Starting phenix.real_space_refine on Wed Aug 5 05:45:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lno_63238/08_2026/9lno_63238_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lno_63238/08_2026/9lno_63238.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lno_63238/08_2026/9lno_63238_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lno_63238/08_2026/9lno_63238_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lno_63238/08_2026/9lno_63238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lno_63238/08_2026/9lno_63238.map" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.104 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 S 33 5.16 5 Cl 1 4.86 5 C 2873 2.51 5 N 637 2.21 5 O 704 1.98 5 H 4157 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8405 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 8341 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 26, 'TRANS': 493} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {' CL': 1, 'CLR': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.25, per 1000 atoms: 0.15 Number of scatterers: 8405 At special positions: 0 Unit cell: (77.35, 67.15, 92.65, 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) Cl 1 17.00 S 33 16.00 O 704 8.00 N 637 7.00 C 2873 6.00 H 4157 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 112 " - pdb=" SG CYS A 471 " distance=2.03 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 166 " 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: 0.61 Conformation dependent library (CDL) restraints added in 283.6 milliseconds 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 964 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 0 sheets defined 76.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 45 through 49 removed outlier: 3.597A pdb=" N SER A 48 " --> pdb=" O PHE A 45 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL A 49 " --> pdb=" O VAL A 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 45 through 49' Processing helix chain 'A' and resid 55 through 69 removed outlier: 3.897A pdb=" N VAL A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE A 62 " --> pdb=" O ASN A 58 " (cutoff:3.500A) Proline residue: A 63 - end of helix Processing helix chain 'A' and resid 74 through 85 removed outlier: 3.503A pdb=" N TYR A 78 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE A 83 " --> pdb=" O PHE A 79 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 84 " --> pdb=" O ILE A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 101 Processing helix chain 'A' and resid 107 through 112 Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 116 through 132 removed outlier: 3.526A pdb=" N LEU A 120 " --> pdb=" O GLN A 116 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER A 122 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL A 123 " --> pdb=" O GLY A 119 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 131 " --> pdb=" O SER A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 147 Processing helix chain 'A' and resid 186 through 195 Processing helix chain 'A' and resid 210 through 231 removed outlier: 3.652A pdb=" N LEU A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N CYS A 216 " --> pdb=" O GLU A 212 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 259 removed outlier: 4.024A pdb=" N THR A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 removed outlier: 3.815A pdb=" N TYR A 269 " --> pdb=" O GLN A 265 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N TYR A 270 " --> pdb=" O GLY A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 280 removed outlier: 3.553A pdb=" N LYS A 279 " --> pdb=" O PHE A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 295 removed outlier: 3.723A pdb=" N MET A 285 " --> pdb=" O PRO A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 309 removed outlier: 3.512A pdb=" N ALA A 304 " --> pdb=" O GLY A 300 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 349 removed outlier: 3.707A pdb=" N ASP A 318 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE