Starting phenix.real_space_refine on Fri Aug 22 15:13:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hin_34823/08_2025/8hin_34823.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hin_34823/08_2025/8hin_34823.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hin_34823/08_2025/8hin_34823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hin_34823/08_2025/8hin_34823.map" model { file = "/net/cci-nas-00/data/ceres_data/8hin_34823/08_2025/8hin_34823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hin_34823/08_2025/8hin_34823.cif" } resolution = 3.3 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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 3155 2.51 5 N 778 2.21 5 O 818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4788 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4512 Classifications: {'peptide': 588} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 560} Chain breaks: 2 Chain: "B" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 231 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'LN9': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.30, per 1000 atoms: 0.27 Number of scatterers: 4788 At special positions: 0 Unit cell: (83.6992, 78.468, 92.8538, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 818 8.00 N 778 7.00 C 3155 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 255 " - pdb=" SG CYS A 511 " distance=2.25 Simple disulfide: pdb=" SG CYS A 345 " - pdb=" SG CYS A 351 " distance=2.31 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 361 " distance=2.31 Simple disulfide: pdb=" SG CYS A 517 " - pdb=" SG CYS A 522 " distance=2.39 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: 0.30 Conformation dependent library (CDL) restraints added in 160.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1124 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 0 sheets defined 79.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 22 through 47 removed outlier: 3.883A pdb=" N ILE A 26 " --> pdb=" O ASN A 22 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE A 37 " --> pdb=" O PHE A 33 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 75 removed outlier: 3.766A pdb=" N LEU A 71 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 92 removed outlier: 3.570A pdb=" N PHE A 81 " --> pdb=" O GLY A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 112 removed outlier: 3.741A pdb=" N GLU A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 103 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE A 104 " --> pdb=" O TRP A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 121 removed outlier: 3.624A pdb=" N VAL A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR A 117 " --> pdb=" O PHE A 113 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY A 121 " --> pdb=" O TYR A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 133 Processing helix chain 'A' and resid 135 through 152 removed outlier: 4.482A pdb=" N ARG A 139 " --> pdb=" O GLY A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 170 Processing helix chain 'A' and resid 173 through 190 Processing helix chain 'A' and resid 197 through 224 Processing helix chain 'A' and resid 224 through 233 removed outlier: 3.632A pdb=" N LEU A 229 " --> pdb=" O GLY A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.823A pdb=" N TYR A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 294 removed outlier: 3.991A pdb=" N ILE A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TRP A 289 " --> pdb=" O ILE A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 306 through 319 removed outlier: 3.593A pdb=" N GLY A 318 " --> pdb=" O CYS A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 328 removed outlier: 3.998A pdb=" N PHE A 326 " --> pdb=" O LEU A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 339 removed outlier: 3.573A pdb=" N GLY A 332 " --> pdb=" O MET A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 347 through 356 removed outlier: 3.630A pdb=" N ARG A 352 " --> pdb=" O PRO A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 363 No H-bonds generated