Starting phenix.real_space_refine on Wed Jul 1 23:45:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jkk_61564/07_2026/9jkk_61564.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jkk_61564/07_2026/9jkk_61564.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jkk_61564/07_2026/9jkk_61564.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jkk_61564/07_2026/9jkk_61564.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jkk_61564/07_2026/9jkk_61564.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jkk_61564/07_2026/9jkk_61564.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.102 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: 6 Type Number sf(0) Gaussians K 2 8.98 5 S 23 5.16 5 Cl 1 4.86 5 C 2795 2.51 5 N 660 2.21 5 O 712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4193 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4187 Classifications: {'peptide': 530} Link IDs: {'PTRANS': 23, 'TRANS': 506} Chain breaks: 2 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 3 Ad-hoc single atom residues: {' CL': 1, ' K': 2} Classifications: {'water': 3} Link IDs: {None: 2} Chain breaks: 3 Time building chain proxies: 1.19, per 1000 atoms: 0.28 Number of scatterers: 4193 At special positions: 0 Unit cell: (76.7403, 66.6207, 85.1733, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 Cl 1 17.00 S 23 16.00 O 712 8.00 N 660 7.00 C 2795 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 189 " distance=2.04 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: 0.29 Conformation dependent library (CDL) restraints added in 147.1 milliseconds 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 976 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 1 sheets defined 70.8% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 66 through 74 removed outlier: 3.856A pdb=" N LEU A 70 " --> pdb=" O LYS A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 93 removed outlier: 3.727A pdb=" N TYR A 88 " --> pdb=" O TRP A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 110 removed outlier: 3.635A pdb=" N ILE A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 119 removed outlier: 4.312A pdb=" N MET A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 125 removed outlier: 3.655A pdb=" N PHE A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 138 Processing helix chain 'A' and resid 139 through 169 removed outlier: 3.577A pdb=" N PHE A 143 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 146 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE A 155 " --> pdb=" O TYR A 151 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL A 158 " --> pdb=" O PHE A 154 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 159 " --> pdb=" O PHE A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 219 removed outlier: 3.668A pdb=" N PHE A 217 " --> pdb=" O ALA A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 227 Processing helix chain 'A' and resid 239 through 256 removed outlier: 3.702A pdb=" N LEU A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL A 247 " --> pdb=" O CYS A 243 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 272 removed outlier: 3.574A pdb=" N THR A 271 " --> pdb=" O TRP A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 285 removed outlier: 3.949A pdb=" N THR A 278 " --> pdb=" O TYR A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 296 removed outlier: 3.907A pdb=" N GLY A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 323 removed outlier: 3.507A pdb=" N VAL A 318 " --> pdb=" O ALA A 314 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N CYS A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 336 Processing helix chain 'A' and resid 343 through 376 removed outlier: 3.625A pdb=" N VAL A 348 " --> pdb=" O ARG A 344 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR A 349 " --> pdb=" O ASP A 345 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A 357 " --> pdb=" O ASN A 353 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 382 removed outlier: 3.521A pdb=" N VAL A 382 " --> pdb=" O ILE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 399 Proline residue: A 395 - end of helix Processing helix chain 'A' and resid 403 through 438 removed outlier: 3.516A pdb=" N TRP A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A 410 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASP A 436 " --> pdb=" O THR A 432 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLU