal model delta harmonic sigma weight residual 180.00 -154.63 -25.37 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA PHE A 515 " pdb=" C PHE A 515 " pdb=" N ALA A 516 " pdb=" CA ALA A 516 " ideal model delta harmonic sigma weight residual 180.00 -162.62 -17.38 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" C37 POV A 712 " pdb=" C38 POV A 712 " pdb=" C39 POV A 712 " pdb="C310 POV A 712 " ideal model delta sinusoidal sigma weight residual -179.61 -92.70 -86.91 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 2881 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 620 0.058 - 0.116: 83 0.116 - 0.173: 8 0.173 - 0.231: 3 0.231 - 0.289: 1 Chirality restraints: 715 Sorted by residual: chirality pdb=" CA ASN A 199 " pdb=" N ASN A 199 " pdb=" C ASN A 199 " pdb=" CB ASN A 199 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA ARG A 196 " pdb=" N ARG A 196 " pdb=" C ARG A 196 " pdb=" CB ARG A 196 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ASP A 327 " pdb=" N ASP A 327 " pdb=" C ASP A 327 " pdb=" CB ASP A 327 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.23e-01 ... (remaining 712 not shown) Planarity restraints: 739 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 473 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.81e+00 pdb=" CD GLU A 473 " -0.042 2.00e-02 2.50e+03 pdb=" OE1 GLU A 473 " 0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU A 473 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 391 " 0.036 5.00e-02 4.00e+02 5.34e-02 4.57e+00 pdb=" N PRO A 392 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 392 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 392 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 68 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO A 69 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 69 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 69 " -0.024 5.00e-02 4.00e+02 ... (remaining 736 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 514 2.75 - 3.29: 4341 3.29 - 3.83: 7077 3.83 - 4.36: 7686 4.36 - 4.90: 14082 Nonbonded interactions: 33700 Sorted by model distance: nonbonded pdb=" OE2 GLU A 78 " pdb=" CG1 ILE A 195 " model vdw 2.214 3.440 nonbonded pdb=" OE1 GLU A 75 " pdb=" CE1 TYR A 225 " model vdw 2.240 3.340 nonbonded pdb=" OE2 GLU A 75 " pdb=" OD1 ASN A 199 " model vdw 2.251 3.040 nonbonded pdb=" ND2 ASN A 98 " pdb=" O GLU A 171 " model vdw 2.258 3.120 nonbonded pdb=" CG GLU A 75 " pdb=" ND2 ASN A 199 " model vdw 2.283 3.520 ... (remaining 33695 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.050 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 3.800 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:0.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.126 4605 Z= 0.189 Angle : 0.610 9.199 6238 Z= 0.367 Chirality : 0.042 0.289 715 Planarity : 0.005 0.053 739 Dihedral : 14.405 86.912 1873 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.49 % Favored : 96.15 % Rotamer: Outliers : 0.90 % Allowed : 17.75 % Favored : 81.35 % 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: 2.24 (0.37), residues: 545 helix: 2.53 (0.28), residues: 362 sheet: None (None), residues: 0 loop : -0.72 (0.44), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 289 TYR 0.012 0.001 TYR A 605 PHE 0.009 0.001 PHE A 426 TRP 0.004 0.001 TRP A 375 HIS 0.002 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 4604) covalent geometry : angle 0.61026 ( 6236) SS BOND : bond 0.00334 ( 1) SS BOND : angle 0.26268 ( 2) hydrogen bonds : bond 0.15948 ( 279) hydrogen bonds : angle 5.27369 ( 831) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.107 Fit side-chains revert: symmetry clash REVERT: A 196 ARG cc_start: 0.6502 (mmt90) cc_final: 0.6189 (mmm-85) REVERT: A 297 LYS cc_start: 0.7711 (ptpt) cc_final: 0.7434 (ptmt) outliers start: 4 outliers final: 3 residues processed: 66 average time/residue: 0.0626 time to fit residues: 5.0485 Evaluate side-chains 64 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 601 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.1980 chunk 48 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN A 395 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.155910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.126362 restraints weight = 5823.391| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.99 r_work: 0.3084 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4605 