Starting phenix.real_space_refine on Wed Aug 5 18:21:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9z66_73834/08_2026/9z66_73834.cif Found real_map, /net/cci-nas-00/data/ceres_data/9z66_73834/08_2026/9z66_73834.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9z66_73834/08_2026/9z66_73834.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9z66_73834/08_2026/9z66_73834.map" model { file = "/net/cci-nas-00/data/ceres_data/9z66_73834/08_2026/9z66_73834.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9z66_73834/08_2026/9z66_73834.cif" } resolution = 3.31 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= 0.006 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: 7 Type Number sf(0) Gaussians P 1 5.49 5 S 28 5.16 5 Na 1 4.78 5 C 3509 2.51 5 N 874 2.21 5 O 980 1.98 5 H 5348 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10741 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 7205 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 20, 'TRANS': 452} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1872 Classifications: {'peptide': 121} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "C" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 1658 Classifications: {'peptide': 111} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 103} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' NA': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.35, per 1000 atoms: 0.13 Number of scatterers: 10741 At special positions: 0 Unit cell: (79.75, 74.675, 119.625, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 28 16.00 P 1 15.00 Na 1 11.00 O 980 8.00 N 874 7.00 C 3509 6.00 H 5348 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS A 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 92 " 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: 0.73 Conformation dependent library (CDL) restraints added in 173.0 milliseconds 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1294 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 7 sheets defined 60.0% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 66 through 100 Processing helix chain 'A' and resid 101 through 110 Processing helix chain 'A' and resid 111 through 115 removed outlier: 4.941A pdb=" N LEU A 114 " --> pdb=" O ASN A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 132 Processing helix chain 'A' and resid 133 through 148 removed outlier: 3.993A pdb=" N SER A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 166 Proline residue: A 157 - end of helix Processing helix chain 'A' and resid 168 through 177 Processing helix chain 'A' and resid 180 through 212 removed outlier: 4.291A pdb=" N HIS A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Proline residue: A 207 - end of helix Processing helix chain 'A' and resid 217 through 224 Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 253 through 263 removed outlier: 4.055A pdb=" N MET A 257 " --> pdb=" O ASP A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 270 removed outlier: 3.513A pdb=" N ARG A 268 " --> pdb=" O ASP A 264 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 363 Processing helix chain 'A' and resid 365 through 376 removed outlier: 4.078A pdb=" N VAL A 369 " --> pdb=" O GLN A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 383 Processing helix chain 'A' and resid 384 through 402 removed outlier: 4.157A pdb=" N TYR A 388 " --> pdb=" O TRP A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 418 Proline residue: A 413 - end of helix Processing helix chain 'A' and resid 421 through 447 Proline residue: A 427 - end of helix Processing helix chain 'A' and resid 451 through 474 Processing helix chain 'A' and resid 476 through 479 Processing helix chain 'A' and resid 480 through 496 removed outlier: 3.706A pdb=" N ARG A 484 " --> pdb=" O ARG A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 509 removed outlier: 4.146A pdb=" N ALA A 501 " --> pdb=" O ARG A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 522 removed outlier: 3.565A pdb=" N LEU A 513 " --> pdb=" O PHE A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 