A 437 " --> pdb=" O GLY A 433 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 443 removed outlier: 3.739A pdb=" N ARG A 443 " --> pdb=" O LEU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 461 removed outlier: 3.952A pdb=" N LEU A 450 " --> pdb=" O GLU A 446 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 451 " --> pdb=" O LEU A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 479 removed outlier: 3.725A pdb=" N VAL A 471 " --> pdb=" O GLY A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 496 removed outlier: 3.678A pdb=" N LEU A 485 " --> pdb=" O GLY A 481 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 513 removed outlier: 3.507A pdb=" N GLN A 510 " --> pdb=" O ASP A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 542 removed outlier: 3.747A pdb=" N VAL A 535 " --> pdb=" O PHE A 531 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE A 540 " --> pdb=" O VAL A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 566 Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' Processing helix chain 'A' and resid 571 through 579 removed outlier: 4.735A pdb=" N ALA A 577 " --> pdb=" O PRO A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 596 removed outlier: 3.510A pdb=" N ALA A 594 " --> pdb=" O LYS A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 605 removed outlier: 3.712A pdb=" N VAL A 604 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP A 605 " --> pdb=" O ARG A 601 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 600 through 605' Processing helix chain 'A' and resid 609 through 613 removed outlier: 3.796A pdb=" N PHE A 612 " --> pdb=" O VAL A 609 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 547 through 548 212 hydrogen bonds defined for protein. 609 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: 0.42 Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 625 1.31 - 1.43: 1310 1.43 - 1.56: 2348 1.56 - 1.69: 0 1.69 - 1.82: 34 Bond restraints: 4317 Sorted by residual: bond pdb=" C ILE A 268 " pdb=" N THR A 269 " ideal model delta sigma weight residual 1.335 1.264 0.070 1.35e-02 5.49e+03 2.72e+01 bond pdb=" C ILE A 352 " pdb=" N ASN A 353 " ideal model delta sigma weight residual 1.335 1.269 0.066 1.38e-02 5.25e+03 2.29e+01 bond pdb=" N ASN A 353 " pdb=" CA ASN A 353 " ideal model delta sigma weight residual 1.458 1.394 0.063 1.33e-02 5.65e+03 2.26e+01 bond pdb=" N THR A 269 " pdb=" CA THR A 269 " ideal model delta sigma weight residual 1.458 1.396 0.062 1.30e-02 5.92e+03 2.25e+01 bond pdb=" C ASN A 353 " pdb=" O ASN A 353 " ideal model delta sigma weight residual 1.236 1.179 0.057 1.29e-02 6.01e+03 1.94e+01 ... (remaining 4312 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 5755 2.95 - 5.91: 113 5.91 - 8.86: 19 8.86 - 11.82: 3 11.82 - 14.77: 2 Bond angle restraints: 5892 Sorted by residual: angle pdb=" CA ASN A 353 " pdb=" C ASN A 353 " pdb=" N SER A 354 " ideal model delta sigma weight residual 118.14 125.48 -7.34 1.31e+00 5.83e-01 3.14e+01 angle pdb=" N ALA A 77 " pdb=" CA ALA A 77 " pdb=" C ALA A 77 " ideal model delta sigma weight residual 114.04 107.37 6.67 1.24e+00 6.50e-01 2.90e+01 angle pdb=" N ILE A 74 " pdb=" CA ILE A 74 " pdb=" C ILE A 74 " ideal model delta sigma weight residual 113.22 107.32 5.90 1.23e+00 6.61e-01 2.30e+01 angle pdb=" N GLY A 585 " pdb=" CA GLY A 585 " pdb=" C GLY A 585 " ideal model delta sigma weight residual 110.60 116.97 -6.37 1.46e+00 4.69e-01 1.91e+01 angle pdb=" C ASN A 353 " pdb=" CA ASN A 353 " pdb=" CB ASN A 353 " ideal model delta sigma weight residual 110.31 119.27 -8.96 2.09e+00 2.29e-01 1.84e+01 ... (remaining 5887 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.38: 2288 15.38 - 30.77: 124 30.77 - 46.15: 24 46.15 - 61.53: 1 61.53 - 76.91: 1 Dihedral angle restraints: 2438 sinusoidal: 911 harmonic: 1527 Sorted by residual: dihedral pdb=" CA CYS A 180 " pdb=" C CYS A 180 " pdb=" N ASN A 181 " pdb=" CA ASN A 181 " ideal model delta harmonic sigma weight residual -180.00 -153.92 -26.08 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA HIS A 616 " pdb=" C HIS A 616 " pdb=" N TRP A 617 " pdb=" CA TRP A 617 " ideal model delta harmonic sigma weight residual 180.00 156.24 23.76 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA PHE A 412 " pdb=" C PHE A 412 " pdb=" N ILE A 413 " pdb=" CA ILE A 413 " ideal model delta harmonic sigma weight residual 180.00 157.42 22.58 