Starting phenix.real_space_refine on Sat May 2 09:34:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jkk_61564/05_2026/9jkk_61564.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jkk_61564/05_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_61564/05_2026/9jkk_61564.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jkk_61564/05_2026/9jkk_61564.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jkk_61564/05_2026/9jkk_61564.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jkk_61564/05_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-2.1rc2-6044/lib/python3.9/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, 6 Unusual residues: {' K': 2, ' CL': 1} Classifications: {'undetermined': 3, 'water': 3} Link IDs: {None: 5} Time building chain proxies: 1.31, per 1000 atoms: 0.31 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: 0.35 Conformation dependent library (CDL) restraints added in 155.3 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: 0.13 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: 0.65 Time building geometry restraints manager: 0.47 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 2.850 nonbonded pdb=" OG SER A 321 " pdb="CL CL A 701 " model vdw 1.560 3.190 nonbonded pdb=" CG ASP A 79 " pdb=" K K A 703 " model vdw 1.867 3.080 nonbonded pdb=" ND2 ASN A 82 " pdb="CL CL A 701 " model vdw 1.951 3.270 nonbonded pdb=" OD1 ASP A 79 " pdb=" K K A 703 " model vdw 2.046 2.850 ... (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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.900 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:7.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 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 covalent geometry : bond 0.00665 ( 4317) covalent geometry : angle 1.07018 ( 5892) SS BOND : bond 0.00405 ( 1) SS BOND : angle 2.61019 ( 2) hydrogen bonds : bond 0.31321 ( 212) hydrogen bonds : angle 11.53530 ( 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 : 0.138 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: 0.4700 time to fit residues: 44.4591 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 : 0.164 ------------------------------------------------------------------------------- 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: 0.9980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 124 ASN A 165 HIS A 181 ASN A 182 ASN A 185 ASN A 188 ASN A 444 HIS A 477 HIS A 503 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.136686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.107782 restraints weight = 4728.439| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.75 r_work: 0.3009 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4318 Z= 0.155 Angle : 0.694 10.686 5894 Z= 0.338 Chirality : 0.042 0.130 668 Planarity : 0.006 0.044 721 Dihedral : 5.646 29.834 569 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.47 % Allowed : 10.11 % Favored : 87.42 % 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: -3.60 (0.31), residues: 524 helix: -2.22 (0.23), residues: 345 sheet: None (None), residues: 0 loop : -2.39 (0.41), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 237 TYR 0.016 0.002 TYR A 575 PHE 0.022 0.002 PHE A 155 TRP 0.013 0.001 TRP A 132 HIS 0.004 0.001 HIS A 444 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 4317) covalent geometry : angle 0.69265 ( 5892) SS BOND : bond 0.00061 ( 1) SS BOND : angle 2.19087 ( 2) hydrogen bonds : bond 0.04640 ( 212) hydrogen bonds : angle 5.63735 ( 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 90 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: A 105 PHE cc_start: 0.8271 (t80) cc_final: 0.8024 (t80) REVERT: A 174 GLU cc_start: 0.8232 (tt0) cc_final: 0.7655 (tp30) REVERT: A 239 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.7351 (mp10) REVERT: A 301 ASP cc_start: 0.8189 (p0) cc_final: 0.7324 (m-30) REVERT: A 307 GLU cc_start: 0.8086 (pt0) cc_final: 0.7868 (pt0) REVERT: A 337 LYS cc_start: 0.8113 (mtpp) cc_final: 0.7699 (mtpp) REVERT: A 373 GLN cc_start: 0.8003 (tp40) cc_final: 0.7796 (tp40) REVERT: A 407 TRP cc_start: 0.8303 (m100) cc_final: 0.7936 (m100) REVERT: A 421 ASP cc_start: 0.8106 (m-30) cc_final: 0.7771 (m-30) REVERT: A 534 PHE cc_start: 0.7628 (t80) cc_final: 0.6797 (t80) REVERT: A 560 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8088 (tp) outliers start: 11 outliers final: 4 residues processed: 88 average time/residue: 0.4590 time to fit residues: 42.0418 Evaluate side-chains 71 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 517 SER Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 560 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 37 optimal weight: 0.1980 chunk 8 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 47 optimal weight: 0.0670 chunk 35 optimal weight: 0.8980 chunk 50 optimal weight: 0.1980 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 45 optimal weight: 0.2980 chunk 38 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 overall best weight: 0.2718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.139616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.110765 restraints weight = 4672.867| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.75 r_work: 0.3047 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4318 Z= 0.107 Angle : 0.605 11.357 5894 Z= 0.292 Chirality : 0.040 0.128 668 Planarity : 0.005 0.039 721 Dihedral : 5.185 28.501 569 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.92 % Allowed : 12.81 % Favored : 84.27 % 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: -2.05 (0.35), residues: 524 helix: -0.96 (0.27), residues: 347 sheet: None (None), residues: 0 loop : -1.96 (0.44), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 588 TYR 0.006 0.001 TYR A 470 PHE 0.015 0.001 PHE A 365 TRP 0.008 0.001 TRP A 132 HIS 0.003 0.000 HIS A 444 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 4317) covalent geometry : angle 0.60493 ( 5892) SS BOND : bond 0.00084 ( 1) SS BOND : angle 1.42408 ( 2) hydrogen bonds : bond 0.03432 ( 212) hydrogen bonds : angle 5.05689 ( 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 83 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.154 Fit side-chains revert: symmetry clash REVERT: A 103 LEU cc_start: 0.8553 (tm) cc_final: 0.8190 (tt) REVERT: A 174 GLU cc_start: 0.8231 (tt0) cc_final: 0.7650 (tp30) REVERT: A 239 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.7320 (mp10) REVERT: A 301 ASP cc_start: 0.8170 (p0) cc_final: 0.7280 (m-30) REVERT: A 337 LYS cc_start: 0.7856 (mtpp) cc_final: 0.7515 (mtpp) REVERT: A 407 TRP cc_start: 0.8212 (m100) cc_final: 0.7827 (m100) REVERT: A 421 ASP cc_start: 0.8018 (m-30) cc_final: 0.7688 (m-30) REVERT: A 534 PHE cc_start: 0.7545 (t80) cc_final: 0.6735 (t80) outliers start: 13 outliers final: 5 residues processed: 78 average time/residue: 0.4997 time to fit residues: 40.4839 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 : 0.165 ------------------------------------------------------------------------------- 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 429 SER Chi-restraints excluded: chain A residue 522 LEU 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: 0.7980 chunk 20 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 27 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.131932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.102495 restraints weight = 4741.732| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.74 r_work: 0.2931 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 4318 Z= 0.194 Angle : 0.695 13.244 5894 Z= 0.331 Chirality : 0.043 0.139 668 Planarity : 0.005 0.043 721 Dihedral : 5.298 28.339 569 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.60 % Allowed : 13.26 % 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: -1.53 (0.36), residues: 524 helix: -0.71 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -1.40 (0.47), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 588 TYR 0.011 0.002 TYR A 548 PHE 0.030 0.002 PHE A 365 TRP 0.020 0.001 TRP A 256 HIS 0.004 0.001 HIS A 444 Details of bonding type rmsd covalent geometry : bond 0.00479 ( 4317) covalent