550 Proline residue: A 532 - end of helix Processing helix chain 'A' and resid 556 through 564 removed outlier: 3.966A pdb=" N SER A 560 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N TRP A 561 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ASP A 562 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N PHE A 563 " --> pdb=" O SER A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 570 Processing helix chain 'A' and resid 571 through 581 Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.506A pdb=" N THR B 91 " --> pdb=" O ASN B 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.580A pdb=" N VAL C 87 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.381A pdb=" N GLU B 10 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N MET B 34 " --> pdb=" O TRP B 50 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N TRP B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N TRP B 36 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA B 40 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.381A pdb=" N GLU B 10 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TYR B 111 " --> pdb=" O ARG B 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'C' and resid 10 through 14 removed outlier: 6.893A pdb=" N MET C 37 " --> pdb=" O TYR C 53 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N TYR C 53 " --> pdb=" O MET C 37 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TRP C 39 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 10 through 14 Processing sheet with id=AA7, first strand: chain 'C' and resid 30 through 31 365 hydrogen bonds defined for protein. 1017 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.90 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5341 1.03 - 1.23: 7 1.23 - 1.42: 2260 1.42 - 1.62: 3211 1.62 - 1.81: 43 Bond restraints: 10862 Sorted by residual: bond pdb=" N ASP A 377 " pdb=" CA ASP A 377 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.21e-02 6.83e+03 7.08e+00 bond pdb=" N CYS A 135 " pdb=" CA CYS A 135 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 5.06e+00 bond pdb=" N CYS A 135 " pdb=" H CYS A 135 " ideal model delta sigma weight residual 0.860 0.902 -0.042 2.00e-02 2.50e+03 4.50e+00 bond pdb=" C ASP A 377 " pdb=" O ASP A 377 " ideal model delta sigma weight residual 1.233 1.251 -0.018 1.28e-02 6.10e+03 1.97e+00 bond pdb=" CA CYS A 135 " pdb=" HA CYS A 135 " ideal model delta sigma weight residual 0.970 0.990 -0.020 2.00e-02 2.50e+03 1.02e+00 ... (remaining 10857 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.95: 19603 5.95 - 11.91: 2 11.91 - 17.86: 0 17.86 - 23.82: 2 23.82 - 29.77: 4 Bond angle restraints: 19611 Sorted by residual: angle pdb="HG21 THR A 436 " pdb=" CG2 THR A 436 " pdb="HG22 THR A 436 " ideal model delta sigma weight residual 109.00 79.23 29.77 3.00e+00 1.11e-01 9.85e+01 angle pdb="HG22 THR A 436 " pdb=" CG2 THR A 436 " pdb="HG23 THR A 436 " ideal model delta sigma weight residual 109.00 79.56 29.44 3.00e+00 1.11e-01 9.63e+01 angle pdb=" CB THR A 436 " pdb=" CG2 THR A 436 " pdb="HG21 THR A 436 " ideal model delta sigma weight residual 110.00 81.17 28.83 3.00e+00 1.11e-01 9.24e+01 angle pdb=" CB THR A 436 " pdb=" CG2 THR A 436 " pdb="HG23 THR A 436 " ideal model delta sigma weight residual 110.00 82.24 27.76 3.00e+00 1.11e-01 8.56e+01 angle pdb=" CB THR A 436 " pdb=" CG2 THR A 436 " pdb="HG22 THR A 436 " ideal model delta sigma weight residual 110.00 132.98 -22.98 3.00e+00 1.11e-01 5.87e+01 ... (remaining 19606 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 4532 17.91 - 35.82: 400 35.82 - 53.73: 151 53.73 - 71.64: 45 71.64 - 89.54: 4 Dihedral angle restraints: 5132 sinusoidal: 2754 harmonic: 2378 Sorted by residual: dihedral pdb=" CB CYS C 23 " pdb=" SG CYS C 23 " pdb=" SG CYS C 92 " pdb=" CB CYS C 92 " ideal model delta sinusoidal sigma weight residual 93.00 62.52 30.48 1 1.00e+01 1.00e-02 1.33e+01 dihedral pdb=" CB CYS A 277 " pdb=" SG CYS A 277 " pdb=" SG CYS A 321 " pdb=" CB CYS A 321 " ideal model delta sinusoidal sigma weight residual 93.00 65.69 27.31 