for 'chain 'A' and resid 361 through 363' Processing helix chain 'A' and resid 364 through 374 Processing helix chain 'A' and resid 377 through 414 removed outlier: 3.817A pdb=" N LEU A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR A 410 " --> pdb=" O THR A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 446 removed outlier: 3.970A pdb=" N VAL A 430 " --> pdb=" O GLY A 426 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) Proline residue: A 442 - end of helix removed outlier: 3.609A pdb=" N ALA A 446 " --> pdb=" O PRO A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 464 Processing helix chain 'A' and resid 464 through 475 Processing helix chain 'A' and resid 481 through 507 removed outlier: 3.681A pdb=" N MET A 495 " --> pdb=" O GLY A 491 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG A 499 " --> pdb=" O MET A 495 " (cutoff:3.500A) Proline residue: A 502 - end of helix removed outlier: 3.520A pdb=" N GLY A 507 " --> pdb=" O GLU A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 547 Processing helix chain 'A' and resid 552 through 556 removed outlier: 3.556A pdb=" N HIS A 555 " --> pdb=" O PRO A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 564 removed outlier: 3.579A pdb=" N ARG A 564 " --> pdb=" O PHE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 578 Processing helix chain 'A' and resid 646 through 671 removed outlier: 3.504A pdb=" N TYR A 671 " --> pdb=" O LEU A 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 54 329 hydrogen bonds defined for protein. 975 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: 0.63 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 713 1.28 - 1.43: 1374 1.43 - 1.57: 2769 1.57 - 1.72: 1 1.72 - 1.86: 57 Bond restraints: 4914 Sorted by residual: bond pdb=" C PHE A 72 " pdb=" O PHE A 72 " ideal model delta sigma weight residual 1.236 1.140 0.096 1.15e-02 7.56e+03 6.95e+01 bond pdb=" C THR A 403 " pdb=" O THR A 403 " ideal model delta sigma weight residual 1.236 1.144 0.093 1.15e-02 7.56e+03 6.48e+01 bond pdb=" C TRP A 276 " pdb=" O TRP A 276 " ideal model delta sigma weight residual 1.241 1.171 0.071 9.80e-03 1.04e+04 5.19e+01 bond pdb=" C PRO A 66 " pdb=" O PRO A 66 " ideal model delta sigma weight residual 1.237 1.154 0.083 1.26e-02 6.30e+03 4.39e+01 bond pdb=" C GLY A 68 " pdb=" O GLY A 68 " ideal model delta sigma weight residual 1.234 1.156 0.078 1.19e-02 7.06e+03 4.27e+01 ... (remaining 4909 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.54: 5762 3.54 - 7.08: 883 7.08 - 10.62: 46 10.62 - 14.16: 7 14.16 - 17.69: 3 Bond angle restraints: 6701 Sorted by residual: angle pdb=" C ASN A 101 " pdb=" CA ASN A 101 " pdb=" CB ASN A 101 " ideal model delta sigma weight residual 110.67 92.98 17.69 1.92e+00 2.71e-01 8.49e+01 angle pdb=" N THR A 411 " pdb=" CA THR A 411 " pdb=" C THR A 411 " ideal model delta sigma weight residual 111.07 101.26 9.81 1.07e+00 8.73e-01 8.41e+01 angle pdb=" C PRO A 518 " pdb=" CA PRO A 518 " pdb=" CB PRO A 518 " ideal model delta sigma weight residual 110.20 96.90 13.30 1.46e+00 4.69e-01 8.30e+01 angle pdb=" N GLY A 418 " pdb=" CA GLY A 418 " pdb=" C GLY A 418 " ideal model delta sigma weight residual 111.03 98.32 12.71 1.40e+00 5.10e-01 8.25e+01 angle pdb=" C PHE A 453 " pdb=" CA PHE A 453 " pdb=" CB PHE A 453 " ideal model delta sigma weight residual 110.81 96.80 14.01 1.60e+00 3.91e-01 7.66e+01 ... (remaining 6696 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 2476 17.64 - 35.28: 295 35.28 - 52.92: 75 52.92 - 70.56: 18 70.56 - 88.20: 7 Dihedral angle restraints: 2871 sinusoidal: 1111 harmonic: 1760 Sorted by residual: dihedral pdb=" CB CYS A 345 " pdb=" SG CYS A 345 " pdb=" SG CYS A 351 " pdb=" CB CYS A 351 " ideal model delta sinusoidal sigma weight residual -86.00 -171.52 85.52 1 1.00e+01 1.00e-02 8.85e+01 dihedral pdb=" CB CYS A 517 " pdb=" SG CYS A 517 " pdb=" SG CYS A 522 " pdb=" CB CYS A 522 " ideal model delta sinusoidal sigma weight residual -86.00 -161.56 75.56 1 1.00e+01 1.00e-02 7.21e+01 dihedral pdb=" C ASN A 101 " pdb=" N ASN A 101 " pdb=" CA ASN A 101 " pdb=" CB