geometry : angle 0.69391 ( 5892) SS BOND : bond 0.00025 ( 1) SS BOND : angle 2.19486 ( 2) hydrogen bonds : bond 0.04061 ( 212) hydrogen bonds : angle 4.93032 ( 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 85 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.156 Fit side-chains REVERT: A 103 LEU cc_start: 0.8517 (tm) cc_final: 0.8154 (tt) REVERT: A 105 PHE cc_start: 0.8376 (t80) cc_final: 0.8074 (t80) REVERT: A 174 GLU cc_start: 0.8407 (tt0) cc_final: 0.7844 (tp30) REVERT: A 239 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7514 (mp10) REVERT: A 301 ASP cc_start: 0.8254 (p0) cc_final: 0.7380 (m-30) REVERT: A 309 SER cc_start: 0.8368 (t) cc_final: 0.7878 (m) REVERT: A 337 LYS cc_start: 0.8286 (mtpp) cc_final: 0.7916 (mtpp) REVERT: A 344 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7647 (ptt180) REVERT: A 373 GLN cc_start: 0.8406 (tp40) cc_final: 0.8200 (tm-30) REVERT: A 407 TRP cc_start: 0.8340 (m100) cc_final: 0.7942 (m100) REVERT: A 421 ASP cc_start: 0.8055 (m-30) cc_final: 0.7806 (m-30) REVERT: A 534 PHE cc_start: 0.7686 (t80) cc_final: 0.6884 (t80) REVERT: A 560 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8126 (tp) REVERT: A 601 ARG cc_start: 0.7417 (tpp80) cc_final: 0.7007 (tpp80) outliers start: 16 outliers final: 6 residues processed: 79 average time/residue: 0.5321 time to fit residues: 43.6055 Evaluate side-chains 75 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 432 THR Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 560 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 31 optimal weight: 0.6980 chunk 12 optimal weight: 0.2980 chunk 39 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.134313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.105069 restraints weight = 4693.767| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.74 r_work: 0.2964 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3104 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= 0.128 Angle : 0.618 12.470 5894 Z= 0.294 Chirality : 0.041 0.128 668 Planarity : 0.004 0.038 721 Dihedral : 5.083 29.078 569 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.92 % Allowed : 16.18 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.37), residues: 524 helix: -0.22 (0.28), residues: 358 sheet: None (None), residues: 0 loop : -1.19 (0.49), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 588 TYR 0.016 0.001 TYR A 274 PHE 0.016 0.001 PHE A 365 TRP 0.009 0.001 TRP A 132 HIS 0.004 0.001 HIS A 444 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 4317) covalent geometry : angle 0.61688 ( 5892) SS BOND : bond 0.00021 ( 1) SS BOND : angle 1.62588 ( 2) hydrogen bonds : bond 0.03390 ( 212) hydrogen bonds : angle 4.77381 ( 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 82 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.149 Fit side-chains revert: symmetry clash REVERT: A 103 LEU cc_start: 0.8414 (tm) cc_final: 0.8082 (tt) REVERT: A 105 PHE cc_start: 0.8324 (t80) cc_final: 0.7985 (t80) REVERT: A 174 GLU cc_start: 0.8367 (tt0) cc_final: 0.7785 (tp30) REVERT: A 239 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7328 (mp10) REVERT: A 301 ASP cc_start: 0.8185 (p0) cc_final: 0.7285 (m-30) REVERT: A 309 SER cc_start: 0.8327 (t) cc_final: 0.7812 (m) REVERT: A 337 LYS cc_start: 0.8023 (mtpp) cc_final: 0.7646 (mtpp) REVERT: A 373 GLN cc_start: 0.8350 (tp40) cc_final: 0.8111 (tm-30) REVERT: A 407 TRP cc_start: 0.8270 (m100) cc_final: 0.7882 (m100) REVERT: A 421 ASP cc_start: 0.8008 (m-30) cc_final: 0.7708 (m-30) REVERT: A 534 PHE cc_start: 0.7614 (t80) cc_final: 0.6811 (t80) outliers start: 13 outliers final: 6 residues processed: 78 average time/residue: 0.4753 time to fit residues: 38.5103 Evaluate side-chains 73 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 501 VAL Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 569 MET 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: 5.9990 chunk 13 optimal weight: 0.4980 chunk 10 optimal weight: 0.2980 chunk 29 optimal weight: 0.0000 chunk 49 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN A 182 ASN A 444 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.135906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.106135 restraints weight = 4762.812| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.77 r_work: 0.2977 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3241 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= 0.117 Angle : 0.607 12.277 5894 Z= 0.292 Chirality : 0.040 0.128 668 Planarity : 0.004 0.037 721 Dihedral : 4.960 29.784 569 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.15 % Allowed : 16.18 % 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: -0.48 (0.38), residues: 524 helix: 0.08 (0.28), residues: 358 sheet: None (None), residues: 0 loop : -0.96 (0.51), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 588 TYR 0.015 0.001 TYR A 274 PHE 0.015 0.001 PHE A 155 TRP 0.009 0.001 TRP A 132 HIS 0.004 0.001 HIS A 444 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 4317) covalent geometry : angle 0.60651 ( 5892) SS BOND : bond 0.00040 ( 1) SS BOND : angle 1.46291 ( 2) hydrogen bonds : bond 0.03210 ( 212) hydrogen bonds : angle 4.63384 ( 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 82 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.159 Fit side-chains REVERT: A 103 LEU cc_start: 0.8375 (tm) cc_final: 0.8125 (tt) REVERT: A 105 PHE cc_start: 0.8292 (t80) cc_final: 0.7908 (t80) REVERT: A 174 GLU cc_start: 0.8340 (tt0) cc_final: 0.7796 (tp30) REVERT: A 218 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8505 (mt-10) REVERT: A 239 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.7281 (mp10) REVERT: A 301 ASP cc_start: 0.8173 (p0) cc_final: 0.7973 (p0) REVERT: A 309 SER cc_start: 0.8303 (t) cc_final: 0.7782 (m) REVERT: A 337 LYS cc_start: 0.7938 (mtpp) cc_final: 0.7561 (mtpp) REVERT: A 373 GLN cc_start: 0.8374 (tp40) cc_final: 0.8135 (tm-30) REVERT: A 407 TRP cc_start: 0.8243 (m100) cc_final: 0.7828 (m100) REVERT: A 421 ASP cc_start: 0.7943 (m-30) cc_final: 0.7667 (m-30) REVERT: A 534 PHE cc_start: 0.7598 (t80) cc_final: 0.6789 (t80) outliers start: 14 outliers final: 4 residues processed: 77 average time/residue: 0.4595 time to fit residues: 36.8083 Evaluate side-chains 69 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.9980 chunk 28 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.134439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.105169 restraints weight = 4790.168| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.76 r_work: 0.2964 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3271 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= 0.130 Angle : 0.617 12.205 5894 Z= 0.294 Chirality : 0.041 0.135 668 Planarity : 0.004 0.046 721 Dihedral : 4.936 28.449 569 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.02 % Allowed : 16.63 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.38), residues: 524 helix: 0.13 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -0.68 (0.52), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 588 TYR 0.014 0.001 TYR A 274 PHE 0.017 0.001 PHE A 155 TRP 0.011 0.001 TRP A 132 HIS 0.002 0.000 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 4317) covalent geometry : angle 0.61629 ( 5892) SS BOND : bond 0.00131 ( 1) SS BOND : angle 1.90211 ( 2) hydrogen bonds : bond 0.03282 ( 212) hydrogen bonds : angle 4.61971 ( 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 76 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.165 Fit side-chains REVERT: A 103 LEU cc_start: 0.8444 (tm) cc_final: 0.8192 (tt) REVERT: A 105 PHE cc_start: 0.8345 (t80) cc_final: 0.7938 (t80) REVERT: A 117 GLU cc_start: 0.8989 (pt0) cc_final: 0.8764 (pt0) REVERT: A 174 GLU cc_start: 0.8333 (tt0) cc_final: 0.7812 (tp30) REVERT: A 301 ASP cc_start: 0.8206 (p0) cc_final: 0.7988 (p0) REVERT: A 309 SER cc_start: 0.8330 (t) cc_final: 0.7828 (m) REVERT: A 337 LYS cc_start: 0.7900 (mtpp) cc_final: 0.7563 (mtpp) REVERT: A 373 GLN cc_start: 0.8436 (tp40) cc_final: 0.8199 (tm-30) REVERT: A 407 TRP cc_start: 0.8279 (m100) cc_final: 0.7921 (m100) REVERT: A 421 ASP cc_start: 0.8044 (m-30) cc_final: 0.7766 (m-30) REVERT: A 534 PHE cc_start: 0.7637 (t80) cc_final: 0.6832 (t80) outliers start: 9 outliers final: 5 residues processed: 74 average time/residue: 0.5048 time to fit residues: 38.8203 Evaluate side-chains 70 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 569 MET 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: 9.9990 chunk 50 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.132366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.103503 restraints weight = 4742.505| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.71 r_work: 0.2943 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4318 Z= 0.149 Angle : 0.636 12.856 5894 Z= 0.301 Chirality : 0.041 0.131 668 Planarity : 0.004 0.037 721 Dihedral : 4.987 29.109 569 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.25 % Allowed : 17.08 % 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: -0.33 (0.38), residues: 524 helix: 0.07 (0.28), residues: 366 sheet: None (None), residues: 0 loop : -0.58 (0.53), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 237 TYR 0.013 0.001 TYR A 274 PHE 0.019 0.001 PHE A 155 TRP 0.013 0.001 TRP A 132 HIS 0.002 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 4317) covalent geometry : angle 0.63506 ( 5892) SS BOND : bond 0.00131 ( 1) SS BOND : angle 2.06478 ( 2) hydrogen bonds : bond 0.03484 ( 212) hydrogen bonds : angle 4.60599 ( 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 69 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.151 Fit side-chains REVERT: A 103 LEU cc_start: 0.8448 (tm) cc_final: 0.8203 (tt) REVERT: A 105 PHE cc_start: 0.8371 (t80) cc_final: 0.7945 (t80) REVERT: A 174 GLU cc_start: 0.8392 (tt0) cc_final: 0.7848 (tp30) REVERT: A 301 ASP cc_start: 0.8202 (p0) cc_final: 0.7987 (p0) REVERT: A 309 SER cc_start: 0.8333 (t) cc_final: 0.7853 (m) REVERT: A 373 GLN cc_start: 0.8403 (tp40) cc_final: 0.8173 (tm-30) REVERT: A 407 TRP cc_start: 0.8298 (m100) cc_final: 0.7944 (m100) REVERT: A 421 ASP cc_start: 0.8003 (m-30) cc_final: 0.7696 (m-30) REVERT: A 534 PHE cc_start: 0.7669 (t80) cc_final: 0.6866 (t80) REVERT: A 601 ARG cc_start: 0.7288 (tpp80) cc_final: 0.7037 (tpp80) outliers start: 10 outliers final: 6 residues processed: 65 average time/residue: 0.4472 time to fit residues: 30.3444 Evaluate side-chains 64 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 569 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 46 optimal weight: 0.0030 chunk 10 optimal weight: 0.2980 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 36 optimal weight: 0.4980 chunk 23 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN 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 = 0.135642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.106473 restraints weight = 4759.570| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.74 r_work: 0.2983 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3481 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= 0.109 Angle : 0.591 12.133 5894 Z= 0.280 Chirality : 0.040 0.128 668 Planarity : 0.004 0.036 721 Dihedral : 4.823 29.345 569 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.57 % Allowed : 18.20 % 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: -0.03 (0.39), residues: 524 helix: 0.30 (0.29), residues: 366 sheet: None (None), residues: 0 loop : -0.51 (0.54), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 237 TYR 0.011 0.001 TYR A 274 PHE 0.014 0.001 PHE A 155 TRP 0.010 0.001 TRP A 132 HIS 0.001 0.000 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 4317) covalent geometry : angle 0.59065 ( 5892) SS BOND : bond 0.00160 ( 1) SS BOND : angle 1.61607 ( 2) hydrogen bonds : bond 0.03075 ( 212) hydrogen bonds : angle 4.55325 ( 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 70 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.109 Fit side-chains REVERT: A 103 LEU cc_start: 0.8424 (tm) cc_final: 0.8205 (tt) REVERT: A 105 PHE cc_start: 0.8360 (t80) cc_final: 0.7908 (t80) REVERT: A 174 GLU cc_start: 0.8354 (tt0) cc_final: 0.7827 (tp30) REVERT: A 309 SER cc_start: 0.8331 (t) cc_final: 0.7819 (m) REVERT: A 373 GLN cc_start: 0.8463 (tp40) cc_final: 0.8237 (tm-30) REVERT: A 407 TRP cc_start: 0.8268 (m100) cc_final: 0.7915 (m100) REVERT: A 421 ASP cc_start: 0.7976 (m-30) cc_final: 0.7698 (m-30) REVERT: A 534 PHE cc_start: 0.7645 (t80) cc_final: 0.6800 (t80) REVERT: A 601 ARG cc_start: 0.7319 (tpp80) cc_final: 0.7005 (tpp80) outliers start: 7 outliers final: 4 residues processed: 68 average time/residue: 0.4218 time to fit residues: 30.0003 Evaluate side-chains 62 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 569 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 17 optimal weight: 0.4980 chunk 11 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.134170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.104995 restraints weight = 4691.199| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.73 r_work: 0.2959 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4318 Z= 0.137 Angle : 0.625 12.584 5894 Z= 0.298 Chirality : 0.041 0.128 668 Planarity : 0.004 0.036 721 Dihedral : 4.857 28.742 569 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.12 % Allowed : 18.65 % 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: -0.04 (0.39), residues: 524 helix: 0.27 (0.28), residues: 367 sheet: None (None), residues: 0 loop : -0.45 (0.54), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 237 TYR 0.012 0.001 TYR A 274 PHE 0.017 0.001 PHE A 155 TRP 0.013 0.001 TRP A 132 HIS 0.002 0.000 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 4317) covalent geometry : angle 0.62470 ( 5892) SS BOND : bond 0.00120 ( 1) SS BOND : angle 1.78623 ( 2) hydrogen bonds : bond 0.03293 ( 212) hydrogen bonds : angle 4.56654 ( 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 63 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.159 Fit side-chains REVERT: A 103 LEU cc_start: 0.8432 (tm) cc_final: 0.8191 (tt) REVERT: A 105 PHE cc_start: 0.8374 (t80) cc_final: 0.7927 (t80) REVERT: A 117 GLU cc_start: 0.8968 (pt0) cc_final: 0.8658 (pt0) REVERT: A 174 GLU cc_start: 0.8375 (tt0) cc_final: 0.7849 (tp30) REVERT: A 309 SER cc_start: 0.8350 (t) cc_final: 0.7852 (m) REVERT: A 373 GLN cc_start: 0.8401 (tp40) cc_final: 0.8176 (tm-30) REVERT: A 407 TRP cc_start: 0.8289 (m100) cc_final: 0.7944 (m100) REVERT: A 421 ASP cc_start: 0.7977 (m-30) cc_final: 0.7686 (m-30) REVERT: A 534 PHE cc_start: 0.7666 (t80) cc_final: 0.6823 (t80) REVERT: A 601 ARG cc_start: 0.7312 (tpp80) cc_final: 0.6963 (tpp80) outliers start: 5 outliers final: 4 residues processed: 61 average time/residue: 0.4198 time to fit residues: 26.7564 Evaluate side-chains 60 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 569 MET 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: 0.5980 chunk 49 optimal weight: 0.4980 chunk 7 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 28 optimal weight: 0.3980 chunk 31 optimal weight: 0.2980 chunk 22 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.135294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.106532 restraints weight = 4715.787| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.71 r_work: 0.2986 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3542 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= 0.112 Angle : 0.601 12.273 5894 Z= 0.286 Chirality : 0.040 0.127 668 Planarity : 0.004 0.036 721 Dihedral : 4.767 29.091 569 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.57 % Allowed : 18.20 % 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: 0.43 (0.29), residues: 366 sheet: None (None), residues: 0 loop : -0.43 (0.54), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 237 TYR 0.011 0.001 TYR A 274 PHE 0.015 0.001 PHE A 155 TRP 0.010 0.001 TRP A 132 HIS 0.001 0.000 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 4317) covalent geometry : angle 0.60031 ( 5892) SS BOND : bond 0.00070 ( 1) SS BOND : angle 1.55114 ( 2) hydrogen bonds : bond 0.03067 ( 212) hydrogen bonds : angle 4.52376 ( 609) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1523.39 seconds wall clock time: 26 minutes 42.03 seconds (1602.03 seconds total)