1 1.00e+01 1.00e-02 1.07e+01 dihedral pdb=" CG ARG A 497 " pdb=" CD ARG A 497 " pdb=" NE ARG A 497 " pdb=" CZ ARG A 497 " ideal model delta sinusoidal sigma weight residual 180.00 136.54 43.46 2 1.50e+01 4.44e-03 1.01e+01 ... (remaining 5129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 650 0.033 - 0.066: 167 0.066 - 0.100: 58 0.100 - 0.133: 20 0.133 - 0.166: 1 Chirality restraints: 896 Sorted by residual: chirality pdb=" CB THR A 376 " pdb=" CA THR A 376 " pdb=" OG1 THR A 376 " pdb=" CG2 THR A 376 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 6.90e-01 chirality pdb=" CA ILE C 62 " pdb=" N ILE C 62 " pdb=" C ILE C 62 " pdb=" CB ILE C 62 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 chirality pdb=" CA ILE A 476 " pdb=" N ILE A 476 " pdb=" C ILE A 476 " pdb=" CB ILE A 476 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.74e-01 ... (remaining 893 not shown) Planarity restraints: 1581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 135 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.63e+00 pdb=" N THR A 136 " 0.028 2.00e-02 2.50e+03 pdb=" CA THR A 136 " -0.007 2.00e-02 2.50e+03 pdb=" H THR A 136 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 474 " -0.021 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO A 475 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 475 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 475 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 156 " 0.019 5.00e-02 4.00e+02 2.87e-02 1.32e+00 pdb=" N PRO A 157 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 157 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 157 " 0.016 5.00e-02 4.00e+02 ... (remaining 1578 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 871 2.22 - 2.81: 22880 2.81 - 3.41: 30009 3.41 - 4.00: 39658 4.00 - 4.60: 60545 Nonbonded interactions: 153963 Sorted by model distance: nonbonded pdb=" O LEU A 506 " pdb=" H LEU A 511 " model vdw 1.620 2.450 nonbonded pdb="HE21 GLN A 547 " pdb=" O LEU A 558 " model vdw 1.667 2.450 nonbonded pdb=" HG SER A 560 " pdb=" OH TYR B 100 " model vdw 1.677 2.450 nonbonded pdb=" O ASN B 52 " pdb=" H GLY B 56 " model vdw 1.687 2.450 nonbonded pdb="HH11 ARG A 181 " pdb=" O ALA A 494 " model vdw 1.698 2.450 ... (remaining 153958 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 3.380 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: 0.040 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.750 Find NCS groups from input model: 0.020 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:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 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 : 0.002 0.032 5517 Z= 0.099 Angle : 0.431 5.974 7519 Z= 0.234 Chirality : 0.037 0.166 896 Planarity : 0.003 0.033 927 Dihedral : 16.456 89.545 1928 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.68 % Allowed : 23.31 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 3.17 (0.33), residues: 697 helix: 3.50 (0.27), residues: 366 sheet: 1.53 (0.51), residues: 117 loop : -0.18 (0.42), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 480 TYR 0.008 0.001 TYR B 27 PHE 0.011 0.001 PHE A 563 TRP 0.004 0.001 TRP B 50 HIS 0.003 0.001 HIS A 462 Details of bonding type rmsd/Z covalent geometry : bond 0.00187 / 0.10 ( 5514) covalent geometry : angle 0.43090 / 0.23 ( 7513) SS BOND : bond 0.00141 / 0.07 ( 3) SS BOND : angle 0.20785 / 0.08 ( 6) hydrogen bonds : bond 0.14755 / 9.84 ( 353) hydrogen bonds : angle 5.69081 / 4.33 ( 1017) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 444 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 113 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 GLU cc_start: 0.6929 (tm-30) cc_final: 0.6640 (tm-30) REVERT: A 257 MET cc_start: 0.3547 (mmm) cc_final: 0.1834 (ptp) REVERT: A 548 LYS cc_start: 0.6246 (mttt) cc_final: 0.6025 (mptt) REVERT: B 87 LYS cc_start: 0.7339 (mtpt) cc_final: 0.7138 (mttt) REVERT: C 32 PHE cc_start: 0.6641 (m-80) cc_final: 0.6417 (m-10) REVERT: C 97 GLU cc_start: 0.7252 (tt0) cc_final: 0.6967 (tt0) outliers start: 4 outliers final: 1 residues