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 2435 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 499 0.060 - 0.119: 142 0.119 - 0.179: 23 0.179 - 0.239: 3 0.239 - 0.299: 1 Chirality restraints: 668 Sorted by residual: chirality pdb=" CA ASN A 353 " pdb=" N ASN A 353 " pdb=" C ASN A 353 " pdb=" CB ASN A 353 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CB ILE A 248 " pdb=" CA ILE A 248 " pdb=" CG1 ILE A 248 " pdb=" CG2 ILE A 248 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA THR A 269 " pdb=" N THR A 269 " pdb=" C THR A 269 " pdb=" CB THR A 269 " both_signs ideal model delta sigma weight residual False 2.53 2.31 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 665 not shown) Planarity restraints: 721 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 365 " 0.014 2.00e-02 2.50e+03 1.87e-02 6.15e+00 pdb=" CG PHE A 365 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE A 365 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE A 365 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 365 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 365 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 365 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 111 " -0.037 5.00e-02 4.00e+02 5.58e-02 4.98e+00 pdb=" N PRO A 112 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 112 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 112 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 493 " 0.011 2.00e-02 2.50e+03 2.12e-02 4.51e+00 pdb=" C ILE A 493 " -0.037 2.00e-02 2.50e+03 pdb=" O ILE A 493 " 0.014 2.00e-02 2.50e+03 pdb=" N GLY A 494 " 0.012 2.00e-02 2.50e+03 ... (remaining 718 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.25: 7 2.25 - 2.98: 1858 2.98 - 3.70: 7280 3.70 - 4.42: 11937 4.42 - 5.14: 20555 Nonbonded interactions: 41637 Sorted by model distance: nonbonded pdb=" OD2 ASP A 79 " pdb=" K K A 703 " model vdw 1.532 3.590 nonbonded pdb=" OG SER A 321 " pdb="CL CL A 701 " model vdw 1.560 3.270 nonbonded pdb=" CG ASP A 79 " pdb=" K K A 703 " model vdw 1.867 3.820 nonbonded pdb=" ND2 ASN A 82 " pdb="CL CL A 701 " model vdw 1.951 3.350 nonbonded pdb=" OD1 ASP A 79 " pdb=" K K A 703 " model vdw 2.046 3.590 ... (remaining 41632 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 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: 5.280 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:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 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 : 0.007 0.074 4318 Z= 0.319 Angle : 1.071 14.771 5894 Z= 0.558 Chirality : 0.056 0.299 668 Planarity : 0.008 0.056 721 Dihedral : 10.032 76.914 1459 Min Nonbonded Distance : 1.532 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % 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: -6.33 (0.22), residues: 524 helix: -4.45 (0.12), residues: 362 sheet: None (None), residues: 0 loop : -2.91 (0.38), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 544 TYR 0.024 0.003 TYR A 115 PHE 0.043 0.003 PHE A 365 TRP 0.021 0.003 TRP A 132 HIS 0.005 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00665 / 0.32 ( 4317) covalent geometry : angle 1.07018 / 0.56 ( 5892) SS BOND : bond 0.00405 / 0.21 ( 1) SS BOND : angle 2.61019 / 1.39 ( 2) hydrogen bonds : bond 0.31321 / 19.23 ( 212) hydrogen bonds : angle 11.53530 / 7.83 ( 609) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.147 Fit side-chains REVERT: A 105 PHE cc_start: 0.8203 (t80) cc_final: 0.7966 (t80) REVERT: A 116 MET cc_start: 0.8432 (ttp) cc_final: 0.8219 (ttm) REVERT: A 174 GLU cc_start: 0.7569 (tt0) cc_final: 0.7307 (tp30) REVERT: A 301 ASP cc_start: 0.7909 (p0) cc_final: 0.7293 (m-30) REVERT: A 336 ASN cc_start: 0.8029 (m-40) cc_final: 0.7709 (m-40) REVERT: A 337 LYS cc_start: 0.7786 (mtpp) cc_final: 0.7499 (mtpp) REVERT: A 343 TYR cc_start: 0.7462 (t80) cc_final: 0.7171 (t80) REVERT: A 355 LEU cc_start: 0.7995 (tp) cc_final: 0.7604 (tp) REVERT: A 407 TRP cc_start: 0.8125 (m100) cc_final: 0.7900 (m-90) REVERT: A 421 ASP cc_start: 0.8063 (m-30) cc_final: 0.7626 (m-30) REVERT: A 534 PHE cc_start: 0.7306 (t80) cc_final: 0.6563 (t80) REVERT: A 575 TYR cc_start: 0.7827 (t80) cc_final: 0.7482 (t80) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.4058 time to fit residues: 38.5611 Evaluate side-chains 72 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.0770 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 ASN