Z= 0.136 Angle : 0.508 5.959 6238 Z= 0.268 Chirality : 0.039 0.181 715 Planarity : 0.005 0.057 739 Dihedral : 8.320 84.799 960 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.94 % Favored : 96.88 % Rotamer: Outliers : 2.47 % Allowed : 14.83 % Favored : 82.70 % 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: 2.35 (0.37), residues: 545 helix: 2.49 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -0.56 (0.46), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 289 TYR 0.012 0.001 TYR A 391 PHE 0.010 0.001 PHE A 540 TRP 0.005 0.001 TRP A 307 HIS 0.003 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 4604) covalent geometry : angle 0.50826 ( 6236) SS BOND : bond 0.00378 ( 1) SS BOND : angle 0.11123 ( 2) hydrogen bonds : bond 0.06348 ( 279) hydrogen bonds : angle 4.01277 ( 831) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.105 Fit side-chains REVERT: A 297 LYS cc_start: 0.7530 (ptpt) cc_final: 0.7328 (ptmt) REVERT: A 309 ASN cc_start: 0.7269 (m110) cc_final: 0.6854 (p0) REVERT: A 381 TYR cc_start: 0.8997 (OUTLIER) cc_final: 0.8508 (t80) REVERT: A 439 ARG cc_start: 0.7759 (ttp-170) cc_final: 0.7442 (ttp-170) REVERT: A 521 MET cc_start: 0.8041 (mmm) cc_final: 0.7719 (mmt) REVERT: A 603 ARG cc_start: 0.8014 (tpp80) cc_final: 0.7116 (tmt170) outliers start: 11 outliers final: 6 residues processed: 68 average time/residue: 0.0534 time to fit residues: 4.5205 Evaluate side-chains 61 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 381 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 10 optimal weight: 0.0770 chunk 50 optimal weight: 0.4980 chunk 38 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 28 optimal weight: 0.0010 overall best weight: 0.4344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.157910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.128766 restraints weight = 5755.789| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.95 r_work: 0.3115 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4605 Z= 0.113 Angle : 0.457 5.522 6238 Z= 0.242 Chirality : 0.037 0.181 715 Planarity : 0.005 0.054 739 Dihedral : 7.696 73.169 955 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.02 % Allowed : 15.96 % Favored : 82.02 % 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: 2.59 (0.37), residues: 545 helix: 2.70 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -0.50 (0.47), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 289 TYR 0.010 0.001 TYR A 391 PHE 0.010 0.001 PHE A 426 TRP 0.007 0.001 TRP A 65 HIS 0.002 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 4604) covalent geometry : angle 0.45707 ( 6236) SS BOND : bond 0.00340 ( 1) SS BOND : angle 0.12625 ( 2) hydrogen bonds : bond 0.05432 ( 279) hydrogen bonds : angle 3.78547 ( 831) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.085 Fit side-chains revert: symmetry clash REVERT: A 102 TYR cc_start: 0.7448 (OUTLIER) cc_final: 0.6455 (t80) REVERT: A 381 TYR cc_start: 0.9006 (OUTLIER) cc_final: 0.8344 (t80) REVERT: A 444 LEU cc_start: 0.8216 (mp) cc_final: 0.7767 (tp) REVERT: A 603 ARG cc_start: 0.8001 (tpp80) cc_final: 0.7075 (tmt170) outliers start: 9 outliers final: 7 residues processed: 63 average time/residue: 0.0473 time to fit residues: 3.7657 Evaluate side-chains 66 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 102 TYR Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 381 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 7 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.151703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.122496 restraints weight = 5780.151| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.94 r_work: 0.3032 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4605 Z= 0.156 Angle : 0.516 5.696 6238 Z= 0.272 Chirality : 0.040 0.181 715 Planarity : 0.005 0.059 739 Dihedral : 8.150 67.530 955 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.92 % Allowed : 15.28 % Favored : 81.80 % 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: 2.44 (0.37), residues: 545 helix: 2.55 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -0.49 (0.47), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 289 TYR 0.016 0.001 TYR A 391 PHE 0.012 0.001 PHE A 540 TRP 0.006 0.001 TRP A 65 HIS 0.004 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 4604) covalent geometry : angle 0.51575 ( 6236) SS BOND : bond 0.00465 ( 