processed: 116 average time/residue: 0.1371 time to fit residues: 20.3807 Evaluate side-chains 81 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 560 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.206772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.153003 restraints weight = 17572.555| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 3.50 r_work: 0.3726 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5517 Z= 0.141 Angle : 0.497 4.228 7519 Z= 0.267 Chirality : 0.039 0.134 896 Planarity : 0.005 0.039 927 Dihedral : 3.413 26.923 743 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.03 % Allowed : 21.28 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 2.70 (0.33), residues: 697 helix: 3.02 (0.27), residues: 369 sheet: 1.30 (0.51), residues: 117 loop : -0.21 (0.41), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 107 TYR 0.012 0.001 TYR C 53 PHE 0.008 0.001 PHE A 464 TRP 0.015 0.001 TRP A 567 HIS 0.004 0.001 HIS A 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 5514) covalent geometry : angle 0.49648 / 0.27 ( 7513) SS BOND : bond 0.00306 / 0.15 ( 3) SS BOND : angle 1.06289 / 0.52 ( 6) hydrogen bonds : bond 0.03863 / 2.61 ( 353) hydrogen bonds : angle 4.86464 / 3.67 ( 1017) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 444 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 GLU cc_start: 0.7480 (tm-30) cc_final: 0.7116 (tm-30) REVERT: A 257 MET cc_start: 0.3528 (mmm) cc_final: 0.1855 (ptp) REVERT: A 274 LYS cc_start: 0.6943 (mmtp) cc_final: 0.6396 (tppp) REVERT: A 462 HIS cc_start: 0.6772 (OUTLIER) cc_final: 0.6430 (t-90) REVERT: A 487 LYS cc_start: 0.6025 (mttm) cc_final: 0.5768 (mmmt) REVERT: A 548 LYS cc_start: 0.5726 (mttt) cc_final: 0.5406 (mptt) REVERT: B 87 LYS cc_start: 0.7095 (mtpt) cc_final: 0.6711 (mttt) REVERT: B 101 TYR cc_start: 0.7061 (t80) cc_final: 0.6826 (t80) REVERT: C 32 PHE cc_start: 0.6723 (m-80) cc_final: 0.6410 (m-10) outliers start: 12 outliers final: 9 residues processed: 107 average time/residue: 0.1471 time to fit residues: 20.5789 Evaluate side-chains 94 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 462 HIS Chi-restraints excluded: chain B residue 100 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 22 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 48 optimal weight: 0.1980 chunk 5 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.202315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.146252 restraints weight = 17625.594| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 3.68 r_work: 0.3567 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5517 Z= 0.123 Angle : 0.479 5.136 7519 Z= 0.255 Chirality : 0.038 0.138 896 Planarity : 0.004 0.048 927 Dihedral : 3.422 21.096 742 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.53 % Allowed : 21.62 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 2.57 (0.33), residues: 697 helix: 2.96 (0.27), residues: 367 sheet: 1.21 (0.51), residues: 117 loop : -0.32 (0.42), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 107 TYR 0.010 0.001 TYR C 53 PHE 0.007 0.001 PHE A 464 TRP 0.019 0.001 TRP A 567 HIS 0.005 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 5514) covalent geometry : angle 0.47792 / 0.25 ( 7513) SS BOND : bond 0.00585 / 0.30 ( 3) SS BOND : angle 1.06321 / 0.55 ( 6) hydrogen bonds : bond 0.03647 / 2.49 ( 353) hydrogen bonds : angle 4.60606 / 3.46 ( 1017) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 444 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 GLU cc_start: 0.7460 (tm-30) cc_final: 0.7069 (tm-30) REVERT: A 257 MET cc_start: 0.3594 (mmm) cc_final: 0.1959 (ptp) REVERT: A 462 HIS cc_start: 0.6538 (OUTLIER) cc_final: 0.6243 (t-90) REVERT: A 548 LYS cc_start: 0.5592 (mttt) cc_final: 0.5221 (mptt) REVERT: B 87 LYS cc_start: 0.6819 (mtpt) cc_final: 0.6458 (mttt) outliers start: 15 outliers final: 9 residues processed: 96 average time/residue: 0.1290 time to fit residues: 16.8459 Evaluate side-chains 90 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 462 HIS Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 