ASN A 101 " ideal model delta harmonic sigma weight residual -122.60 -105.38 -17.22 0 2.50e+00 1.60e-01 4.74e+01 ... (remaining 2868 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 413 0.068 - 0.137: 253 0.137 - 0.205: 88 0.205 - 0.274: 23 0.274 - 0.342: 4 Chirality restraints: 781 Sorted by residual: chirality pdb=" CA PRO A 367 " pdb=" N PRO A 367 " pdb=" C PRO A 367 " pdb=" CB PRO A 367 " both_signs ideal model delta sigma weight residual False 2.72 2.38 0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CA LEU A 170 " pdb=" N LEU A 170 " pdb=" C LEU A 170 " pdb=" CB LEU A 170 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CA ASN A 75 " pdb=" N ASN A 75 " pdb=" C ASN A 75 " pdb=" CB ASN A 75 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 778 not shown) Planarity restraints: 821 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 445 " 0.024 2.00e-02 2.50e+03 4.81e-02 2.31e+01 pdb=" C GLN A 445 " -0.083 2.00e-02 2.50e+03 pdb=" O GLN A 445 " 0.030 2.00e-02 2.50e+03 pdb=" N ALA A 446 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 504 " -0.017 2.00e-02 2.50e+03 3.57e-02 1.28e+01 pdb=" C PHE A 504 " 0.062 2.00e-02 2.50e+03 pdb=" O PHE A 504 " -0.023 2.00e-02 2.50e+03 pdb=" N SER A 505 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 499 " -0.266 9.50e-02 1.11e+02 1.19e-01 8.72e+00 pdb=" NE ARG A 499 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 499 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 499 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 499 " -0.010 2.00e-02 2.50e+03 ... (remaining 818 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 510 2.76 - 3.30: 5056 3.30 - 3.83: 7660 3.83 - 4.37: 10038 4.37 - 4.90: 16102 Nonbonded interactions: 39366 Sorted by model distance: nonbonded pdb=" O GLY A 77 " pdb=" N GLY A 79 " model vdw 2.228 3.120 nonbonded pdb=" ND2 ASN A 250 " pdb=" C1 NAG A 801 " model vdw 2.236 3.550 nonbonded pdb=" O GLY A 77 " pdb=" N HIS A 80 " model vdw 2.246 3.120 nonbonded pdb=" N MET A 62 " pdb=" O MET A 62 " model vdw 2.298 2.496 nonbonded pdb=" O PRO A 246 " pdb=" CB ALA A 247 " model vdw 2.299 3.460 ... (remaining 39361 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 6.420 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 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 : 0.019 0.355 4918 Z= 1.309 Angle : 2.548 36.756 6709 Z= 1.820 Chirality : 0.096 0.342 781 Planarity : 0.008 0.119 821 Dihedral : 16.877 88.204 1735 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.66 % Allowed : 6.73 % Favored : 92.61 % Rotamer: Outliers : 4.58 % Allowed : 14.74 % Favored : 80.68 % Cbeta Deviations : 1.07 % 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 aren not related in a simple way. whole: -3.91 (0.28), residues: 609 helix: -2.24 (0.20), residues: 444 sheet: None (None), residues: 0 loop : -3.08 (0.42), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 336 TYR 0.040 0.004 TYR A 455 PHE 0.026 0.004 PHE A 476 TRP 0.042 0.004 TRP A 276 HIS 0.005 0.002 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.01695 ( 4914) covalent geometry : angle 2.46251 ( 6701) SS BOND : bond 0.28673 ( 4) SS BOND : angle 19.11744 ( 8) hydrogen bonds : bond 0.18872 ( 329) hydrogen bonds : angle 8.18001 ( 975) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.178 Fit side-chains REVERT: A 101 ASN cc_start: 0.7718 (OUTLIER) cc_final: 0.7366 (t0) REVERT: A 117 TYR cc_start: 0.8260 (m-10) cc_final: 0.8018 (m-80) REVERT: A 125 MET cc_start: 0.6594 (ttp) cc_final: 0.6379 (ttp) REVERT: A 130 ARG cc_start: 0.6746 (ttp80) cc_final: 0.6381 (ttt-90) REVERT: A 330 MET cc_start: 0.8358 (mtt) cc_final: 0.8140 (mtt) REVERT: A 333 MET cc_start: 0.8450 (mtp) cc_final: 0.7664 (mtp) REVERT: A 382 MET cc_start: 0.6783 (tpt) cc_final: 0.6356 (tpp) REVERT: A 422 LEU cc_start: 0.5566 (OUTLIER) cc_final: 0.5354 (mt) REVERT: A 506 PHE cc_start: 0.7147 (OUTLIER) cc_final: 0.6728 (t80) REVERT: A 570 ARG cc_start: 0.5734 (ptt-90) cc_final: 0.5463 (ptt-90) REVERT: B 28 GLN cc_start: 0.5671 (OUTLIER) cc_final: 0.5408 (tp40) REVERT: B 31 MET cc_start: 