1) SS BOND : angle 0.06570 ( 2) hydrogen bonds : bond 0.06999 ( 279) hydrogen bonds : angle 3.93198 ( 831) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.106 Fit side-chains revert: symmetry clash REVERT: A 102 TYR cc_start: 0.7639 (OUTLIER) cc_final: 0.6366 (t80) REVERT: A 381 TYR cc_start: 0.9103 (OUTLIER) cc_final: 0.8367 (t80) REVERT: A 444 LEU cc_start: 0.8130 (mp) cc_final: 0.7667 (tp) outliers start: 13 outliers final: 9 residues processed: 69 average time/residue: 0.0510 time to fit residues: 4.4353 Evaluate side-chains 64 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 102 TYR Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 381 TYR Chi-restraints excluded: chain A residue 437 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 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 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.151953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.122729 restraints weight = 5788.947| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.94 r_work: 0.3036 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4605 Z= 0.148 Angle : 0.501 5.659 6238 Z= 0.264 Chirality : 0.039 0.182 715 Planarity : 0.005 0.056 739 Dihedral : 8.175 59.793 955 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.15 % Allowed : 15.96 % Favored : 80.90 % 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: 2.44 (0.37), residues: 545 helix: 2.55 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -0.46 (0.46), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 289 TYR 0.014 0.001 TYR A 391 PHE 0.012 0.001 PHE A 426 TRP 0.007 0.001 TRP A 65 HIS 0.003 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 4604) covalent geometry : angle 0.50081 ( 6236) SS BOND : bond 0.00473 ( 1) SS BOND : angle 0.14255 ( 2) hydrogen bonds : bond 0.06750 ( 279) hydrogen bonds : angle 3.91602 ( 831) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.082 Fit side-chains revert: symmetry clash REVERT: A 102 TYR cc_start: 0.7652 (OUTLIER) cc_final: 0.6418 (t80) REVERT: A 381 TYR cc_start: 0.9048 (OUTLIER) cc_final: 0.8166 (t80) REVERT: A 444 LEU cc_start: 0.8182 (mp) cc_final: 0.7808 (tp) outliers start: 14 outliers final: 10 residues processed: 70 average time/residue: 0.0480 time to fit residues: 4.2182 Evaluate side-chains 66 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 102 TYR Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 381 TYR Chi-restraints excluded: chain A residue 403 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 0.1980 chunk 43 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 27 optimal weight: 0.3980 chunk 39 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.154464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.125127 restraints weight = 5812.725| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.96 r_work: 0.3070 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4605 Z= 0.120 Angle : 0.474 5.626 6238 Z= 0.250 Chirality : 0.038 0.184 715 Planarity : 0.005 0.057 739 Dihedral : 7.799 59.358 955 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.15 % Allowed : 15.96 % Favored : 80.90 % 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: 2.61 (0.37), residues: 545 helix: 2.69 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -0.44 (0.46), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 289 TYR 0.012 0.001 TYR A 391 PHE 0.010 0.001 PHE A 426 TRP 0.007 0.001 TRP A 65 HIS 0.002 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 4604) covalent geometry : angle 0.47439 ( 6236) SS BOND : bond 0.00400 ( 1) SS BOND : angle 0.08987 ( 2) hydrogen bonds : bond 0.05852 ( 279) hydrogen bonds : angle 3.79730 ( 831) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.088 Fit side-chains revert: symmetry clash REVERT: A 102 TYR cc_start: 0.7506 (OUTLIER) cc_final: 0.6407 (t80) REVERT: A 324 LYS cc_start: 0.7609 (tttm) cc_final: 0.7402 (tptt) REVERT: A 381 TYR cc_start: 0.9027 (OUTLIER) cc_final: 0.8195 (t80) REVERT: A 444 LEU cc_start: 0.8130 (mp) cc_final: 0.7744 (tp) outliers start: 14 outliers final: 12 residues processed: 67 average time/residue: 0.0572 time to fit residues: 4.7928 Evaluate side-chains 71 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 102 TYR Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 381 TYR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 437 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 0.0770 chunk 7 optimal weight: 0.6980 chunk 37 optimal weight: 0.2980 chunk 15 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 26 optimal weight: 6.