A 320 " --> pdb=" O TYR A 316 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA A 321 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU A 322 " --> pdb=" O ASP A 318 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N CYS A 323 " --> pdb=" O CYS A 319 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE A 340 " --> pdb=" O VAL A 336 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 355 removed outlier: 3.957A pdb=" N VAL A 355 " --> pdb=" O ILE A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 372 removed outlier: 3.931A pdb=" N THR A 372 " --> pdb=" O PRO A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 411 removed outlier: 4.126A pdb=" N CYS A 382 " --> pdb=" O GLN A 378 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 383 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE A 384 " --> pdb=" O TRP A 380 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE A 389 " --> pdb=" O PHE A 385 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP A 394 " --> pdb=" O PHE A 390 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 437 removed outlier: 4.251A pdb=" N LEU A 423 " --> pdb=" O GLY A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 441 Processing helix chain 'A' and resid 443 through 455 removed outlier: 4.284A pdb=" N ILE A 447 " --> pdb=" O GLY A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 474 removed outlier: 3.650A pdb=" N LEU A 464 " --> pdb=" O CYS A 460 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 490 removed outlier: 3.800A pdb=" N ASN A 484 " --> pdb=" O ARG A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 503 Processing helix chain 'A' and resid 503 through 519 removed outlier: 3.589A pdb=" N LYS A 519 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 528 Processing helix chain 'A' and resid 532 through 548 removed outlier: 3.617A pdb=" N TYR A 536 " --> pdb=" O PRO A 532 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER A 537 " --> pdb=" O PRO A 533 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE A 538 " --> pdb=" O TRP A 534 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N SER A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET A 547 " --> pdb=" O ALA A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 561 removed outlier: 3.507A pdb=" N LEU A 552 " --> pdb=" O VAL A 548 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE A 553 " --> pdb=" O CYS A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 572 229 hydrogen bonds defined for protein. 666 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.92 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4141 1.03 - 1.23: 49 1.23 - 1.43: 1866 1.43 - 1.62: 2443 1.62 - 1.82: 46 Bond restraints: 8545 Sorted by residual: bond pdb=" N GLU A 52 " pdb=" H GLU A 52 " ideal model delta sigma weight residual 0.860 0.950 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" N VAL A 528 " pdb=" CA VAL A 528 " ideal model delta sigma weight residual 1.459 1.494 -0.035 9.10e-03 1.21e+04 1.48e+01 bond pdb=" N ILE A 365 " pdb=" CA ILE A 365 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.71e+00 bond pdb=" N ASN A 69 " pdb=" CA ASN A 69 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.17e-02 7.31e+03 8.88e+00 bond pdb=" N PHE A 364 " pdb=" CA PHE A 364 " ideal model delta sigma weight residual 1.456 1.492 -0.037 1.26e-02 6.30e+03 8.54e+00 ... (remaining 8540 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 15057 1.58 - 3.15: 292 3.15 - 4.73: 31 4.73 - 6.30: 3 6.30 - 7.88: 3 Bond angle restraints: 15386 Sorted by residual: angle pdb=" N ALA A 366 " pdb=" CA ALA A 366 " pdb=" C ALA A 366 " ideal model delta sigma weight residual 112.93 107.73 5.20 1.33e+00 5.65e-01 1.53e+01 angle pdb=" N VAL A 49 " pdb=" CA VAL A 49 " pdb=" C VAL A 49 " ideal model delta sigma weight residual 113.47 109.56 3.91 1.01e+00 9.80e-01 1.50e+01 angle pdb=" N VAL A 528 " pdb=" CA VAL A 528 " pdb=" CB VAL A 528 " ideal model delta sigma weight residual 112.33 108.05 4.28 1.19e+00 7.06e-01 