0.6562 (mmm) cc_final: 0.5633 (ptt) REVERT: B 54 TRP cc_start: 0.5243 (m100) cc_final: 0.4961 (m100) outliers start: 23 outliers final: 6 residues processed: 115 average time/residue: 0.0866 time to fit residues: 12.3188 Evaluate side-chains 88 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain B residue 28 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 4.9990 chunk 24 optimal weight: 0.1980 chunk 48 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 GLN A 268 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.145865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.122294 restraints weight = 5163.718| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.22 r_work: 0.3155 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4918 Z= 0.147 Angle : 0.669 7.529 6709 Z= 0.341 Chirality : 0.044 0.199 781 Planarity : 0.005 0.051 821 Dihedral : 8.043 61.356 736 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.59 % Allowed : 16.53 % Favored : 79.88 % 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 aren not related in a simple way. whole: -0.37 (0.34), residues: 609 helix: 0.29 (0.24), residues: 450 sheet: None (None), residues: 0 loop : -1.60 (0.51), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 379 TYR 0.012 0.002 TYR A 256 PHE 0.019 0.001 PHE A 453 TRP 0.024 0.002 TRP B 30 HIS 0.003 0.001 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 4914) covalent geometry : angle 0.66728 ( 6701) SS BOND : bond 0.00630 ( 4) SS BOND : angle 1.55537 ( 8) hydrogen bonds : bond 0.04280 ( 329) hydrogen bonds : angle 5.23859 ( 975) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.193 Fit side-chains REVERT: A 44 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7703 (mtm) REVERT: A 60 ARG cc_start: 0.7252 (ptm-80) cc_final: 0.6958 (ttt-90) REVERT: A 125 MET cc_start: 0.6502 (ttp) cc_final: 0.6261 (ttp) REVERT: A 325 MET cc_start: 0.8813 (tmm) cc_final: 0.8596 (tpp) REVERT: A 328 MET cc_start: 0.8615 (mtm) cc_final: 0.8095 (mtm) REVERT: A 427 ARG cc_start: 0.7022 (mtt-85) cc_final: 0.6512 (mtp180) REVERT: A 506 PHE cc_start: 0.8617 (OUTLIER) cc_final: 0.7924 (t80) REVERT: A 667 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7709 (mt) REVERT: B 31 MET cc_start: 0.6949 (mmm) cc_final: 0.6136 (ptt) outliers start: 18 outliers final: 10 residues processed: 89 average time/residue: 0.0888 time to fit residues: 9.8110 Evaluate side-chains 85 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 667 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 57 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.145086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.121263 restraints weight = 5237.198| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.23 r_work: 0.3171 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4918 Z= 0.139 Angle : 0.616 7.828 6709 Z= 0.311 Chirality : 0.042 0.192 781 Planarity : 0.005 0.055 821 Dihedral : 6.724 64.213 723 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.18 % Allowed : 16.33 % Favored : 79.48 % 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 aren not related in a simple way. whole: 0.61 (0.35), residues: 609 helix: 1.00 (0.25), residues: 452 sheet: None (None), residues: 0 loop : -1.23 (0.52), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 564 TYR 0.015 0.001 TYR A 256 PHE 0.009 0.001 PHE A 230 TRP 0.018 0.001 TRP B 30 HIS 0.004 0.001 HIS A 555 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 4914) covalent geometry : angle 0.61538 ( 6701) SS BOND : bond 0.00373 ( 4) SS BOND : angle 1.20639 ( 8) hydrogen bonds : bond 0.03972 ( 329) hydrogen bonds : angle 4.88126 ( 975) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.177 Fit side-chains REVERT: A 60 ARG cc_start: 0.7229 (ptm-80) cc_final: 0.6995 (tmt170) REVERT: A 99 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7292 (mm-30) REVERT: A 125 MET cc_start: 0.6457 (ttp) cc_final: 0.6189 (ttp) REVERT: A 300 ARG cc_start: 0.8021 (mmt-90) cc_final: 0.7746 (mmt-90) REVERT: A 325 MET cc_start: 0.8913 (tmm) cc_final: 0.8649 (tpp) REVERT: A 352 ARG cc_start: 0.7633 (ttm-80) cc_final: 0.7424 (ttm-80) REVERT: A 427 ARG cc_start: 0.7125 (mtt-85) cc_final: 0.6538 (mtp180) REVERT: A 552 PRO cc_start: 0.7549 (Cg_exo) cc_final: 0.7329 (Cg_endo) REVERT: A 564 ARG cc_start: 0.7005 (ptt-90) cc_final: 0.6591 (ptt90) REVERT: A 667 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7832 (mt) REVERT: B 31 MET cc_start: 0.6879 (mmm) cc_final: 0.6217 (ptt) outliers start: 21 outliers final: 16 residues processed: 93 average time/residue: 0.0734 time to fit residues: 8.5452 Evaluate side-chains 94 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 667 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 37 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 24 optimal weight: 0.0000 chunk 15 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.7186 ------------------------------------------------------------------------------- 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 = 0.3563 r_free = 0.3563 target = 0.146682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.121790 restraints weight = 5255.293| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.36 r_work: 0.3143 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4918 Z= 0.118 Angle : 0.579 6.885 6709 Z= 0.292 Chirality : 0.041 0.180 781 Planarity : 0.005 0.052 821 Dihedral : 6.463 62.493 723 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.18 % Allowed : 18.53 % Favored : 77.29 % 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 aren not related in a simple way. whole: 1.11 (0.36), residues: 609 helix: 1.30 (0.25), residues: 456 sheet: None (None), residues: 0 loop : -0.84 (0.54), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 564 TYR 0.038 0.001 TYR A 256 PHE 0.007 0.001 PHE A 398 TRP 0.015 0.001 TRP B 30 HIS 0.002 0.001 HIS A 555 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 4914) covalent geometry : angle 0.57718 ( 6701) SS BOND : bond 0.00137 ( 4) SS BOND : angle 1.54201 ( 8) hydrogen bonds : bond 0.03490 ( 329) hydrogen bonds : angle 4.71209 ( 975) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.101 Fit side-chains REVERT: A 44 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.6339 (tmm) REVERT: A 60 ARG cc_start: 0.7401 (ptm-80) cc_final: 0.7038 (ttt-90) REVERT: A 150 TYR cc_start: 0.8270 (m-10) cc_final: 0.7925 (m-10) REVERT: A 300 ARG cc_start: 0.8116 (mmt-90) cc_final: 0.7848 (mmt-90) REVERT: A 325 MET cc_start: 0.8887 (tmm) cc_final: 0.8559 (tpp) REVERT: A 352 ARG cc_start: 0.7681 (ttm-80) cc_final: 0.7470 (ttm-80) REVERT: A 387 LEU cc_start: 0.8010 (mt) cc_final: 0.7697 (mt) REVERT: A 505 SER cc_start: 0.8473 (t) cc_final: 0.8041 (t) REVERT: A 667 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7759 (mt) outliers start: 21 outliers final: 13 residues processed: 97 average time/residue: 0.0802 time to fit residues: 9.6432 Evaluate side-chains 89 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 667 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 8 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 52 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3565 r_free = 0.3565 target = 0.146493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.121224 restraints weight = 5270.844| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.39 r_work: 0.3134 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4918 Z= 0.123 Angle : 0.578 9.158 6709 Z= 0.290 Chirality : 0.041 0.171 781 Planarity : 0.004 0.049 821 Dihedral : 6.018 60.473 721 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.18 % Allowed : 18.33 % Favored : 77.49 % 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 aren not related in a simple way. whole: 1.40 (0.36), residues: 609 helix: 1.45 (0.25), residues: 456 sheet: None (None), residues: 0 loop : -0.55 (0.56), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 564 TYR 0.025 0.001 TYR A 256 PHE 0.009 0.001 PHE A 520 TRP 0.015 0.001 TRP B 30 HIS 0.005 0.001 HIS A 555 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 4914) covalent geometry : angle 0.57584 ( 6701) SS BOND : bond 0.00280 ( 4) SS BOND : angle 1.46196 ( 8) hydrogen