Starting phenix.real_space_refine on Thu Jul 2 03:07:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wrp_37785/07_2026/8wrp_37785.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wrp_37785/07_2026/8wrp_37785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wrp_37785/07_2026/8wrp_37785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wrp_37785/07_2026/8wrp_37785.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wrp_37785/07_2026/8wrp_37785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wrp_37785/07_2026/8wrp_37785.map" } resolution = 2.83 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= 0.017 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: 5 Type Number sf(0) Gaussians P 77 5.49 5 S 9 5.16 5 C 3698 2.51 5 N 1141 2.21 5 O 1341 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6266 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 821 Classifications: {'RNA': 39} Modifications used: {'rna2p_pyr': 8, 'rna3p_pur': 15, 'rna3p_pyr': 16} Link IDs: {'rna2p': 8, 'rna3p': 30} Chain: "C" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 582 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "D" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 203 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 4660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4660 Classifications: {'peptide': 583} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 38, 'TRANS': 544} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.52, per 1000 atoms: 0.24 Number of scatterers: 6266 At special positions: 0 Unit cell: (82.5, 91.08, 122.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 9 16.00 P 77 15.00 O 1341 8.00 N 1141 7.00 C 3698 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.40 Conformation dependent library (CDL) restraints added in 294.4 milliseconds 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1088 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 3 sheets defined 50.4% alpha, 10.6% beta 21 base pairs and 49 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 75 through 90 removed outlier: 3.533A pdb=" N GLY A 90 " --> pdb=" O GLU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 99 Processing helix chain 'A' and resid 105 through 117 removed outlier: 4.119A pdb=" N ARG A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 169 removed outlier: 4.415A pdb=" N LEU A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL A 143 " --> pdb=" O ARG A 139 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ILE A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG A 150 " --> pdb=" O LYS A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.557A pdb=" N SER A 237 " --> pdb=" O ASN A 234 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A 238 " --> pdb=" O ARG A 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 234 through 238' Processing helix chain 'A' and resid 266 through 270 Processing helix chain 'A' and resid 281 through 292 removed outlier: 3.937A pdb=" N GLU A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 319 Processing helix chain 'A' and resid 327 through 333 Processing helix chain 'A' and resid 367 through 381 removed outlier: 4.158A pdb=" N LYS A 371 " --> pdb=" O GLY A 367 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU A 372 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 450 removed outlier: 3.974A pdb=" N ASP A 428 " --> pdb=" O ASP A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 463 removed outlier: 3.686A pdb=" N GLU A 458 " --> pdb=" O GLU A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 477 removed outlier: 3.941A pdb=" N LEU A 473 " --> pdb=" O GLU A 469 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 474 " --> pdb=" O THR A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 488 removed outlier: 4.052A pdb=" N MET A 488 " --> pdb=" O TRP A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 502 Processing helix chain 'A' and resid 527 through 536 Processing helix chain 'A' and resid 542 through 558 removed outlier: 3.501A pdb=" N ALA A 546 " --> pdb=" O GLU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 588 removed outlier: 4.024A pdb=" N VAL A 562 " --> pdb=" O SER A 558 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG A 563 " --> pdb=" O THR A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 618 Processing helix chain 'A' and resid 626 through 642 removed outlier: 4.526A pdb=" N VAL A 630 " --> pdb=" O TRP A 626 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 638 " --> pdb=" O ALA A 634 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ALA A 