22 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 0.0980 chunk 23 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 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 = 0.4245 r_free = 0.4245 target = 0.194447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.137358 restraints weight = 17774.809| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 3.65 r_work: 0.3494 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 5517 Z= 0.177 Angle : 0.521 4.694 7519 Z= 0.284 Chirality : 0.040 0.130 896 Planarity : 0.005 0.060 927 Dihedral : 3.772 35.019 742 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.86 % Allowed : 21.45 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 2.26 (0.33), residues: 697 helix: 2.72 (0.27), residues: 369 sheet: 0.91 (0.52), residues: 117 loop : -0.42 (0.42), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 107 TYR 0.023 0.002 TYR A 496 PHE 0.014 0.001 PHE A 464 TRP 0.022 0.002 TRP A 567 HIS 0.006 0.002 HIS A 462 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 ( 5514) covalent geometry : angle 0.52048 / 0.28 ( 7513) SS BOND : bond 0.00616 / 0.32 ( 3) SS BOND : angle 0.72573 / 0.40 ( 6) hydrogen bonds : bond 0.03862 / 2.65 ( 353) hydrogen bonds : angle 4.56776 / 3.44 ( 1017) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 444 is missing expected H atoms. Skipping. Evaluate side-chains 101 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7812 (mm) REVERT: A 216 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7215 (tm-30) REVERT: A 257 MET cc_start: 0.3586 (mmm) cc_final: 0.1861 (ptp) REVERT: A 548 LYS cc_start: 0.5875 (mttt) cc_final: 0.5476 (mptt) REVERT: B 87 LYS cc_start: 0.6881 (mtpt) cc_final: 0.6516 (mttt) REVERT: C 97 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7029 (pt0) outliers start: 11 outliers final: 4 residues processed: 98 average time/residue: 0.1144 time to fit residues: 15.5044 Evaluate side-chains 87 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain C residue 97 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 10 optimal weight: 0.5980 chunk 40 optimal weight: 0.1980 chunk 49 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 17 optimal weight: 0.0030 chunk 18 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 42 optimal weight: 0.2980 overall best weight: 0.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 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 = 0.4247 r_free = 0.4247 target = 0.195084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.140715 restraints weight = 17262.194| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 3.50 r_work: 0.3538 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5517 Z= 0.107 Angle : 0.470 3.997 7519 Z= 0.251 Chirality : 0.038 0.150 896 Planarity : 0.004 0.039 927 Dihedral : 3.604 26.391 742 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.86 % Allowed : 21.45 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 2.41 (0.33), residues: 697 helix: 2.84 (0.27), residues: 369 sheet: 0.92 (0.51), residues: 117 loop : -0.30 (0.43), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 497 TYR 0.011 0.001 TYR C 53 PHE 0.008 0.001 PHE A 464 TRP 0.019 0.001 TRP A 567 HIS 0.002 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 5514) covalent geometry : angle 0.46882 / 0.25 ( 7513) SS BOND : bond 0.00249 / 0.13 ( 3) SS BOND : angle 1.34566 / 0.71 ( 6) hydrogen bonds : bond 0.03484 / 2.40 ( 353) hydrogen bonds : angle 4.38904 / 3.31 ( 1017) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 444 is missing expected H atoms. Skipping. Evaluate side-chains 92 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7729 (mm) REVERT: A 216 GLU cc_start: 0.7485 (tm-30) cc_final: 0.7100 (tm-30) REVERT: A 257 MET cc_start: 0.3578 (mmm) cc_final: 0.1865 (ptp) REVERT: A 462 HIS cc_start: 0.6986 (OUTLIER) cc_final: 0.6760 (t70) REVERT: A 548 LYS cc_start: 0.5710 (mttt) cc_final: 0.5322 (mptt) REVERT: B 87 LYS cc_start: 0.6940 (mtpt) cc_final: 0.6564 (mttt) REVERT: C 97 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.6938 (pt0) outliers start: 11 outliers final: 5 residues processed: 90 average time/residue: 0.1048 time to fit residues: 13.2709 Evaluate side-chains 88 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 462 HIS Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 97 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 63 optimal weight: 0.0970 chunk 48 optimal weight: 0.0770 chunk 67 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 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 = 0.4251 r_free = 0.4251 target = 0.195620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.139240 restraints weight = 17576.539| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 3.67 r_work: 0.3515 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5517 Z= 0.114 Angle : 0.464 4.507 7519 Z= 0.247 Chirality : 0.038 0.157 896 Planarity : 0.004 0.038 927 Dihedral : 3.524 20.017 742 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.20 % Allowed : 21.28 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 2.43 (0.33), residues: 697 helix: 2.87 (0.27), residues: 369 sheet: 0.90 (0.51), residues: 117 loop : -0.30 (0.43), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 18 TYR 0.011 0.001 TYR C 53 PHE 0.007 0.001 PHE B 95 TRP 0.024 0.001 TRP A 567 HIS 0.002 0.001 HIS A 462 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 5514) covalent geometry : angle 0.46309 / 0.25 ( 7513) SS BOND : bond 0.00197 / 0.10 ( 3) SS BOND : angle 0.93671 / 0.49 ( 6) hydrogen bonds : bond 0.03425 / 2.36 ( 353) hydrogen bonds : angle 4.31446 / 3.26 ( 1017) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 444 is missing expected H atoms. Skipping. Evaluate side-chains 99 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 GLU cc_start: 0.7535 (tm-30) cc_final: 0.7167 (tm-30) REVERT: A 257 MET cc_start: 0.3645 (mmm) cc_final: 0.1935 (ptp) REVERT: A 393 VAL cc_start: 0.8796 (t) cc_final: 0.8549 (p) REVERT: A 462 HIS cc_start: 0.6998 (OUTLIER) cc_final: 0.6625 (t70) REVERT: A 548 LYS cc_start: 0.5841 (mttt) cc_final: 0.5444 (mptt) REVERT: B 87 LYS cc_start: 0.7031 (mtpt) cc_final: 0.6666 (mttt) REVERT: C 97 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6856 (pt0) outliers start: 13 outliers final: 9 residues processed: 95 average time/residue: 0.1019 time to fit residues: 13.6666 Evaluate side-chains 95 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 462 HIS Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 97 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 32 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 17 optimal weight: 0.2980 chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 0.1980 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.195048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.138761 restraints weight = 17558.291| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 3.64 r_work: 0.3506 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5517 Z= 0.113 Angle : 0.472 4.962 7519 Z= 0.251 Chirality : 0.038 0.180 896 Planarity : 0.004 0.037 927 Dihedral : 3.505 15.123 742 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.20 % Allowed : 22.13 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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 (0.33), residues: 697 helix: 2.88 (0.27), residues: 368 sheet: 1.05 (0.48), residues: 128 loop : -0.38 (0.45), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 18 TYR 0.011 0.001 TYR C 53 PHE 0.007 0.001 PHE A 464 TRP 0.023 0.001 TRP A 567 HIS 0.003 0.001 HIS A 462 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 5514) covalent geometry : angle 0.47153 / 0.25 ( 7513) SS BOND : bond 0.00168 / 0.08 ( 3) SS BOND : angle 0.83621 / 0.44 ( 6) hydrogen bonds : bond 0.03417 / 2.36 ( 353) hydrogen bonds : angle 4.26829 / 3.23 ( 1017) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 444 is missing expected H atoms. Skipping. Evaluate side-chains 95 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 GLU cc_start: 0.7509 (tm-30) cc_final: 0.7150 (tm-30) REVERT: A 257 MET cc_start: 0.3656 (mmm) cc_final: 0.1943 (ptp) REVERT: A 393 VAL cc_start: 0.8758 (t) cc_final: 0.8530 (p) REVERT: A 423 GLU cc_start: 0.7077 (mp0) cc_final: 0.6868 (mp0) REVERT: A 548 LYS cc_start: 0.5862 (mttt) cc_final: 0.5456 (mptt) REVERT: B 73 GLU cc_start: 0.6569 (mp0) cc_final: 0.5756 (mp0) REVERT: B 87 LYS cc_start: 0.6998 (mtpt) cc_final: 0.6641 (mttt) REVERT: C 97 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.6884 (pt0) outliers start: 13 outliers final: 11 residues processed: 91 average time/residue: 0.1209 time to fit residues: 15.4622 Evaluate side-chains 94 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 97 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 52 optimal weight: 0.3980 chunk 69 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.190879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.134881 restraints weight = 17672.029| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 3.59 r_work: 0.3466 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5517 Z= 0.139 Angle : 0.480 5.032 7519 Z= 0.259 Chirality : 0.039 0.141 896 Planarity : 0.004 0.035 927 Dihedral : 3.566 13.861 742 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.53 % Allowed : 21.96 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 2.34 (0.33), residues: 697 helix: 2.82 (0.27), residues: 368 sheet: 0.91 (0.48), residues: 128 loop : -0.47 (0.44), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 18 TYR 0.010 0.001 TYR C 53 PHE 0.008 0.001 PHE A 464 TRP 0.028 0.001 TRP A 567 HIS 0.004 0.001 HIS C 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 5514) covalent geometry : angle 0.47992 / 0.26 ( 7513) SS BOND : bond 0.00211 / 0.11 ( 3) SS BOND : angle 0.69160 / 0.35 ( 6) hydrogen bonds : bond 0.03591 / 2.48 ( 353) hydrogen bonds : angle 4.33241 / 3.27 ( 1017) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 444 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 GLU cc_start: 0.7553 (tm-30) cc_final: 0.7187 (tm-30) REVERT: A 393 VAL cc_start: 0.8726 (t) cc_final: 0.8514 (p) REVERT: A 423 GLU cc_start: 0.7210 (mp0) cc_final: 0.6991 (mp0) REVERT: A 548 LYS cc_start: 0.5998 (mttt) cc_final: 0.5579 (mptt) REVERT: B 73 GLU cc_start: 0.6630 (mp0) cc_final: 0.5781 (mp0) REVERT: B 87 LYS cc_start: 0.7084 (mtpt) cc_final: 0.6745 (mttt) outliers start: 15 outliers final: 13 residues processed: 93 average time/residue: 0.0970 time to fit residues: 13.2090 Evaluate side-chains 93 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 56 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 25 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 30 optimal weight: 0.1980 chunk 20 optimal weight: 0.2980 chunk 49 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 27 optimal weight: 0.4980 chunk 12 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.190191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.137896 restraints weight = 17139.161| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 3.30 r_work: 0.3505 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5517 Z= 0.113 Angle : 0.469 5.256 7519 Z= 0.249 Chirality : 0.038 0.132 896 Planarity : 0.004 0.036 927 Dihedral : 3.552 13.445 742 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.03 % Allowed : 22.47 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 2.32 (0.33), residues: 697 helix: 2.77 (0.27), residues: 369 sheet: 0.93 (0.48), residues: 128 loop : -0.45 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 18 TYR 0.012 0.001 TYR C 53 PHE 0.007 0.001 PHE A 464 TRP 0.028 0.001 TRP A 567 HIS 0.003 0.001 HIS A 462 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 5514) covalent geometry : angle 0.46857 / 0.25 ( 7513) SS BOND : bond 0.00166 / 0.08 ( 3) SS BOND : angle 0.55103 / 0.28 ( 6) hydrogen bonds : bond 0.03422 / 2.36 ( 353) hydrogen bonds : angle 4.30222 / 3.24 ( 1017) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 444 is missing expected H atoms. Skipping. Evaluate side-chains 91 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 GLU cc_start: 0.7539 (tm-30) cc_final: 0.7173 (tm-30) REVERT: A 257 MET cc_start: 0.3710 (mmm) cc_final: 