bonds : bond 0.03501 ( 329) hydrogen bonds : angle 4.61488 ( 975) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.167 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.6206 (tmm) REVERT: A 60 ARG cc_start: 0.7461 (ptm-80) cc_final: 0.7082 (ttt-90) REVERT: A 150 TYR cc_start: 0.8409 (m-10) cc_final: 0.7986 (m-10) REVERT: A 325 MET cc_start: 0.8938 (tmm) cc_final: 0.8580 (tpp) REVERT: A 387 LEU cc_start: 0.8077 (mt) cc_final: 0.7740 (mt) REVERT: A 505 SER cc_start: 0.8527 (t) cc_final: 0.8047 (t) REVERT: A 667 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7770 (mt) outliers start: 21 outliers final: 18 residues processed: 93 average time/residue: 0.0713 time to fit residues: 8.3254 Evaluate side-chains 97 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 667 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 5 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 26 optimal weight: 0.0870 chunk 25 optimal weight: 0.9990 overall best weight: 0.7564 ------------------------------------------------------------------------------- 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 = 0.3578 r_free = 0.3578 target = 0.147627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.122377 restraints weight = 5324.378| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.38 r_work: 0.3155 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4918 Z= 0.113 Angle : 0.555 8.418 6709 Z= 0.280 Chirality : 0.040 0.172 781 Planarity : 0.004 0.048 821 Dihedral : 5.938 60.860 721 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.78 % Allowed : 19.52 % Favored : 76.69 % 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 aren not related in a simple way. whole: 1.62 (0.36), residues: 609 helix: 1.61 (0.25), residues: 456 sheet: None (None), residues: 0 loop : -0.46 (0.56), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 564 TYR 0.024 0.001 TYR A 256 PHE 0.010 0.001 PHE A 520 TRP 0.016 0.001 TRP B 30 HIS 0.003 0.001 HIS A 555 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 4914) covalent geometry : angle 0.55384 ( 6701) SS BOND : bond 0.00263 ( 4) SS BOND : angle 1.20431 ( 8) hydrogen bonds : bond 0.03336 ( 329) hydrogen bonds : angle 4.53849 ( 975) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.172 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.6409 (tmm) REVERT: A 60 ARG cc_start: 0.7457 (ptm-80) cc_final: 0.7143 (ttt90) REVERT: A 150 TYR cc_start: 0.8414 (m-10) cc_final: 0.8061 (m-10) REVERT: A 325 MET cc_start: 0.8921 (tmm) cc_final: 0.8581 (tpp) REVERT: A 387 LEU cc_start: 0.8019 (mt) cc_final: 0.7510 (mt) REVERT: A 483 GLN cc_start: 0.7854 (mm-40) cc_final: 0.7442 (mm-40) REVERT: A 667 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7783 (mt) outliers start: 19 outliers final: 13 residues processed: 92 average time/residue: 0.0741 time to fit residues: 8.5323 Evaluate side-chains 91 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 667 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 39 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.3532 r_free = 0.3532 target = 0.143796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.118446 restraints weight = 5252.455| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.23 r_work: 0.3148 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 4918 Z= 0.183 Angle : 0.644 7.320 6709 Z= 0.329 Chirality : 0.044 0.180 781 Planarity : 0.005 0.047 821 Dihedral : 6.393 65.035 721 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.18 % Allowed : 18.92 % Favored : 76.89 % 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 aren not related in a simple way. whole: 1.27 (0.35), residues: 609 helix: 1.36 (0.25), residues: 455 sheet: None (None), residues: 0 loop : -0.58 (0.55), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 564 TYR 0.028 0.002 TYR A 256 PHE 0.016 0.001 PHE A 534 TRP 0.014 0.001 TRP B 30 HIS 0.004 0.001 HIS A 555 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 4914) covalent geometry : angle 0.63750 ( 6701) SS BOND : bond 0.00242 ( 4) SS BOND : angle 2.76474 ( 8) hydrogen bonds : bond 