1.30e+01 angle pdb=" N LYS A 68 " pdb=" CA LYS A 68 " pdb=" C LYS A 68 " ideal model delta sigma weight residual 111.33 107.31 4.02 1.21e+00 6.83e-01 1.10e+01 angle pdb=" N VAL A 528 " pdb=" CA VAL A 528 " pdb=" C VAL A 528 " ideal model delta sigma weight residual 113.47 110.29 3.18 1.01e+00 9.80e-01 9.93e+00 ... (remaining 15381 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 3667 17.94 - 35.88: 348 35.88 - 53.82: 125 53.82 - 71.76: 27 71.76 - 89.70: 12 Dihedral angle restraints: 4179 sinusoidal: 2208 harmonic: 1971 Sorted by residual: dihedral pdb=" CB CYS A 112 " pdb=" SG CYS A 112 " pdb=" SG CYS A 471 " pdb=" CB CYS A 471 " ideal model delta sinusoidal sigma weight residual -86.00 -139.91 53.91 1 1.00e+01 1.00e-02 3.95e+01 dihedral pdb=" CB CYS A 157 " pdb=" SG CYS A 157 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual -86.00 -119.75 33.75 1 1.00e+01 1.00e-02 1.62e+01 dihedral pdb=" CA PHE A 385 " pdb=" C PHE A 385 " pdb=" N ILE A 386 " pdb=" CA ILE A 386 " ideal model delta harmonic sigma weight residual 180.00 163.67 16.33 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 4176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 575 0.059 - 0.117: 89 0.117 - 0.176: 2 0.176 - 0.234: 1 0.234 - 0.293: 2 Chirality restraints: 669 Sorted by residual: chirality pdb=" CA ASN A 527 " pdb=" N ASN A 527 " pdb=" C ASN A 527 " pdb=" CB ASN A 527 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CA ILE A 365 " pdb=" N ILE A 365 " pdb=" C ILE A 365 " pdb=" CB ILE A 365 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA VAL A 528 " pdb=" N VAL A 528 " pdb=" C VAL A 528 " pdb=" CB VAL A 528 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 666 not shown) Planarity restraints: 1205 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 51 " -0.044 2.00e-02 2.50e+03 8.04e-02 6.46e+01 pdb=" N GLU A 52 " 0.139 2.00e-02 2.50e+03 pdb=" CA GLU A 52 " -0.037 2.00e-02 2.50e+03 pdb=" H GLU A 52 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 365 " -0.024 2.00e-02 2.50e+03 4.42e-02 1.96e+01 pdb=" N ALA A 366 " 0.076 2.00e-02 2.50e+03 pdb=" CA ALA A 366 " -0.020 2.00e-02 2.50e+03 pdb=" H ALA A 366 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 70 " 0.019 2.00e-02 2.50e+03 3.64e-02 1.32e+01 pdb=" N GLY A 71 " -0.063 2.00e-02 2.50e+03 pdb=" CA GLY A 71 " 0.017 2.00e-02 2.50e+03 pdb=" H GLY A 71 " 0.026 2.00e-02 2.50e+03 ... (remaining 1202 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 756 2.23 - 2.82: 17350 2.82 - 3.41: 21246 3.41 - 4.01: 27965 4.01 - 4.60: 44444 Nonbonded interactions: 111761 Sorted by model distance: nonbonded pdb=" O PHE A 553 " pdb=" HG1 THR A 557 " model vdw 1.635 2.450 nonbonded pdb=" O GLU A 193 " pdb=" H GLY A 198 " model vdw 1.671 2.450 nonbonded pdb="HH12 ARG A 195 " pdb=" OE2 GLU A 212 " model vdw 1.714 2.450 nonbonded pdb=" O THR A 561 " pdb=" HE ARG A 568 " model vdw 1.740 2.450 nonbonded pdb=" HH TYR A 67 " pdb=" O ILE A 352 " model vdw 1.741 2.450 ... (remaining 111756 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: 1.440 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: 0.050 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.060 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4390 Z= 0.191 Angle : 0.604 7.266 5992 Z= 0.357 Chirality : 0.041 0.293 669 Planarity : 0.004 0.051 718 Dihedral : 16.492 89.703 1624 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.66 % Allowed : 19.82 % Favored : 79.52 % 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: 0.19 (0.39), residues: 514 helix: 0.96 (0.31), residues: 339 sheet: None (None), residues: 0 loop : -1.51 (0.45), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 210 TYR 0.013 0.001 TYR A 64 PHE 0.018 0.001 PHE A 463 TRP 0.008 0.001 TRP A 494 HIS 0.001 0.000 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.19 ( 4388) covalent geometry : angle 0.60076 / 0.36 ( 5988) SS BOND : bond 0.00527 / 0.26 ( 2) SS BOND : angle 2.41707 / 1.22 ( 4) hydrogen bonds : bond 0.18493 / 11.66 ( 229) hydrogen bonds : angle 6.50796 / 4.43 ( 666) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 95 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7629 (mm-30) cc_final: 0.6943 (pt0) REVERT: A 226 PHE cc_start: 0.7464 (m-80) cc_final: 0.7246 (m-10) REVERT: A 401 GLU cc_start: 0.7442 (mm-30) cc_final: 0.6424 (tt0) REVERT: A 409 ASP cc_start: 0.7364 (t0) cc_final: 0.7070 (m-30) REVERT: A 414 GLN cc_start: 0.6660 (mp10) cc_final: 0.6183 (mp10) REVERT: A 431 MET cc_start: 0.6863 (mtm) cc_final: 0.6444 (mmp) REVERT: A 560 LYS cc_start: 0.7011 (ttmm) cc_final: 0.6756 (mtpt) REVERT: A 566 ARG cc_start: 0.5833 (mmt180) cc_final: 0.5163 (ttp-110) REVERT: A 583 LYS cc_start: 0.5558 (pttm) cc_final: 0.4837 (mttp) outliers start: 3 outliers final: 1 residues processed: 96 average time/residue: 0.1812 time to fit residues: 21.4861 Evaluate side-chains 65 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.120344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.102841 restraints weight = 15945.486| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.61 r_work: 0.3024 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4390 Z= 0.171 Angle : 0.596 5.157 5992 Z= 0.315 Chirality : 0.040 0.147 669 Planarity : 0.005 0.044 718 Dihedral : 6.328 55.964 700 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.89 % Favored : 95.91 % Rotamer: Outliers : 1.54 % Allowed : 19.82 % Favored : 78.63 % 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 (0.38), residues: 514 helix: 0.64 (0.30), residues: 349 sheet: None (None), residues: 0 loop : -1.64 (0.46), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 194 TYR 0.016 0.002 TYR A 64 PHE 0.016 0.002 PHE A 463 TRP 0.015 0.001 TRP A 380 HIS 0.003 0.001 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 ( 4388) covalent geometry : angle 0.59252 / 0.31 ( 5988) SS BOND : bond 0.01134 / 0.55 ( 2) SS BOND : angle 2.45845 / 1.33 ( 4) hydrogen bonds : bond 0.05014 / 2.98 ( 229) hydrogen bonds : angle 4.40398 / 3.06 ( 666) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: A 64 TYR cc_start: 0.9142 (OUTLIER) cc_final: 0.7660 (p90) REVERT: A 164 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7424 (pt0) REVERT: A 268 ILE cc_start: 0.7997 (tt) cc_final: 0.7752 (tt) REVERT: A 409 ASP cc_start: 0.7790 (t0) cc_final: 0.7440 (m-30) REVERT: A 414 GLN cc_start: 0.7169 (mp10) cc_final: 0.6862 (mp10) REVERT: A 431 MET cc_start: 0.8000 (mtm) cc_final: 0.7623 (mmp) REVERT: A 496 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8221 (mt) REVERT: A 562 ARG cc_start: 0.6680 (mmt180) cc_final: 0.6414 (mmt180) REVERT: A 566 ARG cc_start: 0.6004 (mmt180) cc_final: 0.5769 (ttp-110) outliers start: 7 outliers final: 3 residues processed: 64 average time/residue: 0.1676 time to fit residues: 13.5731 Evaluate side-chains 59 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 496 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 7 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 571 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.137257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.118897 restraints weight = 15495.836| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.78 r_work: 0.3038 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4390 Z= 0.114 Angle : 0.483 4.357 5992 Z= 0.251 Chirality : 0.036 0.116 669 Planarity : 0.004 0.043 718 Dihedral : 5.448 52.521 700 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.11 % Favored : 96.69 % Rotamer: Outliers : 0.66 % Allowed : 19.82 % Favored : 79.52 % 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: 0.31 (0.40), residues: 514 helix: 1.00 (0.30), residues: 355 sheet: None (None), residues: 0 loop : -1.58 (0.47), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 568 TYR 0.013 0.001 TYR A 64 PHE 0.013 0.001 PHE A 463 TRP 0.006 0.001 TRP A 380 HIS 0.001 0.000 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 ( 4388) covalent geometry : angle 0.48121 / 0.25 ( 5988) SS BOND : bond 0.00350 / 0.18 ( 2) SS BOND : angle 1.74123 / 0.95 ( 4) hydrogen bonds : bond 0.04354 / 2.59 ( 229) hydrogen bonds : angle 4.16089 / 2.89 ( 666) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 409 ASP cc_start: 0.7739 (t0) cc_final: 0.7373 (m-30) REVERT: A 414 GLN cc_start: 0.6974 (mp10) cc_final: 0.6723 (mp10) REVERT: A 431 MET cc_start: 0.8019 (mtm) cc_final: 0.7587 (mmp) REVERT: A 496 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8254 (mt) REVERT: A 566 ARG cc_start: 0.6033 (mmt180) cc_final: 0.5670 (ttp-110) outliers start: 3 outliers final: 2 residues processed: 56 average time/residue: 0.1755 time to fit residues: 12.4056 Evaluate side-chains 54 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 496 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 35 optimal weight: 0.1980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 526 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.136615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.118314 restraints weight = 15801.792| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.80 r_work: 0.2947 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4390 Z= 0.106 Angle : 0.477 4.186 5992 Z= 0.246 Chirality : 0.036 0.120 669 Planarity : 0.004 0.043 718 Dihedral : 4.899 53.092 700 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.11 % Favored : 96.69 % Rotamer: Outliers : 0.88 % Allowed : 19.38 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.40), residues: 514 helix: 1.07 (0.30), residues: 356 sheet: None (None), residues: 0 loop : -1.56 (0.49), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 61 TYR 0.013 0.001 TYR A 64 PHE 0.014 0.001 PHE A 463 TRP 0.005 0.001 TRP A 192 HIS 0.001 0.000 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 4388) covalent geometry : angle 0.47537 / 0.24 ( 5988) SS BOND : bond 0.00344 / 0.18 ( 2) SS BOND : angle 1.78266 / 0.97 ( 4) hydrogen bonds : bond 0.03847 / 2.24 ( 229) hydrogen bonds : angle 3.98997 / 2.78 ( 666) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8152 (tt0) cc_final: 0.7899 (tt0) REVERT: A 229 TRP cc_start: 0.7326 (t60) cc_final: 0.6928 (t60) REVERT: A 409 ASP cc_start: 0.7698 (t0) cc_final: 0.7362 (m-30) REVERT: A 414 GLN cc_start: 0.6852 (mp10) cc_final: 0.6628 (mp10) REVERT: A 431 MET cc_start: 0.8104 (mtm) cc_final: 0.7665 (mmt) REVERT: A 445 MET cc_start: 0.8549 (tpp) cc_final: 0.7891 (tpt) REVERT: A 496 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8306 (mt) REVERT: A 566 ARG cc_start: 0.6048 (mmt180) cc_final: 0.5642 (ttp-110) outliers start: 4 outliers final: 3 residues processed: 56 average time/residue: 0.1663 time to fit residues: 11.7224 Evaluate side-chains 56 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 526 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3433 r_free = 0.3433 target = 0.126944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.107297 restraints weight = 16077.358| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.89 r_work: 0.2878 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 4390 Z= 0.185 Angle : 0.546 5.087 5992 Z= 0.286 Chirality : 0.039 0.137 669 Planarity : 0.004 0.044 718 Dihedral : 5.257 54.220 700 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.50 % Favored : 96.30 % Rotamer: Outliers : 1.76 % Allowed : 18.50 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.39), residues: 514 helix: 0.96 (0.30), residues: 357 sheet: None (None), residues: 0 loop : -1.66 (0.50), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 421 TYR 0.017 0.001 TYR A 64 PHE 0.016 0.001 PHE A 553 TRP 0.006 0.001 TRP A 192 HIS 0.003 0.001 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.18 ( 4388) covalent geometry : angle 0.54263 / 0.29 ( 5988) SS BOND : bond 0.00309 / 0.16 ( 2) SS BOND : angle 2.23508 / 1.21 ( 4) hydrogen bonds : bond 0.04958 / 2.93 ( 229) hydrogen bonds : angle 4.15562 / 2.90 ( 666) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8173 (tt0) cc_final: 0.7888 (tt0) REVERT: A 229 TRP cc_start: 0.7417 (t60) cc_final: 0.7005 (t60) REVERT: A 376 LEU cc_start: 0.7242 (tp) cc_final: 0.6919 (mp) REVERT: A 409 