Starting phenix.real_space_refine on Thu Jun 5 01:32:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hin_34823/06_2025/8hin_34823.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hin_34823/06_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_34823/06_2025/8hin_34823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hin_34823/06_2025/8hin_34823.map" model { file = "/net/cci-nas-00/data/ceres_data/8hin_34823/06_2025/8hin_34823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hin_34823/06_2025/8hin_34823.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 3.47, per 1000 atoms: 0.72 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: 1.06 Conformation dependent library (CDL) restraints added in 555.6 milliseconds 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: 0.48 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: 1.31 Time building geometry restraints manager: 1.24 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: 0.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.580 Find NCS groups from input model: 0.040 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: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.750 ------------------------------------------------------------------------------- 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 : 12.04 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.042 0.004 TRP A 276 HIS 0.005 0.002 HIS A 264 PHE 0.026 0.004 PHE A 476 TYR 0.040 0.004 TYR A 455 ARG 0.012 0.001 ARG A 336 Details of bonding type rmsd hydrogen bonds : bond 0.18872 ( 329) hydrogen bonds : angle 8.18001 ( 975) SS BOND : bond 0.28673 ( 4) SS BOND : angle 19.11744 ( 8) covalent geometry : bond 0.01695 ( 4914) covalent geometry : angle 2.46251 ( 6701) *********************** 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 : 0.526 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: 0.1949 time to fit residues: 27.7330 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 : 0.491 ------------------------------------------------------------------------------- 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 50 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 47 optimal weight: 0.0970 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 = 0.3553 r_free = 0.3553 target = 0.145994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.121790 restraints weight = 5114.671| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.16 r_work: 0.3348 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2357 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= 0.141 Angle : 0.667 7.724 6709 Z= 0.339 Chirality : 0.044 0.191 781 Planarity : 0.005 0.051 821 Dihedral : 8.065 61.320 736 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.34), residues: 609 helix: 0.24 (0.24), residues: 456 sheet: None (None), residues: 0 loop : -1.55 (0.52), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 30 HIS 0.003 0.001 HIS A 268 PHE 0.019 0.001 PHE A 453 TYR 0.012 0.001 TYR A 256 ARG 0.003 0.001 ARG A 379 Details of bonding type rmsd hydrogen bonds : bond 0.04259 ( 329) hydrogen bonds : angle 5.24353 ( 975) SS BOND : bond 0.00267 ( 4) SS BOND : angle 1.52496 ( 8) covalent geometry : bond 0.00308 ( 4914) covalent geometry : angle 0.66567 ( 6701) *********************** 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 97 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.487 Fit side-chains REVERT: A 44 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7727 (mtm) REVERT: A 60 ARG cc_start: 0.7276 (ptm-80) cc_final: 0.7022 (ttt-90) REVERT: A 125 MET cc_start: 0.6473 (ttp) cc_final: 0.6246 (ttp) REVERT: A 328 MET cc_start: 0.8534 (mtm) cc_final: 0.7998 (mtm) REVERT: A 427 ARG cc_start: 0.7054 (mtt-85) cc_final: 0.6554 (mtp180) REVERT: A 506 PHE cc_start: 0.8620 (OUTLIER) cc_final: 0.7963 (t80) REVERT: A 667 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7722 (mt) REVERT: B 31 MET cc_start: 0.6901 (mmm) cc_final: 0.6172 (ptt) outliers start: 18 outliers final: 10 residues processed: 90 average time/residue: 0.1950 time to fit residues: 21.7975 Evaluate side-chains 84 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 39 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 1 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3545 r_free = 0.3545 target = 0.145139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.121326 restraints weight = 5195.686| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.24 r_work: 0.3170 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: 0.7651 moved from start: 0.2865 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 : 0.617 7.870 6709 Z= 0.311 Chirality : 0.042 0.191 781 Planarity : 0.005 0.055 821 Dihedral : 6.696 64.616 723 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.98 % Allowed : 17.33 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.35), residues: 609 helix: 1.03 (0.25), residues: 452 sheet: None (None), residues: 0 loop : -1.25 (0.52), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 30 HIS 0.004 0.001 HIS A 555 PHE 0.010 0.001 PHE A 326 TYR 0.014 0.001 TYR A 256 ARG 0.008 0.001 ARG A 564 Details of bonding type rmsd hydrogen bonds : bond 0.03948 ( 329) hydrogen bonds : angle 4.86217 ( 975) SS BOND : bond 0.00139 ( 4) SS BOND : angle 1.36734 ( 8) covalent geometry : bond 0.00316 ( 4914) covalent geometry : angle 0.61595 ( 6701) *********************** 