A 124 ASN A 165 HIS A 181 ASN A 182 ASN A 185 ASN A 188 ASN A 477 HIS A 503 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.137814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.108983 restraints weight = 4729.382| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.75 r_work: 0.3027 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4318 Z= 0.140 Angle : 0.683 10.595 5894 Z= 0.333 Chirality : 0.041 0.136 668 Planarity : 0.006 0.042 721 Dihedral : 5.602 29.854 569 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 1.80 % Allowed : 10.56 % Favored : 87.64 % 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: -3.52 (0.31), residues: 524 helix: -2.23 (0.23), residues: 349 sheet: None (None), residues: 0 loop : -2.18 (0.42), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 237 TYR 0.015 0.001 TYR A 575 PHE 0.020 0.002 PHE A 155 TRP 0.012 0.001 TRP A 132 HIS 0.004 0.001 HIS A 444 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 4317) covalent geometry : angle 0.68163 / 0.33 ( 5892) SS BOND : bond 0.00054 / 0.03 ( 1) SS BOND : angle 2.08844 / 1.11 ( 2) hydrogen bonds : bond 0.04574 / 2.87 ( 212) hydrogen bonds : angle 5.64319 / 3.75 ( 609) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.151 Fit side-chains revert: symmetry clash REVERT: A 105 PHE cc_start: 0.8300 (t80) cc_final: 0.8078 (t80) REVERT: A 116 MET cc_start: 0.8552 (ttp) cc_final: 0.8341 (ttm) REVERT: A 174 GLU cc_start: 0.8225 (tt0) cc_final: 0.7655 (tp30) REVERT: A 239 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.7354 (mp10) REVERT: A 301 ASP cc_start: 0.8168 (p0) cc_final: 0.7313 (m-30) REVERT: A 307 GLU cc_start: 0.8047 (pt0) cc_final: 0.7823 (pt0) REVERT: A 337 LYS cc_start: 0.7958 (mtpp) cc_final: 0.7565 (mtpp) REVERT: A 339 THR cc_start: 0.8209 (OUTLIER) cc_final: 0.7622 (t) REVERT: A 373 GLN cc_start: 0.8011 (tp40) cc_final: 0.7797 (tp40) REVERT: A 407 TRP cc_start: 0.8295 (m100) cc_final: 0.7934 (m100) REVERT: A 421 ASP cc_start: 0.8062 (m-30) cc_final: 0.7709 (m-30) REVERT: A 534 PHE cc_start: 0.7614 (t80) cc_final: 0.6791 (t80) outliers start: 8 outliers final: 2 residues processed: 84 average time/residue: 0.4714 time to fit residues: 41.1973 Evaluate side-chains 67 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 555 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 37 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 1 optimal weight: 0.0030 chunk 47 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 49 optimal weight: 0.4980 overall best weight: 0.4390 ------------------------------------------------------------------------------- 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 = 0.3502 r_free = 0.3502 target = 0.138531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.109579 restraints weight = 4681.742| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.76 r_work: 0.3029 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4318 Z= 0.117 Angle : 0.622 11.519 5894 Z= 0.299 Chirality : 0.040 0.138 668 Planarity : 0.005 0.039 721 Dihedral : 5.210 28.587 569 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 3.60 % Allowed : 11.69 % Favored : 84.72 % 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: -2.09 (0.35), residues: 524 helix: -1.05 (0.26), residues: 353 sheet: None (None), residues: 0 loop : -1.81 (0.45), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 588 TYR 0.007 0.001 TYR A 575 PHE 0.019 0.001 PHE A 76 TRP 0.010 0.001 TRP A 132 HIS 0.006 0.001 HIS A 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 4317) covalent geometry : angle 0.62157 / 0.30 ( 5892) SS BOND : bond 0.00086 / 0.05 ( 1) SS BOND : angle 1.41042 / 0.75 ( 2) hydrogen bonds : bond 0.03580 / 2.26 ( 212) hydrogen bonds : angle 5.06340 / 3.38 ( 609) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: A 103 LEU cc_start: 0.8536 (tm) cc_final: 0.8163 (tt) REVERT: A 105 PHE cc_start: 0.8258 (t80) cc_final: 0.7964 (t80) REVERT: A 116 MET cc_start: 0.8611 (ttp) cc_final: 0.8321 (ttm) REVERT: A 174 GLU cc_start: 0.8230 (tt0) cc_final: 0.7650 (tp30) REVERT: A 218 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8310 (mt-10) REVERT: A 239 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.7331 (mp10) REVERT: A 301 ASP cc_start: 0.8162 (p0) cc_final: 0.7285 (m-30) REVERT: A 307 GLU cc_start: 0.8130 (pt0) cc_final: 0.7925 (pt0) REVERT: A 337 LYS cc_start: 0.7932 (mtpp) cc_final: 0.7612 (mtpp) REVERT: A 407 TRP cc_start: 0.8260 (m100) cc_final: 0.7906 (m100) REVERT: A 421 ASP cc_start: 0.7979 (m-30) cc_final: 0.7654 (m-30) REVERT: A 534 PHE cc_start: 0.7554 (t80) cc_final: 0.6724 (t80) outliers start: 16 outliers final: 5 residues processed: 80 average time/residue: 0.4713 time to fit residues: 39.2660 Evaluate side-chains 69 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 555 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 39 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 6 optimal weight: 0.4980 chunk 47 optimal weight: 1.9990 chunk 7 optimal weight: 0.0770 chunk 43 optimal weight: 1.