0.04013 ( 329) hydrogen bonds : angle 4.72086 ( 975) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.114 Fit side-chains REVERT: A 44 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.6225 (tmm) REVERT: A 60 ARG cc_start: 0.7252 (ptm-80) cc_final: 0.7044 (ttt-90) REVERT: A 325 MET cc_start: 0.9113 (tmm) cc_final: 0.8646 (tpp) REVERT: A 387 LEU cc_start: 0.8078 (mt) cc_final: 0.7707 (mt) REVERT: A 667 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7788 (mt) outliers start: 21 outliers final: 15 residues processed: 94 average time/residue: 0.0745 time to fit residues: 8.6976 Evaluate side-chains 96 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 667 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 42 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 3 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 45 optimal weight: 0.0000 chunk 35 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.6384 ------------------------------------------------------------------------------- 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 = 0.3579 r_free = 0.3579 target = 0.147914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.122725 restraints weight = 5216.803| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.23 r_work: 0.3360 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4918 Z= 0.115 Angle : 0.579 8.339 6709 Z= 0.292 Chirality : 0.040 0.173 781 Planarity : 0.004 0.048 821 Dihedral : 6.433 69.689 721 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.39 % Allowed : 20.12 % Favored : 76.49 % 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 aren not related in a simple way. whole: 1.62 (0.36), residues: 609 helix: 1.64 (0.25), residues: 455 sheet: None (None), residues: 0 loop : -0.53 (0.55), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 564 TYR 0.028 0.001 TYR A 256 PHE 0.008 0.001 PHE A 534 TRP 0.018 0.001 TRP B 30 HIS 0.004 0.001 HIS A 555 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 4914) covalent geometry : angle 0.57522 ( 6701) SS BOND : bond 0.00221 ( 4) SS BOND : angle 1.88270 ( 8) hydrogen bonds : bond 0.03344 ( 329) hydrogen bonds : angle 4.54475 ( 975) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.175 Fit side-chains REVERT: A 44 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.6211 (tmm) REVERT: A 325 MET cc_start: 0.8931 (tmm) cc_final: 0.8613 (tpp) REVERT: A 387 LEU cc_start: 0.8024 (mt) cc_final: 0.7525 (mt) REVERT: A 483 GLN cc_start: 0.7828 (mm-40) cc_final: 0.7482 (mm-40) REVERT: A 667 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7832 (mt) outliers start: 17 outliers final: 13 residues processed: 82 average time/residue: 0.0705 time to fit residues: 7.3597 Evaluate side-chains 87 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 667 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 0.0170 overall best weight: 1.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.146432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.121237 restraints weight = 5142.065| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.24 r_work: 0.3344 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4918 Z= 0.137 Angle : 0.596 7.490 6709 Z= 0.302 Chirality : 0.041 0.176 781 Planarity : 0.005 0.047 821 Dihedral : 6.452 71.730 721 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.99 % Allowed : 20.92 % Favored : 76.10 % 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 aren not related in a simple way. whole: 1.54 (0.36), residues: 609 helix: 1.55 (0.25), residues: 455 sheet: None (None), residues: 0 loop : -0.48 (0.55), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 300 TYR 0.027 0.001 TYR A 256 PHE 0.012 0.001 PHE A 534 TRP 0.017 0.001 TRP B 30 HIS 0.003 0.001 HIS A 555 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 4914) covalent geometry : angle 0.59314 ( 6701) SS BOND : bond 0.00354 ( 4) SS BOND : angle 1.85166 ( 8) hydrogen bonds : bond 0.03602 ( 329) hydrogen bonds : angle 4.60689 ( 975) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.122 Fit side-chains REVERT: A 44 