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.144568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.113738 restraints weight = 5780.797| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.03 r_work: 0.3072 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4605 Z= 0.114 Angle : 0.462 5.644 6238 Z= 0.242 Chirality : 0.037 0.183 715 Planarity : 0.005 0.056 739 Dihedral : 7.524 57.586 955 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.37 % Allowed : 15.51 % Favored : 81.12 % 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: 2.64 (0.37), residues: 545 helix: 2.73 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -0.47 (0.46), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 289 TYR 0.011 0.001 TYR A 391 PHE 0.009 0.001 PHE A 426 TRP 0.007 0.001 TRP A 65 HIS 0.002 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 4604) covalent geometry : angle 0.46236 ( 6236) SS BOND : bond 0.00372 ( 1) SS BOND : angle 0.10671 ( 2) hydrogen bonds : bond 0.05478 ( 279) hydrogen bonds : angle 3.72970 ( 831) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.083 Fit side-chains revert: symmetry clash REVERT: A 102 TYR cc_start: 0.7441 (OUTLIER) cc_final: 0.6406 (t80) REVERT: A 381 TYR cc_start: 0.9014 (OUTLIER) cc_final: 0.8184 (t80) REVERT: A 444 LEU cc_start: 0.8099 (mp) cc_final: 0.7740 (tp) outliers start: 15 outliers final: 13 residues processed: 67 average time/residue: 0.0502 time to fit residues: 4.1899 Evaluate side-chains 69 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 102 TYR Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 381 TYR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 481 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 17 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.151295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.122297 restraints weight = 5851.881| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.92 r_work: 0.3020 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4605 Z= 0.156 Angle : 0.506 5.779 6238 Z= 0.266 Chirality : 0.039 0.181 715 Planarity : 0.005 0.057 739 Dihedral : 7.955 58.549 955 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.60 % Allowed : 15.96 % Favored : 80.45 % 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: 2.47 (0.36), residues: 545 helix: 2.60 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -0.53 (0.45), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 289 TYR 0.016 0.001 TYR A 391 PHE 0.013 0.001 PHE A 426 TRP 0.005 0.001 TRP A 65 HIS 0.003 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 4604) covalent geometry : angle 0.50591 ( 6236) SS BOND : bond 0.00462 ( 1) SS BOND : angle 0.14203 ( 2) hydrogen bonds : bond 0.06959 ( 279) hydrogen bonds : angle 3.94297 ( 831) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.090 Fit side-chains revert: symmetry clash REVERT: A 65 TRP cc_start: 0.8476 (m100) cc_final: 0.8116 (m100) REVERT: A 102 TYR cc_start: 0.7688 (OUTLIER) cc_final: 0.6359 (t80) REVERT: A 381 TYR cc_start: 0.9113 (OUTLIER) cc_final: 0.8231 (t80) REVERT: A 437 SER cc_start: 0.8476 (OUTLIER) cc_final: 0.8196 (m) REVERT: A 444 LEU cc_start: 0.8199 (mp) cc_final: 0.7860 (tp) outliers start: 16 outliers final: 12 residues processed: 67 average time/residue: 0.0555 time to fit residues: 4.5680 Evaluate side-chains 68 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 102 TYR Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 381 TYR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 481 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 50 optimal weight: 0.0000 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.138335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.107084 restraints weight = 5689.398| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.03 r_work: 0.3033 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4605 Z= 0.126 Angle : 0.485 5.683 6238 Z= 0.256 Chirality : 0.038 0.184 715 Planarity : 0.004 0.055 739 Dihedral : 7.686 59.424 955 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.82 % Allowed : 15.96 % Favored : 80.22 % 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: 2.55 (0.36), residues: 545 helix: 2.67 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -0.53 (0.44), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 289 TYR 0.012 0.001 TYR A 391 PHE 0.011 0.001 PHE A 426 TRP 0.005 0.001 TRP A 65 HIS 0.003 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 4604) covalent geometry : angle 0.48496 ( 6236) SS BOND : bond 0.00413 ( 1) SS BOND : angle 0.10944 ( 2) hydrogen bonds : bond 0.06129 ( 279) hydrogen bonds : angle 3.85366 ( 831) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 0.084 Fit side-chains revert: symmetry clash REVERT: A 65 TRP cc_start: 0.8410 (m100) cc_final: 0.8046 (m100) REVERT: A 102 TYR cc_start: 0.7568 (OUTLIER) cc_final: 0.6368 (t80) REVERT: A 381 TYR cc_start: 0.9036 (OUTLIER) cc_final: 0.8127 (t80) REVERT: A 437 SER cc_start: 0.8409 (OUTLIER) cc_final: 0.8145 (m) REVERT: A 444 LEU cc_start: 0.8127 (mp) cc_final: 0.7825 (tp) outliers start: 17 outliers final: 12 residues processed: 63 average time/residue: 0.0545 time to fit residues: 4.2330 Evaluate side-chains 67 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 102 TYR Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 381 TYR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 481 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 2 optimal weight: 0.4980 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.137208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.106038 restraints weight = 5759.089| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.02 r_work: 0.3019 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4605 Z= 0.140 Angle : 0.498 5.729 6238 Z= 0.262 Chirality : 0.038 0.182 715 Planarity : 0.005 0.057 739 Dihedral : 7.755 59.572 955 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.37 % Allowed : 16.40 % Favored : 80.22 % 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: 2.48 (0.36), residues: 545 helix: 2.62 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -0.56 (0.44), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 289 TYR 0.014 0.001 TYR A 391 PHE 0.012 0.001 PHE A 426 TRP 0.005 0.001 TRP A 65 HIS 0.003 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 4604) covalent geometry : angle 0.49835 ( 6236) SS BOND : bond 0.00431 ( 1) SS BOND : angle 0.12906 ( 2) hydrogen bonds : bond 0.06480 ( 279) hydrogen bonds : angle 3.90095 ( 831) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.083 Fit side-chains revert: symmetry clash REVERT: A 65 TRP cc_start: 0.8405 (m100) cc_final: 0.8027 (m100) REVERT: A 102 TYR cc_start: 0.7604 (OUTLIER) cc_final: 0.6334 (t80) REVERT: A 381 TYR cc_start: 0.9037 (OUTLIER) cc_final: 0.8138 (t80) REVERT: A 437 SER cc_start: 0.8381 (OUTLIER) cc_final: 0.8120 (m) REVERT: A 444 LEU cc_start: 0.8109 (mp) cc_final: 0.7815 (tp) outliers start: 15 outliers final: 12 residues processed: 60 average time/residue: 0.0521 time to fit residues: 3.8800 Evaluate side-chains 65 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 102 TYR Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 381 TYR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 481 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.2980 chunk 20 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 34 optimal weight: 0.1980 chunk 38 optimal weight: 3.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.140456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.109278 restraints weight = 5700.296| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.04 r_work: 0.3061 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4605 Z= 0.114 Angle : 0.467 5.683 6238 Z= 0.246 Chirality : 0.037 0.185 715 Planarity : 0.004 0.056 739 Dihedral : 7.360 58.689 955 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.37 % Allowed : 16.40 % Favored : 80.22 % 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: 2.60 (0.36), residues: 545 helix: 2.65 (0.27), residues: 376 sheet: None (None), residues: 0 loop : -0.49 (0.45), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 289 TYR 0.010 0.001 TYR A 391 PHE 0.010 0.001 PHE A 426 TRP 0.005 0.001 TRP A 65 HIS 0.002 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 4604) covalent geometry : angle 0.46667 ( 6236) SS BOND : bond 0.00371 ( 1) SS BOND : angle 0.09180 ( 2) hydrogen bonds : bond 0.05505 ( 279) hydrogen bonds : angle 3.77631 ( 831) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 802.84 seconds wall clock time: 21 minutes 14.19 seconds (1274.19 seconds total)