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.3493 r_free = 0.3493 target = 0.138131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.108354 restraints weight = 4639.689| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.77 r_work: 0.3006 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4318 Z= 0.119 Angle : 0.607 11.466 5894 Z= 0.291 Chirality : 0.040 0.140 668 Planarity : 0.004 0.038 721 Dihedral : 5.003 29.163 569 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.47 % Allowed : 14.38 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.37), residues: 524 helix: -0.46 (0.28), residues: 363 sheet: None (None), residues: 0 loop : -1.23 (0.49), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 588 TYR 0.006 0.001 TYR A 470 PHE 0.018 0.001 PHE A 365 TRP 0.011 0.001 TRP A 132 HIS 0.004 0.001 HIS A 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 4317) covalent geometry : angle 0.60671 / 0.29 ( 5892) SS BOND : bond 0.00030 / 0.02 ( 1) SS BOND : angle 1.60210 / 0.85 ( 2) hydrogen bonds : bond 0.03318 / 2.11 ( 212) hydrogen bonds : angle 4.76547 / 3.19 ( 609) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.151 Fit side-chains REVERT: A 103 LEU cc_start: 0.8435 (tm) cc_final: 0.8091 (tt) REVERT: A 105 PHE cc_start: 0.8294 (t80) cc_final: 0.7880 (t80) REVERT: A 116 MET cc_start: 0.8698 (ttp) cc_final: 0.8402 (ttm) REVERT: A 174 GLU cc_start: 0.8253 (tt0) cc_final: 0.7672 (tp30) REVERT: A 218 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8503 (mt-10) REVERT: A 239 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.7343 (mp10) REVERT: A 301 ASP cc_start: 0.8169 (p0) cc_final: 0.7257 (m-30) REVERT: A 337 LYS cc_start: 0.8042 (mtpp) cc_final: 0.7677 (mtpp) REVERT: A 373 GLN cc_start: 0.8347 (tp40) cc_final: 0.8112 (tm-30) REVERT: A 407 TRP cc_start: 0.8281 (m100) cc_final: 0.7920 (m100) REVERT: A 421 ASP cc_start: 0.7933 (m-30) cc_final: 0.7576 (m-30) REVERT: A 534 PHE cc_start: 0.7603 (t80) cc_final: 0.6790 (t80) REVERT: A 601 ARG cc_start: 0.7385 (tpp80) cc_final: 0.7181 (tpp80) outliers start: 11 outliers final: 5 residues processed: 75 average time/residue: 0.5001 time to fit residues: 39.0811 Evaluate side-chains 66 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 555 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 0.0030 chunk 39 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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 = 0.3476 r_free = 0.3476 target = 0.136804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.107367 restraints weight = 4644.779| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.74 r_work: 0.2995 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4318 Z= 0.121 Angle : 0.604 11.621 5894 Z= 0.289 Chirality : 0.040 0.134 668 Planarity : 0.004 0.035 721 Dihedral : 4.920 28.620 569 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.15 % Allowed : 15.73 % 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: -0.70 (0.38), residues: 524 helix: -0.13 (0.28), residues: 363 sheet: None (None), residues: 0 loop : -0.96 (0.50), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 588 TYR 0.006 0.001 TYR A 297 PHE 0.017 0.001 PHE A 365 TRP 0.007 0.001 TRP A 520 HIS 0.003 0.001 HIS A 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 ( 4317) covalent geometry : angle 0.60383 / 0.29 ( 5892) SS BOND : bond 0.00051 / 0.03 ( 1) SS BOND : angle 1.49845 / 0.80 ( 2) hydrogen bonds : bond 0.03268 / 2.09 ( 212) hydrogen bonds : angle 4.69310 / 3.16 ( 609) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.158 Fit side-chains REVERT: A 103 LEU cc_start: 0.8397 (tm) cc_final: 0.8039 (tt) REVERT: A 105 PHE cc_start: 0.8324 (t80) cc_final: 0.7964 (t80) REVERT: A 116 MET cc_start: 0.8699 (ttp) cc_final: 0.8382 (ttm) REVERT: A 174 GLU cc_start: 0.8315 (tt0) cc_final: 0.7726 (tp30) REVERT: A 218 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8480 (mt-10) REVERT: A 239 GLN cc_start: 0.7621 (OUTLIER) cc_final: 0.7312 (mp10) REVERT: A 301 ASP cc_start: 0.8167 (p0) cc_final: 0.7948 (p0) REVERT: A 337 LYS cc_start: 0.8005 (mtpp) cc_final: 0.7646 (mtpp) REVERT: A 373 GLN cc_start: 0.8355 (tp40) cc_final: 0.8103 (tm-30) REVERT: A 407 TRP cc_start: 0.8272 (m100) cc_final: 0.7874 (m100) REVERT: A 534 PHE cc_start: 0.7585 (t80) cc_final: 0.6779 (t80) REVERT: A 601 ARG cc_start: 0.7383 (tpp80) cc_final: 0.7155 (tpp80) outliers start: 14 outliers final: 9 residues processed: 75 average time/residue: 0.4887 time to fit residues: 38.0650 Evaluate side-chains 74 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 609 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 3.9990 chunk 13 optimal weight: 0.0770 chunk 10 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 = 0.3471 r_free = 0.3471 target = 0.136317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.106633 restraints weight = 4711.335| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.76 r_work: 0.2986 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4318 Z= 0.124 Angle : 0.605 12.015 5894 Z= 0.289 Chirality : 0.040 0.136 668 Planarity : 0.004 0.037 721 Dihedral : 4.885 29.466 569 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.70 % Allowed : 16.85 % 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: -0.38 (0.38), residues: 524 helix: 0.05 (0.29), residues: 364 sheet: None (None), residues: 0 loop : -0.67 (0.52), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 588 TYR 0.006 0.001 TYR A 297 PHE 0.017 0.001 PHE A 365 TRP 0.007 0.001 TRP A 132 HIS 0.003 0.001 HIS A 444 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.12 ( 4317) covalent geometry : angle 0.60463 / 0.29 ( 5892) SS BOND : bond 0.00033 / 0.02 ( 1) SS BOND : angle 1.50439 / 0.80 ( 2) hydrogen bonds : bond 0.03271 / 2.10 ( 212) hydrogen bonds : angle 4.61906 / 3.11 ( 609) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.191 Fit side-chains REVERT: A 103 LEU cc_start: 0.8408 (tm) cc_final: 0.8158 (tt) REVERT: A 105 PHE cc_start: 0.8295 (t80) cc_final: 0.7878 (t80) REVERT: A 116 MET cc_start: 0.8728 (ttp) cc_final: 0.8409 (ttm) REVERT: A 174 GLU cc_start: 0.8344 (tt0) cc_final: 0.7792 (tp30) REVERT: A 239 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.7327 (mp10) REVERT: A 337 LYS cc_start: 0.8047 (mtpp) cc_final: 0.7679 (mtpp) REVERT: A 373 GLN cc_start: 0.8344 (tp40) cc_final: 0.8116 (tm-30) REVERT: A 407 TRP cc_start: 0.8252 (m100) cc_final: 0.7878 (m100) REVERT: A 534 PHE cc_start: 0.7627 (t80) cc_final: 0.6817 (t80) outliers start: 12 outliers final: 7 residues processed: 76 average time/residue: 0.4981 time to fit residues: 39.4078 Evaluate side-chains 67 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 609 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 2 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 31 optimal weight: 0.0060 chunk 4 optimal weight: 0.6980 chunk 50 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 182 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.135718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.106366 restraints weight = 4710.971| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.75 r_work: 0.2977 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4318 Z= 0.126 Angle : 0.609 12.225 5894 Z= 0.291 Chirality : 0.041 0.135 668 Planarity : 0.004 0.035 721 Dihedral : 4.851 28.828 569 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.92 % Allowed : 16.40 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.39), residues: 524 helix: 0.17 (0.29), residues: 364 sheet: None (None), residues: 0 loop : -0.59 (0.53), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 237 TYR 0.006 0.001 TYR A 297 PHE 0.016 0.001 PHE A 365 TRP 0.009 0.001 TRP A 132 HIS 0.003 0.001 HIS A 444 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 4317) covalent geometry : angle 0.60864 / 0.29 ( 5892) SS BOND : bond 0.00003 / 0.00 ( 1) SS BOND : angle 1.50729 / 0.80 ( 2) hydrogen bonds : bond 0.03242 / 2.10 ( 212) hydrogen bonds : angle 4.60857 / 3.09 ( 609) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.160 Fit side-chains REVERT: A 103 LEU cc_start: 0.8432 (tm) cc_final: 0.8183 (tt) REVERT: A 105 PHE cc_start: 0.8311 (t80) cc_final: 0.7875 (t80) REVERT: A 116 MET cc_start: 