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.6209 (tmm) REVERT: A 60 ARG cc_start: 0.7234 (ttt-90) cc_final: 0.6957 (tmt170) REVERT: A 67 VAL cc_start: 0.7789 (OUTLIER) cc_final: 0.7411 (p) REVERT: A 325 MET cc_start: 0.9015 (tmm) cc_final: 0.8640 (tpp) REVERT: A 387 LEU cc_start: 0.8117 (mt) cc_final: 0.7836 (mt) REVERT: A 667 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7802 (mt) outliers start: 15 outliers final: 12 residues processed: 79 average time/residue: 0.0759 time to fit residues: 7.3976 Evaluate side-chains 85 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 667 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 0.0770 chunk 58 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 3 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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 = 0.3596 r_free = 0.3596 target = 0.149259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.123323 restraints weight = 5185.226| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.30 r_work: 0.3180 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4918 Z= 0.114 Angle : 0.565 7.575 6709 Z= 0.286 Chirality : 0.040 0.176 781 Planarity : 0.004 0.047 821 Dihedral : 6.298 70.222 721 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.59 % Allowed : 20.32 % Favored : 76.10 % 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 aren not related in a simple way. whole: 1.79 (0.36), residues: 609 helix: 1.79 (0.25), residues: 449 sheet: None (None), residues: 0 loop : -0.50 (0.54), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 300 TYR 0.026 0.001 TYR A 256 PHE 0.008 0.001 PHE A 534 TRP 0.020 0.001 TRP B 30 HIS 0.002 0.001 HIS A 555 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 4914) covalent geometry : angle 0.56334 ( 6701) SS BOND : bond 0.00223 ( 4) SS BOND : angle 1.35363 ( 8) hydrogen bonds : bond 0.03292 ( 329) hydrogen bonds : angle 4.51217 ( 975) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.116 Fit side-chains REVERT: A 44 MET cc_start: 0.7493 (OUTLIER) cc_final: 0.5986 (tmm) REVERT: A 67 VAL cc_start: 0.7711 (OUTLIER) cc_final: 0.7315 (p) REVERT: A 325 MET cc_start: 0.8859 (tmm) cc_final: 0.8530 (tpp) REVERT: A 387 LEU cc_start: 0.8120 (mt) cc_final: 0.7639 (mt) REVERT: A 667 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7826 (mt) outliers start: 18 outliers final: 14 residues processed: 86 average time/residue: 0.0783 time to fit residues: 8.4326 Evaluate side-chains 84 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 667 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 27 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 0.0870 chunk 54 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 overall best weight: 2.1564 ------------------------------------------------------------------------------- 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 = 0.3522 r_free = 0.3522 target = 0.143108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.118043 restraints weight = 5242.455| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.23 r_work: 0.3143 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 4918 Z= 0.198 Angle : 0.667 7.719 6709 Z= 0.340 Chirality : 0.045 0.181 781 Planarity : 0.005 0.046 821 Dihedral : 6.697 75.853 721 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.39 % Allowed : 20.72 % Favored : 75.90 % 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 aren not related in a simple way. whole: 1.20 (0.35), residues: 609 helix: 1.27 (0.25), residues: 455 sheet: None (None), residues: 0 loop : -0.48 (0.55), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 564 TYR 0.029 0.002 TYR A 256 PHE 0.017 0.002 PHE A 534 TRP 0.014 0.002 TRP B 30 HIS 0.004 0.001 HIS A 555 Details of bonding type rmsd covalent geometry : bond 0.00471 ( 4914) covalent geometry : angle 0.66171 ( 6701) SS BOND : bond 0.00291 ( 4) SS BOND : angle 2.40852 ( 8) hydrogen bonds : bond 0.04207 ( 329) hydrogen bonds : angle 4.81020 ( 975) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1163.22 seconds wall clock time: 20 minutes 30.76 seconds (1230.76 seconds total)