639 " --> pdb=" O PHE A 635 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU A 640 " --> pdb=" O SER A 636 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 198 through 199 removed outlier: 3.956A pdb=" N ILE A 347 " --> pdb=" O ASP A 342 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASN A 64 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL A 306 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLN A 68 " --> pdb=" O TRP A 304 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N TRP A 304 " --> pdb=" O GLN A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 410 through 417 removed outlier: 3.979A pdb=" N GLN A 412 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS A 405 " --> pdb=" O GLN A 412 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N PHE A 401 " --> pdb=" O LEU A 416 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLY A 385 " --> pdb=" O ALA A 593 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL A 595 " --> pdb=" O GLY A 385 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N VAL A 387 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N ILE A 647 " --> pdb=" O ILE A 592 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE A 594 " --> pdb=" O ILE A 647 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 510 through 515 removed outlier: 3.509A pdb=" N VAL A 524 " --> pdb=" O GLU A 511 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY A 520 " --> pdb=" O LYS A 515 " (cutoff:3.500A) 219 hydrogen bonds defined for protein. 615 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 96 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 49 stacking parallelities Total time for adding SS restraints: 0.79 Time building geometry restraints manager: 0.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1563 1.33 - 1.45: 1579 1.45 - 1.57: 3255 1.57 - 1.69: 151 1.69 - 1.81: 13 Bond restraints: 6561 Sorted by residual: bond pdb=" C3' DG D -8 " pdb=" C2' DG D -8 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C1' DC C 7 " pdb=" N1 DC C 7 " ideal model delta sigma weight residual 1.468 1.505 -0.037 1.40e-02 5.10e+03 6.83e+00 bond pdb=" C3' DT D -1 " pdb=" C2' DT D -1 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.23e+00 bond pdb=" C1' DC D 0 " pdb=" N1 DC D 0 " ideal model delta sigma weight residual 1.468 1.503 -0.035 1.40e-02 5.10e+03 6.21e+00 bond pdb=" C3' DT C 3 " pdb=" C2' DT C 3 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.38e+00 ... (remaining 6556 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 8899 1.63 - 3.27: 285 3.27 - 4.90: 28 4.90 - 6.54: 10 6.54 - 8.17: 1 Bond angle restraints: 9223 Sorted by residual: angle pdb=" N3 DT C 4 " pdb=" C4 DT C 4 " pdb=" O4 DT C 4 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT C 3 " pdb=" C4 DT C 3 " pdb=" O4 DT C 3 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT D -1 " pdb=" C4 DT D -1 " pdb=" O4 DT D -1 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT C -7 " pdb=" C4 DT C -7 " pdb=" O4 DT C -7 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 angle pdb=" N3 DT D -9 " pdb=" C4 DT D -9 " pdb=" O4 DT D -9 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.65e+01 ... (remaining 9218 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 3656 35.81 - 71.62: 279 71.62 - 107.43: 25 107.43 - 143.25: 0 143.25 - 179.06: 4 Dihedral angle restraints: 3964 sinusoidal: 2281 harmonic: 1683 Sorted by residual: dihedral pdb=" O4' U B -9 " pdb=" C1' U B -9 " pdb=" N1 U B -9 " pdb=" C2 U B -9 " ideal model delta sinusoidal sigma weight residual 232.00 52.94 179.06 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C B 8 " pdb=" C1' C B 8 " pdb=" N1 C B 8 " pdb=" C2 C B 8 " ideal model delta sinusoidal sigma weight residual 232.00 57.73 174.27 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" CA ASN A 463 " pdb=" C ASN A 463 " pdb=" N GLN A 464 " pdb=" CA GLN A 464 " ideal model delta harmonic sigma weight residual 180.00 156.05 23.95 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 3961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 869 0.055 - 0.109: 152 0.109 - 0.164: 24 0.164 - 0.219: 1 0.219 - 0.273: 2 Chirality restraints: 1048 Sorted by residual: chirality pdb=" CA GLN A 541 " pdb=" N GLN A 541 " pdb=" C GLN A 541 " pdb=" CB GLN A 541 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C2' C B 4 " pdb=" C3' C B 4 " pdb=" O2' C B 4 " pdb=" C1' C B 4 " both_signs ideal model delta sigma weight residual False -2.75 -2.51 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CG LEU A 564 " pdb=" CB LEU A 564 " pdb=" CD1 LEU A 564 " pdb=" CD2 LEU A 564 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.78e-01 ... (remaining 1045 not shown) Planarity restraints: 908 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 395 " 0.056 5.00e-02 4.00e+02 8.41e-02 1.13e+01 pdb=" N PRO A 396 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 396 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 396 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 273 " -0.045 5.00e-02 4.00e+02 6.79e-02 7.38e+00 pdb=" N PRO A 274 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 274 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 274 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 70 " 0.036 5.00e-02 4.00e+02 5.47e-02 4.79e+00 pdb=" N PRO A 71 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 71 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 71 " 0.030 5.00e-02 4.00e+02 ... (remaining 905 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1283 2.78 - 3.31: 5772 3.31 - 3.84: 11047 3.84 - 4.37: 13217 4.37 - 4.90: 19921 Nonbonded interactions: 51240 Sorted by model distance: nonbonded pdb=" O TRP A 112 " pdb=" OG1 THR A 116 " model vdw 2.254 3.040 nonbonded pdb=" O2' C B -6 " pdb=" OP2 C B -5 " model vdw 2.295 3.040 nonbonded pdb=" OP2 U B 1 " pdb=" NH1 ARG A 319 " model vdw 2.353 3.120 nonbonded pdb=" O TRP A 264 " pdb=" NE1 TRP A 270 " model vdw 2.365 3.120 nonbonded pdb=" OD1 ASN A 577 " pdb=" NH1 ARG A 642 " model vdw 2.384 3.120 ... (remaining 51235 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: 4.390 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.230 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:9.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 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 : 0.004 0.055 6561 Z= 0.287 Angle : 0.651 8.172 9223 Z= 0.446 Chirality : 0.044 0.273 1048 Planarity : 0.006 0.084 908 Dihedral : 21.670 179.057 2876 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.36), residues: 579 helix: 1.13 (0.33), residues: 249 sheet: -0.92 (0.66), residues: 64 loop : -0.01 (0.41), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 267 TYR 0.013 0.002 TYR A 432 PHE 0.012 0.001 PHE A 137 TRP 0.014 0.002 TRP A 626 HIS 0.007 0.001 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.29 ( 6561) covalent geometry : angle 0.65075 / 0.45 ( 9223) hydrogen bonds : bond 0.20605 / 17.81 ( 269) hydrogen bonds : angle 7.21334 / 9.76 ( 711) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 427 LYS cc_start: 0.6973 (mppt) cc_final: 0.6741 (mptt) REVERT: A 554 LEU cc_start: 0.8092 (mt) cc_final: 0.7869 (mt) REVERT: A 629 GLN cc_start: 0.6983 (tp40) cc_final: 0.6651 (tp40) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.5644 time to fit residues: 63.6212 Evaluate side-chains 95 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.0980 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 0.0060 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 27 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN A 258 ASN A 269 ASN A 632 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.170513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.133438 restraints weight = 8297.881| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.98 r_work: 0.3388 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 6561 Z= 0.205 Angle : 0.644 6.298 9223 Z= 0.360 Chirality : 0.046 0.211 1048 Planarity : 0.007 0.068 908 Dihedral : 25.241 178.806 1685 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.00 % Allowed : 11.85 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.36), residues: 579 helix: 1.33 (0.32), residues: 252 sheet: -0.41 (0.68), residues: 66 loop : -0.06 (0.41), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 276 TYR 0.022 0.003 TYR A 529 PHE 0.012 0.001 PHE A 635 TRP 0.014 0.001 TRP A 249 HIS 0.008 0.002 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.21 ( 6561) covalent geometry : angle 0.64429 / 0.36 ( 9223) hydrogen bonds : bond 0.06358 / 6.07 ( 269) hydrogen bonds : angle 4.50075 / 5.52 ( 711) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: A 86 GLU cc_start: 0.7783 (tt0) cc_final: 0.7421 (mt-10) REVERT: A 95 GLU cc_start: 0.7281 (mt-10) cc_final: 0.6972 (mt-10) REVERT: A 203 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7981 (mt0) REVERT: A 427 LYS cc_start: 0.7669 (mppt) cc_final: 0.7173 (mptt) REVERT: A 585 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.8039 (ttp-170) REVERT: A 629 GLN cc_start: 0.7558 (tp40) cc_final: 0.7269 (tp40) outliers start: 5 outliers final: 2 residues processed: 98 average time/residue: 