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: 20 poor density : 82 time to evaluate : 0.533 Fit side-chains REVERT: A 60 ARG cc_start: 0.7222 (ptm-80) cc_final: 0.7001 (tmt170) REVERT: A 125 MET cc_start: 0.6470 (ttp) cc_final: 0.6174 (ttp) REVERT: A 300 ARG cc_start: 0.8018 (mmt-90) cc_final: 0.7744 (mmt-90) REVERT: A 352 ARG cc_start: 0.7634 (ttm-80) cc_final: 0.7423 (ttm-80) REVERT: A 427 ARG cc_start: 0.7121 (mtt-85) cc_final: 0.6533 (mtp180) REVERT: A 552 PRO cc_start: 0.7535 (Cg_exo) cc_final: 0.7313 (Cg_endo) REVERT: A 571 GLU cc_start: 0.6076 (tp30) cc_final: 0.5868 (tm-30) REVERT: A 667 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7904 (mt) REVERT: B 31 MET cc_start: 0.6884 (mmm) cc_final: 0.6227 (ptt) outliers start: 20 outliers final: 14 residues processed: 93 average time/residue: 0.2042 time to fit residues: 23.5973 Evaluate side-chains 93 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 10 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 39 optimal weight: 0.2980 chunk 29 optimal weight: 0.7980 chunk 5 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 34 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.146676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.121986 restraints weight = 5239.658| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.35 r_work: 0.3144 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4918 Z= 0.116 Angle : 0.579 7.256 6709 Z= 0.291 Chirality : 0.040 0.176 781 Planarity : 0.004 0.051 821 Dihedral : 6.429 62.174 723 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.78 % Allowed : 18.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.36), residues: 609 helix: 1.35 (0.25), residues: 455 sheet: None (None), residues: 0 loop : -0.88 (0.54), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 30 HIS 0.002 0.000 HIS A 555 PHE 0.008 0.001 PHE A 398 TYR 0.037 0.001 TYR A 256 ARG 0.008 0.000 ARG A 564 Details of bonding type rmsd hydrogen bonds : bond 0.03432 ( 329) hydrogen bonds : angle 4.67306 ( 975) SS BOND : bond 0.00158 ( 4) SS BOND : angle 1.61793 ( 8) covalent geometry : bond 0.00251 ( 4914) covalent geometry : angle 0.57633 ( 6701) *********************** 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: 19 poor density : 86 time to evaluate : 0.484 Fit side-chains REVERT: A 44 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.7682 (mtm) REVERT: A 60 ARG cc_start: 0.7415 (ptm-80) cc_final: 0.7051 (tmt170) REVERT: A 150 TYR cc_start: 0.8287 (m-10) cc_final: 0.7943 (m-10) REVERT: A 300 ARG cc_start: 0.8106 (mmt-90) cc_final: 0.7827 (mmt-90) REVERT: A 352 ARG cc_start: 0.7658 (ttm-80) cc_final: 0.7446 (ttm-80) REVERT: A 387 LEU cc_start: 0.8003 (mt) cc_final: 0.7693 (mt) REVERT: A 427 ARG cc_start: 0.7118 (mtt-85) cc_final: 0.6488 (mtp180) REVERT: A 505 SER cc_start: 0.8447 (t) cc_final: 0.8014 (t) REVERT: A 667 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7832 (mt) outliers start: 19 outliers final: 12 residues processed: 98 average time/residue: 0.1897 time to fit residues: 23.1468 Evaluate side-chains 89 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 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 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 49 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.142275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.118623 restraints weight = 5353.591| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.20 r_work: 0.3133 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 4918 Z= 0.198 Angle : 0.675 8.473 6709 Z= 0.344 Chirality : 0.045 0.182 781 Planarity : 0.005 0.051 821 Dihedral : 6.546 62.420 721 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.18 % Allowed : 19.52 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.35), residues: 609 helix: 1.09 (0.25), residues: 456 sheet: None (None), residues: 0 loop : -0.72 (0.55), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 30 HIS 0.005 0.001 HIS A 555 PHE 0.016 0.002 PHE A 534 TYR 0.032 0.002 TYR A 256 ARG 0.006 0.000 ARG A 564 Details of bonding type rmsd hydrogen bonds : bond 0.04284 ( 329) hydrogen bonds : angle 4.85458 ( 975) SS BOND : bond 0.00186 ( 4) SS BOND : angle 2.89077 ( 8) covalent geometry : bond 0.00473 ( 4914) covalent geometry : angle 0.66801 ( 6701) *********************** 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 96 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.559 Fit side-chains REVERT: A 44 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.6252 (tmm) REVERT: A 60 ARG cc_start: 0.7221 (ptm-80) cc_final: 0.7017 (ttt-90) REVERT: A 667 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7913 (mt) outliers start: 21 outliers final: 16 residues processed: 89 average time/residue: 0.2000 time to fit residues: 22.2161 Evaluate side-chains 93 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.514 ------------------------------------------------------------------------------- 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 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 265 LEU Chi-restraints excluded: chain A residue 279 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 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 655 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 0 optimal weight: 9.9990 chunk 28 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 35 optimal weight: 8.