0.8730 (ttp) cc_final: 0.8410 (ttm) REVERT: A 174 GLU cc_start: 0.8336 (tt0) cc_final: 0.7804 (tp30) REVERT: A 218 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8465 (mt-10) REVERT: A 337 LYS cc_start: 0.7960 (mtpp) cc_final: 0.7600 (mtpp) REVERT: A 373 GLN cc_start: 0.8414 (tp40) cc_final: 0.8162 (tm-30) REVERT: A 407 TRP cc_start: 0.8263 (m100) cc_final: 0.7894 (m100) REVERT: A 421 ASP cc_start: 0.7987 (m-30) cc_final: 0.7661 (m-30) REVERT: A 534 PHE cc_start: 0.7629 (t80) cc_final: 0.6815 (t80) outliers start: 13 outliers final: 8 residues processed: 72 average time/residue: 0.4365 time to fit residues: 32.7586 Evaluate side-chains 69 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 609 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 51 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 49 optimal weight: 0.1980 chunk 15 optimal weight: 0.6980 chunk 24 optimal weight: 0.0570 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 611 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.136596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.107192 restraints weight = 4699.330| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.75 r_work: 0.2999 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4318 Z= 0.115 Angle : 0.598 11.979 5894 Z= 0.285 Chirality : 0.040 0.130 668 Planarity : 0.004 0.034 721 Dihedral : 4.823 29.115 569 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.47 % Allowed : 16.85 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.39), residues: 524 helix: 0.28 (0.29), residues: 364 sheet: None (None), residues: 0 loop : -0.58 (0.53), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 601 TYR 0.008 0.001 TYR A 156 PHE 0.015 0.001 PHE A 155 TRP 0.008 0.001 TRP A 132 HIS 0.002 0.001 HIS A 444 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 ( 4317) covalent geometry : angle 0.59680 / 0.28 ( 5892) SS BOND : bond 0.00116 / 0.06 ( 1) SS BOND : angle 1.79043 / 0.94 ( 2) hydrogen bonds : bond 0.03123 / 2.01 ( 212) hydrogen bonds : angle 4.54065 / 3.05 ( 609) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.094 Fit side-chains REVERT: A 103 LEU cc_start: 0.8424 (tm) cc_final: 0.8198 (tt) REVERT: A 105 PHE cc_start: 0.8326 (t80) cc_final: 0.7875 (t80) REVERT: A 116 MET cc_start: 0.8732 (ttp) cc_final: 0.8391 (ttm) REVERT: A 174 GLU cc_start: 0.8333 (tt0) cc_final: 0.7825 (tp30) REVERT: A 218 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8424 (mt-10) REVERT: A 337 LYS cc_start: 0.7905 (mtpp) cc_final: 0.7562 (mtpp) REVERT: A 373 GLN cc_start: 0.8405 (tp40) cc_final: 0.8169 (tm-30) REVERT: A 407 TRP cc_start: 0.8265 (m100) cc_final: 0.7865 (m100) REVERT: A 534 PHE cc_start: 0.7628 (t80) cc_final: 0.6830 (t80) outliers start: 11 outliers final: 5 residues processed: 68 average time/residue: 0.4268 time to fit residues: 30.1605 Evaluate side-chains 65 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 609 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 182 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.135048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.105818 restraints weight = 4767.905| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.75 r_work: 0.2974 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4318 Z= 0.128 Angle : 0.614 13.121 5894 Z= 0.292 Chirality : 0.041 0.133 668 Planarity : 0.004 0.035 721 Dihedral : 4.832 29.115 569 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.02 % Allowed : 17.30 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.39), residues: 524 helix: 0.35 (0.29), residues: 360 sheet: None (None), residues: 0 loop : -0.60 (0.53), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 237 TYR 0.007 0.001 TYR A 156 PHE 0.017 0.001 PHE A 155 TRP 0.010 0.001 TRP A 132 HIS 0.002 0.001 HIS A 444 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 4317) covalent geometry : angle 0.61304 / 0.29 ( 5892) SS BOND : bond 0.00206 / 0.11 ( 1) SS BOND : angle 1.84924 / 0.97 ( 2) hydrogen bonds : bond 0.03239 / 2.10 ( 212) hydrogen bonds : angle 4.57389 / 3.07 ( 609) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.093 Fit side-chains REVERT: A 103 LEU cc_start: 0.8411 (tm) cc_final: 0.8178 (tt) REVERT: A 105 PHE cc_start: 0.8342 (t80) cc_final: 0.7862 (t80) REVERT: A 116 MET cc_start: 0.8810 (ttp) cc_final: 0.8461 (ttm) REVERT: A 117 GLU cc_start: 0.8922 (pt0) cc_final: 0.8675 (pt0) REVERT: A 174 GLU cc_start: 