0.5634 time to fit residues: 57.8625 Evaluate side-chains 98 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 94 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 585 ARG Chi-restraints excluded: chain A residue 631 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 3 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN A 632 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.170540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.132443 restraints weight = 8207.433| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.93 r_work: 0.3380 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6561 Z= 0.195 Angle : 0.615 6.321 9223 Z= 0.346 Chirality : 0.046 0.207 1048 Planarity : 0.006 0.068 908 Dihedral : 25.445 179.990 1685 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.61 % Allowed : 12.85 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.36), residues: 579 helix: 1.53 (0.32), residues: 249 sheet: -0.71 (0.66), residues: 69 loop : 0.03 (0.42), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 276 TYR 0.017 0.002 TYR A 529 PHE 0.011 0.002 PHE A 635 TRP 0.013 0.002 TRP A 249 HIS 0.008 0.001 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.19 ( 6561) covalent geometry : angle 0.61513 / 0.35 ( 9223) hydrogen bonds : bond 0.05354 / 5.15 ( 269) hydrogen bonds : angle 4.10812 / 4.89 ( 711) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7788 (mt-10) REVERT: A 95 GLU cc_start: 0.7325 (mt-10) cc_final: 0.6997 (mt-10) REVERT: A 203 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7935 (mt0) REVERT: A 425 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7618 (tt) REVERT: A 427 LYS cc_start: 0.7661 (mppt) cc_final: 0.7435 (mppt) REVERT: A 463 ASN cc_start: 0.8849 (m110) cc_final: 0.8560 (m110) REVERT: A 549 ASP cc_start: 0.8086 (m-30) cc_final: 0.7776 (m-30) REVERT: A 564 LEU cc_start: 0.7939 (mt) cc_final: 0.7730 (mt) REVERT: A 585 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.8032 (ttp-170) REVERT: A 629 GLN cc_start: 0.7539 (tp40) cc_final: 0.7196 (tp40) outliers start: 13 outliers final: 7 residues processed: 100 average time/residue: 0.5394 time to fit residues: 56.5834 Evaluate side-chains 107 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 529 TYR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 585 ARG Chi-restraints excluded: chain A residue 631 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 50 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 63 optimal weight: 0.0970 chunk 22 optimal weight: 0.1980 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN A 138 ASN A 269 ASN A 541 GLN A 632 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.171394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.132984 restraints weight = 8268.913| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.84 r_work: 0.3399 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6561 Z= 0.163 Angle : 0.572 5.933 9223 Z= 0.324 Chirality : 0.043 0.217 1048 Planarity : 0.006 0.066 908 Dihedral : 25.453 178.862 1685 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.81 % Allowed : 13.86 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.36), residues: 579 helix: 1.71 (0.32), residues: 250 sheet: -0.65 (0.66), residues: 69 loop : 0.04 (0.42), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 111 TYR 0.016 0.002 TYR A 432 PHE 0.010 0.001 PHE A 137 TRP 0.012 0.001 TRP A 249 HIS 0.004 0.001 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 ( 6561) covalent geometry : angle 0.57213 / 0.32 ( 9223) hydrogen bonds : bond 0.04894 / 4.61 ( 269) hydrogen bonds : angle 3.92941 / 4.68 ( 711) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7582 (mt-10) REVERT: A 86 GLU cc_start: 0.7759 (tt0) cc_final: 0.7344 (mt-10) REVERT: A 95 GLU cc_start: 0.7309 (mt-10) cc_final: 0.6901 (mt-10) REVERT: A 203 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7904 (mt0) REVERT: A 425 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7598 (tt) REVERT: A 427 LYS cc_start: 0.7634 (mppt) cc_final: 0.7368 (mppt) REVERT: A 463 ASN cc_start: 0.8851 (m110) cc_final: 0.8575 (m110) REVERT: A 549 ASP cc_start: 0.8060 (m-30) cc_final: 0.7733 (m-30) REVERT: A 564 LEU cc_start: 0.7939 (mt) cc_final: 0.7736 (mt) REVERT: A 585 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.8035 (ttp-170) REVERT: A 629 GLN cc_start: 0.7506 (tp40) cc_final: 0.7142 (tp40) outliers start: 14 outliers final: 5 residues processed: 104 average time/residue: 0.5676 time to fit residues: 61.7854 Evaluate side-chains 107 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 