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.147980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.123276 restraints weight = 5166.959| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.20 r_work: 0.3359 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3355 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= 0.122 Angle : 0.582 6.822 6709 Z= 0.295 Chirality : 0.041 0.173 781 Planarity : 0.004 0.050 821 Dihedral : 6.293 64.594 721 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.98 % Allowed : 20.32 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.36), residues: 609 helix: 1.41 (0.25), residues: 456 sheet: None (None), residues: 0 loop : -0.56 (0.56), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 30 HIS 0.003 0.001 HIS A 555 PHE 0.008 0.001 PHE A 534 TYR 0.028 0.001 TYR A 256 ARG 0.006 0.000 ARG A 564 Details of bonding type rmsd hydrogen bonds : bond 0.03534 ( 329) hydrogen bonds : angle 4.61409 ( 975) SS BOND : bond 0.00191 ( 4) SS BOND : angle 2.07008 ( 8) covalent geometry : bond 0.00273 ( 4914) covalent geometry : angle 0.57839 ( 6701) *********************** 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 94 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.483 Fit side-chains REVERT: A 44 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.6349 (tmm) REVERT: A 387 LEU cc_start: 0.8168 (mt) cc_final: 0.7823 (mt) REVERT: A 427 ARG cc_start: 0.7078 (mtt-85) cc_final: 0.6517 (mtp180) REVERT: A 667 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7980 (mt) outliers start: 20 outliers final: 15 residues processed: 88 average time/residue: 0.1914 time to fit residues: 21.0777 Evaluate side-chains 91 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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 243 SER Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain A residue 357 THR 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 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 24 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 55 optimal weight: 20.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.147838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.123782 restraints weight = 5111.865| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.20 r_work: 0.3386 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4918 Z= 0.130 Angle : 0.584 7.061 6709 Z= 0.297 Chirality : 0.041 0.174 781 Planarity : 0.004 0.048 821 Dihedral : 6.361 67.324 721 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.38 % Allowed : 19.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.36), residues: 609 helix: 1.46 (0.25), residues: 456 sheet: None (None), residues: 0 loop : -0.48 (0.56), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 30 HIS 0.004 0.001 HIS A 555 PHE 0.011 0.001 PHE A 534 TYR 0.027 0.001 TYR A 256 ARG 0.006 0.000 ARG A 564 Details of bonding type rmsd hydrogen bonds : bond 0.03578 ( 329) hydrogen bonds : angle 4.62005 ( 975) SS BOND : bond 0.00186 ( 4) SS BOND : angle 1.90874 ( 8) covalent geometry : bond 0.00297 ( 4914) covalent geometry : angle 0.58024 ( 6701) *********************** 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 95 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.484 Fit side-chains REVERT: A 44 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.6289 (tmm) REVERT: A 387 LEU cc_start: 0.8111 (mt) cc_final: 0.7760 (mt) REVERT: A 667 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7830 (mt) outliers start: 22 outliers final: 16 residues processed: 86 average time/residue: 0.1857 time to fit residues: 20.1104 Evaluate side-chains 89 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 243 SER Chi-restraints excluded: chain A residue 256 TYR 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 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 44 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.3542 r_free = 0.3542 target = 0.144790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.119699 restraints weight = 5227.712| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.22 r_work: 0.3316 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4918 Z= 0.147 Angle : 0.615 10.094 6709 Z= 0.309 Chirality : 0.042 0.177 781 Planarity : 0.005 0.048 821 Dihedral : 6.406 68.114 721 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.59 % Allowed : 20.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.36), residues: 609 helix: 1.41 (0.25), residues: 456 sheet: None (None), residues: 0 loop : -0.41 (0.57), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 30 HIS 0.004 0.001 HIS A 555 PHE 0.013 0.001 PHE A 534 TYR 0.027 0.002 TYR A 256 ARG 0.007 0.000 ARG A 564 Details of bonding type rmsd hydrogen bonds : bond 0.03759 ( 329) hydrogen bonds : angle 4.65856 ( 975) SS BOND : bond 0.00237 ( 4) SS BOND : angle 1.99635 ( 8) covalent geometry : bond 0.00344 ( 4914) covalent geometry : angle 0.61136 ( 6701) *********************** 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: 18 poor density : 70 time to evaluate : 0.640 Fit side-chains REVERT: A 44 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.6226 (tmm) REVERT: A 387 LEU cc_start: 0.8020 (mt) cc_final: 0.7652 (mt) REVERT: A 667 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7879 (mt) outliers start: 18 outliers final: 14 residues processed: 82 average time/residue: 0.2449 time to fit residues: 25.1462 Evaluate side-chains 83 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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 243 SER Chi-restraints excluded: chain A residue 256 TYR 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 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 6 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 = 0.3549 r_free = 0.3549 target = 0.145551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.120500 restraints weight = 5132.861| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.22 r_work: 0.3348 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4918 Z= 0.135 Angle : 0.603 10.129 6709 Z= 0.304 Chirality : 0.042 0.177 781 Planarity : 0.005 0.048 821 Dihedral : 6.359 68.375 721 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.38 % Allowed : 19.