ASP cc_start: 0.7751 (OUTLIER) cc_final: 0.7440 (m-30) REVERT: A 414 GLN cc_start: 0.6889 (mp10) cc_final: 0.6651 (mp10) REVERT: A 431 MET cc_start: 0.8067 (mtm) cc_final: 0.7588 (mmt) REVERT: A 566 ARG cc_start: 0.5991 (mmt180) cc_final: 0.5548 (ttp-110) REVERT: A 576 ASP cc_start: 0.8427 (t0) cc_final: 0.8168 (t0) outliers start: 8 outliers final: 4 residues processed: 59 average time/residue: 0.1445 time to fit residues: 11.1807 Evaluate side-chains 58 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 521 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 7 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3509 r_free = 0.3509 target = 0.132261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.114402 restraints weight = 15675.058| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.69 r_work: 0.3061 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4390 Z= 0.108 Angle : 0.484 4.284 5992 Z= 0.252 Chirality : 0.036 0.119 669 Planarity : 0.004 0.044 718 Dihedral : 4.947 53.685 700 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.31 % Favored : 96.50 % Rotamer: Outliers : 0.88 % Allowed : 18.50 % Favored : 80.62 % 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: 0.49 (0.40), residues: 514 helix: 1.16 (0.30), residues: 357 sheet: None (None), residues: 0 loop : -1.62 (0.50), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 568 TYR 0.013 0.001 TYR A 64 PHE 0.015 0.001 PHE A 463 TRP 0.004 0.001 TRP A 192 HIS 0.001 0.000 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 ( 4388) covalent geometry : angle 0.47925 / 0.25 ( 5988) SS BOND : bond 0.00369 / 0.19 ( 2) SS BOND : angle 2.54201 / 1.27 ( 4) hydrogen bonds : bond 0.03977 / 2.33 ( 229) hydrogen bonds : angle 3.99472 / 2.79 ( 666) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8103 (tt0) cc_final: 0.7821 (tt0) REVERT: A 229 TRP cc_start: 0.7395 (t60) cc_final: 0.7035 (t60) REVERT: A 376 LEU cc_start: 0.7220 (tp) cc_final: 0.6955 (mp) REVERT: A 409 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7423 (m-30) REVERT: A 414 GLN cc_start: 0.6918 (mp10) cc_final: 0.6715 (mp10) REVERT: A 431 MET cc_start: 0.7979 (mtm) cc_final: 0.7520 (mmt) REVERT: A 566 ARG cc_start: 0.5837 (mmt180) cc_final: 0.5488 (ttp-110) outliers start: 4 outliers final: 3 residues processed: 52 average time/residue: 0.1559 time to fit residues: 10.4941 Evaluate side-chains 53 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 409 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 46 optimal weight: 0.1980 chunk 17 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3563 r_free = 0.3563 target = 0.135876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.118032 restraints weight = 15644.399| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.70 r_work: 0.2924 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4390 Z= 0.109 Angle : 0.478 4.256 5992 Z= 0.248 Chirality : 0.036 0.120 669 Planarity : 0.004 0.043 718 Dihedral : 4.892 54.167 700 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.09 % Favored : 95.72 % Rotamer: Outliers : 0.88 % Allowed : 18.72 % Favored : 80.40 % 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: 0.58 (0.40), residues: 514 helix: 1.26 (0.30), residues: 357 sheet: None (None), residues: 0 loop : -1.68 (0.49), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 568 TYR 0.013 0.001 TYR A 64 PHE 0.014 0.001 PHE A 463 TRP 0.005 0.001 TRP A 192 HIS 0.001 0.000 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 ( 4388) covalent geometry : angle 0.47508 / 0.25 ( 5988) SS BOND : bond 0.00465 / 0.23 ( 2) SS BOND : angle 2.07735 / 1.08 ( 4) hydrogen bonds : bond 0.03889 / 2.28 ( 229) hydrogen bonds : angle 3.94901 / 2.75 ( 666) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8105 (tt0) cc_final: 0.7811 (tt0) REVERT: A 229 TRP cc_start: 0.7384 (t60) cc_final: 0.7046 (t60) REVERT: A 376 LEU cc_start: 0.7285 (tp) cc_final: 0.6997 (mp) REVERT: A 409 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7402 (m-30) REVERT: A 414 GLN cc_start: 0.6892 (mp10) cc_final: 0.6678 (mp10) REVERT: A 431 MET cc_start: 0.8032 (mtm) cc_final: 0.7589 (mmt) REVERT: A 566 ARG cc_start: 0.5872 (mmt180) cc_final: 0.5503 (ttp-110) REVERT: A 576 ASP cc_start: 0.8360 (t0) cc_final: 0.8096 (t0) outliers start: 4 outliers final: 3 residues processed: 53 average time/residue: 0.1550 time to fit residues: 10.6467 Evaluate side-chains 54 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 409 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3313 r_free = 0.3313 target = 0.120695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.100577 restraints weight = 16066.344| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.99 r_work: 0.2960 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.5224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4390 Z= 0.110 Angle : 0.478 4.454 5992 Z= 0.247 Chirality : 0.036 0.121 669 Planarity : 0.004 0.042 718 Dihedral : 4.883 54.449 700 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.50 % Favored : 96.30 % Rotamer: Outliers : 0.88 % Allowed : 18.72 % Favored : 80.40 % 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: 0.59 (0.40), residues: 514 helix: 1.27 (0.30), residues: 357 sheet: None (None), residues: 0 loop : -1.68 (0.49), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 568 TYR 0.013 0.001 TYR A 64 PHE 0.014 0.001 PHE A 463 TRP 0.005 0.001 TRP A 192 HIS 0.001 0.000 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.11 ( 4388) covalent geometry : angle 0.47524 / 0.25 ( 5988) SS BOND : bond 0.00424 / 0.21 ( 2) SS BOND : angle 1.96392 / 1.05 ( 4) hydrogen bonds : bond 0.03876 / 2.28 ( 229) hydrogen bonds : angle 3.93214 / 2.75 ( 666) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8187 (tt0) cc_final: 0.7891 (tt0) REVERT: A 229 TRP cc_start: 0.7332 (t60) cc_final: 0.6978 (t60) REVERT: A 376 LEU cc_start: 0.7185 (tp) cc_final: 0.6948 (mp) REVERT: A 409 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7417 (m-30) REVERT: A 431 MET cc_start: 0.8026 (mtm) cc_final: 0.7537 (mmt) REVERT: A 566 ARG cc_start: 0.5863 (mmt180) cc_final: 0.5449 (ttp-110) REVERT: A 570 ARG cc_start: 0.6136 (mmp80) cc_final: 0.5796 (mmp-170) REVERT: A 576 ASP cc_start: 0.8400 (t0) cc_final: 0.8091 (t0) outliers start: 4 outliers final: 3 residues processed: 53 average time/residue: 0.1532 time to fit residues: 10.5338 Evaluate side-chains 55 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 409 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 30 optimal weight: 0.0670 chunk 50 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 = 0.3529 r_free = 0.3529 target = 0.133986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.115203 restraints weight = 15448.578| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.85 r_work: 0.2993 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.5274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4390 Z= 0.095 Angle : 0.470 4.859 5992 Z= 0.244 Chirality : 0.036 0.116 669 Planarity : 0.004 0.042 718 Dihedral : 4.761 54.427 700 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.50 % Favored : 96.30 % Rotamer: Outliers : 0.88 % Allowed : 18.94 % Favored : 80.18 % 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: 0.68 (0.40), residues: 514 helix: 1.34 (0.30), residues: 358 sheet: None (None), residues: 0 loop : -1.67 (0.49), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 413 TYR 0.012 0.001 TYR A 64 PHE 0.014 0.001 PHE A 463 TRP 0.004 0.001 TRP A 192 HIS 0.001 0.000 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 ( 4388) covalent geometry : angle 0.46848 / 0.24 ( 5988) SS BOND : bond 0.00353 / 0.18 ( 2) SS BOND : angle 1.70229 / 0.91 ( 4) hydrogen bonds : bond 0.03496 / 2.06 ( 229) hydrogen bonds : angle 3.87004 / 2.70 ( 666) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8112 (tt0) cc_final: 0.7842 (tt0) REVERT: A 164 GLU cc_start: 0.8720 (mm-30) cc_final: 0.7893 (pt0) REVERT: A 229 TRP cc_start: 0.7320 (t60) cc_final: 0.6997 (t60) REVERT: A 376 LEU cc_start: 0.7196 (tp) cc_final: 0.6946 (mp) REVERT: A 409 ASP cc_start: 0.7764 (OUTLIER) cc_final: 0.7404 (m-30) REVERT: A 431 MET cc_start: 0.8005 (mtm) cc_final: 0.7547 (mmt) REVERT: A 566 ARG cc_start: 0.5823 (mmt180) cc_final: 0.5450 (ttp-110) REVERT: A 570 ARG cc_start: 0.6118 (mmp80) cc_final: 0.5782 (mmp-170) REVERT: A 576 ASP cc_start: 0.8366 (t0) cc_final: 0.8085 (t0) outliers start: 4 outliers final: 2 residues processed: 52 average time/residue: 0.1495 time to fit residues: 9.9771 Evaluate side-chains 52 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 409 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 46 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3338 r_free = 0.3338 target = 0.122287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.102292 restraints weight = 16006.596| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.97 r_work: 0.2968 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4390 Z= 0.109 Angle : 0.477 4.223 5992 Z= 0.246 Chirality : 0.036 0.120 669 Planarity : 0.004 0.042 718 Dihedral : 4.801 54.769 700 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.50 % Favored : 96.30 % Rotamer: Outliers : 0.66 % Allowed : 18.72 % Favored : 80.62 % 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: 0.67 (0.40), residues: 514 helix: 1.32 (0.30), residues: 358 sheet: None (None), residues: 0 loop : -1.65 (0.49), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 568 TYR 0.013 0.001 TYR A 64 PHE 0.014 0.001 PHE A 463 TRP 0.005 0.001 TRP A 192 HIS 0.001 0.000 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 ( 4388) covalent geometry : angle 0.47464 / 0.25 ( 5988) SS BOND : bond 0.00352 / 0.18 ( 2) SS BOND : angle 1.87618 / 1.00 ( 4) hydrogen bonds : bond 0.03723 / 2.19 ( 229) hydrogen bonds : angle 3.88720 / 2.71 ( 666) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8134 (tt0) cc_final: 0.7866 (tt0) REVERT: A 164 GLU cc_start: 0.8749 (mm-30) cc_final: 0.7890 (pt0) REVERT: A 229 TRP cc_start: 0.7328 (t60) cc_final: 0.7009 (t60) REVERT: A 376 LEU cc_start: 0.7214 (tp) cc_final: 0.6950 (mp) REVERT: A 409 ASP cc_start: 0.7761 (OUTLIER) cc_final: 0.7403 (m-30) REVERT: A 431 MET cc_start: 0.8034 (mtm) cc_final: 0.7570 (mmt) REVERT: A 566 ARG cc_start: 0.5858 (mmt180) cc_final: 0.5460 (ttp-110) REVERT: A 570 ARG cc_start: 0.6144 (mmp80) cc_final: 0.5808 (mmp-170) REVERT: A 576 ASP cc_start: 0.8374 (t0) cc_final: 0.8095 (t0) outliers start: 3 outliers final: 2 residues processed: 52 average time/residue: 0.1565 time to fit residues: 10.4654 Evaluate side-chains 53 residues out of total 455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 409 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 36 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3349 r_free = 0.3349 target = 0.122244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.102402 restraints weight = 15863.703| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.93 r_work: 0.2950 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.5368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4390 Z= 0.130 Angle : 0.506 5.098 5992 Z= 0.262 Chirality : 0.037 0.125 669 Planarity : 0.004 0.042 718 Dihedral : 4.996 55.465 700 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.09 % Favored : 95.72 % Rotamer: Outliers : 0.88 % Allowed : 18.94 % Favored : 80.18 % 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: 0.61 (0.39), residues: 514 helix: 1.29 (0.30), residues: 356 sheet: None (None), residues: 0 loop : -1.68 (0.49), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 194 TYR 0.015 0.001 TYR A 64 PHE 0.014 0.001 PHE A 463 TRP 0.006 0.001 TRP A 192 HIS 0.001 0.001 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.13 ( 4388) covalent geometry : angle 0.50308 / 0.26 ( 5988) SS BOND : bond 0.00417 / 0.21 ( 2) SS BOND : angle 2.10810 / 1.13 ( 4) hydrogen bonds : bond 0.04159 / 2.45 ( 229) hydrogen bonds : angle 3.96796 / 2.77 ( 666) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2281.63 seconds wall clock time: 39 minutes 26.57 seconds (2366.57 seconds total)