0.8317 (tt0) cc_final: 0.7790 (tp30) REVERT: A 218 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8458 (mt-10) REVERT: A 309 SER cc_start: 0.8339 (t) cc_final: 0.7816 (m) REVERT: A 337 LYS cc_start: 0.8014 (mtpp) cc_final: 0.7653 (mtpp) REVERT: A 373 GLN cc_start: 0.8373 (tp40) cc_final: 0.8140 (tm-30) REVERT: A 407 TRP cc_start: 0.8265 (m100) cc_final: 0.7906 (m100) REVERT: A 534 PHE cc_start: 0.7637 (t80) cc_final: 0.6795 (t80) REVERT: A 601 ARG cc_start: 0.7215 (tpp80) cc_final: 0.6956 (tpp80) outliers start: 9 outliers final: 5 residues processed: 69 average time/residue: 0.4708 time to fit residues: 33.7220 Evaluate side-chains 67 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 609 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.1980 chunk 32 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3456 r_free = 0.3456 target = 0.135036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.106134 restraints weight = 4691.815| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.73 r_work: 0.2977 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4318 Z= 0.125 Angle : 0.619 14.201 5894 Z= 0.291 Chirality : 0.041 0.132 668 Planarity : 0.004 0.035 721 Dihedral : 4.815 29.071 569 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.02 % Allowed : 17.75 % 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: 0.02 (0.39), residues: 524 helix: 0.39 (0.29), residues: 360 sheet: None (None), residues: 0 loop : -0.60 (0.52), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 237 TYR 0.007 0.001 TYR A 156 PHE 0.016 0.001 PHE A 155 TRP 0.010 0.001 TRP A 132 HIS 0.002 0.001 HIS A 444 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.12 ( 4317) covalent geometry : angle 0.61783 / 0.29 ( 5892) SS BOND : bond 0.00120 / 0.06 ( 1) SS BOND : angle 1.71754 / 0.91 ( 2) hydrogen bonds : bond 0.03201 / 2.08 ( 212) hydrogen bonds : angle 4.57611 / 3.09 ( 609) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.152 Fit side-chains REVERT: A 103 LEU cc_start: 0.8385 (tm) cc_final: 0.8155 (tt) REVERT: A 105 PHE cc_start: 0.8338 (t80) cc_final: 0.7867 (t80) REVERT: A 116 MET cc_start: 0.8790 (ttp) cc_final: 0.8387 (ttm) REVERT: A 117 GLU cc_start: 0.8948 (pt0) cc_final: 0.8722 (pt0) REVERT: A 174 GLU cc_start: 0.8347 (tt0) cc_final: 0.7802 (tp30) REVERT: A 218 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8433 (mt-10) REVERT: A 309 SER cc_start: 0.8330 (t) cc_final: 0.7812 (m) REVERT: A 337 LYS cc_start: 0.8016 (mtpp) cc_final: 0.7651 (mtpp) REVERT: A 373 GLN cc_start: 0.8442 (tp40) cc_final: 0.8209 (tm-30) REVERT: A 407 TRP cc_start: 0.8265 (m100) cc_final: 0.7906 (m100) REVERT: A 534 PHE cc_start: 0.7619 (t80) cc_final: 0.6760 (t80) REVERT: A 601 ARG cc_start: 0.7287 (tpp80) cc_final: 0.7015 (tpp80) outliers start: 9 outliers final: 6 residues processed: 68 average time/residue: 0.4043 time to fit residues: 28.7688 Evaluate side-chains 68 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 598 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 28 optimal weight: 0.0070 chunk 31 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 44 optimal weight: 0.4980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 ASN A 239 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.135746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.106772 restraints weight = 4727.520| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.74 r_work: 0.2988 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4318 Z= 0.116 Angle : 0.608 13.563 5894 Z= 0.287 Chirality : 0.040 0.131 668 Planarity : 0.004 0.034 721 Dihedral : 4.763 29.252 569 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.02 % Allowed : 17.75 % 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: 0.15 (0.39), residues: 524 helix: 0.50 (0.29), residues: 360 sheet: None (None), residues: 0 loop : -0.57 (0.52), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 237 TYR 0.008 0.001 TYR A 156 PHE 0.015 0.001 PHE A 155 TRP 0.009 0.001 TRP A 132 HIS 0.002 0.001 HIS A 444 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 4317) covalent geometry : angle 0.60789 / 0.29 ( 5892) SS BOND : bond 0.00128 / 0.07 ( 1) SS BOND : angle 1.57148 / 0.83 ( 2) hydrogen bonds : bond 0.03095 / 2.00 ( 212) hydrogen bonds : angle 4.52660 / 3.05 ( 609) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1481.79 seconds wall clock time: 25 minutes 56.76 seconds (1556.76 seconds total)