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.36), residues: 609 helix: 1.46 (0.25), residues: 455 sheet: None (None), residues: 0 loop : -0.39 (0.57), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 30 HIS 0.004 0.001 HIS A 555 PHE 0.011 0.001 PHE A 534 TYR 0.027 0.001 TYR A 256 ARG 0.007 0.000 ARG A 564 Details of bonding type rmsd hydrogen bonds : bond 0.03632 ( 329) hydrogen bonds : angle 4.62842 ( 975) SS BOND : bond 0.00275 ( 4) SS BOND : angle 1.72717 ( 8) covalent geometry : bond 0.00312 ( 4914) covalent geometry : angle 0.60047 ( 6701) *********************** 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 88 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.607 Fit side-chains REVERT: A 44 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.6207 (tmm) REVERT: A 67 VAL cc_start: 0.7821 (OUTLIER) cc_final: 0.7430 (p) REVERT: A 387 LEU cc_start: 0.7961 (mt) cc_final: 0.7629 (mt) REVERT: A 553 ARG cc_start: 0.7955 (ttp80) cc_final: 0.7682 (ttt90) REVERT: A 667 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7965 (mt) outliers start: 22 outliers final: 15 residues processed: 82 average time/residue: 0.2549 time to fit residues: 25.9884 Evaluate side-chains 84 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 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 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 45 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 376 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.148022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.124551 restraints weight = 5143.358| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.22 r_work: 0.3213 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3788 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= 0.116 Angle : 0.580 10.560 6709 Z= 0.291 Chirality : 0.041 0.176 781 Planarity : 0.004 0.048 821 Dihedral : 6.201 67.938 721 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.19 % Allowed : 20.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.36), residues: 609 helix: 1.71 (0.25), residues: 449 sheet: None (None), residues: 0 loop : -0.41 (0.56), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 30 HIS 0.003 0.001 HIS A 555 PHE 0.008 0.001 PHE A 534 TYR 0.026 0.001 TYR A 256 ARG 0.007 0.000 ARG A 564 Details of bonding type rmsd hydrogen bonds : bond 0.03345 ( 329) hydrogen bonds : angle 4.52937 ( 975) SS BOND : bond 0.00313 ( 4) SS BOND : angle 1.31198 ( 8) covalent geometry : bond 0.00257 ( 4914) covalent geometry : angle 0.57812 ( 6701) ********************** 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 85 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.525 Fit side-chains REVERT: A 44 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.6138 (tmm) REVERT: A 67 VAL cc_start: 0.7800 (OUTLIER) cc_final: 0.7404 (p) REVERT: A 387 LEU cc_start: 0.7960 (mt) cc_final: 0.7474 (mt) REVERT: A 667 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7850 (mt) outliers start: 16 outliers final: 13 residues processed: 80 average time/residue: 0.1870 time to fit residues: 19.0060 Evaluate side-chains 81 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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 357 THR 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 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 37 optimal weight: 0.6980 chunk 9 optimal weight: 0.0570 chunk 13 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 4 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 = 0.3602 r_free = 0.3602 target = 0.150089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.124349 restraints weight = 5169.378| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.41 r_work: 0.3174 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 4918 Z= 0.119 Angle : 0.602 10.296 6709 Z= 0.303 Chirality : 0.040 0.174 781 Planarity : 0.004 0.048 821 Dihedral : 6.399 70.949 721 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.59 % Allowed : 20.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.36), residues: 609 helix: 1.73 (0.25), residues: 448 sheet: None (None), residues: 0 loop : -0.44 (0.55), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 30 HIS 0.002 0.001 HIS A 555 PHE 0.008 0.001 PHE A 534 TYR 0.025 0.001 TYR A 256 ARG 0.005 0.000 ARG A 300 Details of bonding type rmsd hydrogen bonds : bond 0.03290 ( 329) hydrogen bonds : angle 4.59732 ( 975) SS BOND : bond 0.00397 ( 4) SS BOND : angle 3.41558 ( 8) covalent geometry : bond 0.00271 ( 4914) covalent geometry : angle 0.59031 ( 6701) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2861.14 seconds wall clock time: 50 minutes 40.60 seconds (3040.60 seconds total)