0.1968 (ptp) REVERT: A 393 VAL cc_start: 0.8767 (t) cc_final: 0.8561 (p) REVERT: A 548 LYS cc_start: 0.6091 (mttt) cc_final: 0.5682 (mptt) REVERT: B 73 GLU cc_start: 0.6795 (mp0) cc_final: 0.5922 (mp0) REVERT: B 87 LYS cc_start: 0.7167 (mtpt) cc_final: 0.6828 (mttt) outliers start: 12 outliers final: 11 residues processed: 88 average time/residue: 0.1073 time to fit residues: 13.7039 Evaluate side-chains 90 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 18 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 52 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 18 optimal weight: 0.2980 chunk 36 optimal weight: 0.2980 chunk 61 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 0.0870 chunk 9 optimal weight: 0.1980 chunk 66 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 overall best weight: 0.2958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 251 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.193250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.137391 restraints weight = 17682.865| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 3.62 r_work: 0.3496 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5517 Z= 0.100 Angle : 0.472 6.789 7519 Z= 0.248 Chirality : 0.038 0.131 896 Planarity : 0.004 0.035 927 Dihedral : 3.499 12.885 742 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.86 % Allowed : 22.80 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 2.41 (0.33), residues: 697 helix: 2.84 (0.27), residues: 369 sheet: 0.99 (0.48), residues: 128 loop : -0.44 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 18 TYR 0.012 0.001 TYR C 53 PHE 0.006 0.001 PHE B 95 TRP 0.031 0.001 TRP A 567 HIS 0.003 0.001 HIS A 462 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 ( 5514) covalent geometry : angle 0.47193 / 0.25 ( 7513) SS BOND : bond 0.00130 / 0.06 ( 3) SS BOND : angle 0.45042 / 0.23 ( 6) hydrogen bonds : bond 0.03292 / 2.27 ( 353) hydrogen bonds : angle 4.22051 / 3.17 ( 1017) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 444 is missing expected H atoms. Skipping. Evaluate side-chains 90 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 GLU cc_start: 0.7514 (tm-30) cc_final: 0.7143 (tm-30) REVERT: A 548 LYS cc_start: 0.5929 (mttt) cc_final: 0.5495 (mptt) REVERT: B 73 GLU cc_start: 0.6707 (mp0) cc_final: 0.5832 (mp0) REVERT: B 87 LYS cc_start: 0.7096 (mtpt) cc_final: 0.6757 (mttt) outliers start: 11 outliers final: 10 residues processed: 87 average time/residue: 0.0970 time to fit residues: 12.1507 Evaluate side-chains 89 residues out of total 592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 18 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 0.0980 chunk 55 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 63 optimal weight: 0.0870 chunk 30 optimal weight: 0.2980 chunk 47 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.192371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.136555 restraints weight = 17808.250| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 3.62 r_work: 0.3490 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5517 Z= 0.108 Angle : 0.464 6.209 7519 Z= 0.246 Chirality : 0.038 0.133 896 Planarity : 0.004 0.034 927 Dihedral : 3.471 12.991 742 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.86 % Allowed : 22.80 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % 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: 2.37 (0.33), residues: 697 helix: 2.80 (0.27), residues: 369 sheet: 1.00 (0.48), residues: 128 loop : -0.45 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 497 TYR 0.011 0.001 TYR C 53 PHE 0.007 0.001 PHE A 464 TRP 0.027 0.001 TRP A 567 HIS 0.003 0.001 HIS A 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 5514) covalent geometry : angle 0.46407 / 0.25 ( 7513) SS BOND : bond 0.00156 / 0.08 ( 3) SS BOND : angle 0.42646 / 0.21 ( 6) hydrogen bonds : bond 0.03323 / 2.29 ( 353) hydrogen bonds : angle 4.21905 / 3.18 ( 1017) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2536.76 seconds wall clock time: 43 minutes 37.44 seconds (2617.44 seconds total)