529 TYR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 585 ARG Chi-restraints excluded: chain A residue 631 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 56 optimal weight: 0.9980 chunk 33 optimal weight: 0.0770 chunk 4 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 6 optimal weight: 0.5980 chunk 32 optimal weight: 0.4980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN A 195 ASN A 269 ASN A 632 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.171145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.133567 restraints weight = 8324.053| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.89 r_work: 0.3397 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6561 Z= 0.173 Angle : 0.578 6.290 9223 Z= 0.326 Chirality : 0.043 0.213 1048 Planarity : 0.006 0.064 908 Dihedral : 25.435 178.426 1685 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.81 % Allowed : 15.26 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.36), residues: 579 helix: 1.75 (0.32), residues: 248 sheet: -0.70 (0.64), residues: 71 loop : 0.08 (0.42), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 111 TYR 0.017 0.002 TYR A 432 PHE 0.010 0.001 PHE A 137 TRP 0.017 0.001 TRP A 436 HIS 0.004 0.001 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 ( 6561) covalent geometry : angle 0.57829 / 0.33 ( 9223) hydrogen bonds : bond 0.04804 / 4.56 ( 269) hydrogen bonds : angle 3.90807 / 4.59 ( 711) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.154 Fit side-chains revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7763 (mt-10) REVERT: A 86 GLU cc_start: 0.7758 (tt0) cc_final: 0.7439 (mt-10) REVERT: A 95 GLU cc_start: 0.7336 (mt-10) cc_final: 0.6979 (mt-10) REVERT: A 203 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7905 (mt0) REVERT: A 292 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7803 (pt0) REVERT: A 425 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7618 (tt) REVERT: A 427 LYS cc_start: 0.7645 (mppt) cc_final: 0.7359 (mppt) REVERT: A 463 ASN cc_start: 0.8881 (m110) cc_final: 0.8592 (m110) REVERT: A 549 ASP cc_start: 0.8065 (m-30) cc_final: 0.7725 (m-30) REVERT: A 585 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.8047 (ttp-170) REVERT: A 629 GLN cc_start: 0.7529 (tp40) cc_final: 0.7174 (tp40) outliers start: 14 outliers final: 7 residues processed: 105 average time/residue: 0.5365 time to fit residues: 58.9032 Evaluate side-chains 105 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 529 TYR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 585 ARG Chi-restraints excluded: chain A residue 631 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 24 optimal weight: 0.0060 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.0060 chunk 44 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 27 optimal weight: 0.0670 chunk 56 optimal weight: 0.2980 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 overall best weight: 0.4752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN A 269 ASN A 632 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.171537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.134125 restraints weight = 8323.310| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.84 r_work: 0.3407 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6561 Z= 0.157 Angle : 0.570 6.509 9223 Z= 0.322 Chirality : 0.043 0.215 1048 Planarity : 0.006 0.064 908 Dihedral : 25.421 178.308 1685 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.21 % Allowed : 17.07 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.36), residues: 579 helix: 1.82 (0.32), residues: 248 sheet: -0.65 (0.65), residues: 69 loop : 0.08 (0.42), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 111 TYR 0.019 0.002 TYR A 432 PHE 0.011 0.001 PHE A 627 TRP 0.068 0.003 TRP A 626 HIS 0.003 0.001 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 ( 6561) covalent geometry : angle 0.56951 / 0.32 ( 9223) hydrogen bonds : bond 0.04675 / 4.42 ( 269) hydrogen bonds : angle 3.85737 / 4.51 ( 711) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7778 (mt-10) REVERT: A 86 GLU cc_start: 0.7750 (tt0) cc_final: 0.7422 (mt-10) REVERT: A 95 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6984 (mt-10) REVERT: A 203 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7896 (mt0) REVERT: A 280 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8005 (tp) REVERT: A 292 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7789 (mt-10) REVERT: A 425 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7642 (tt) REVERT: A 463 ASN cc_start: 0.8870 (m110) cc_final: 0.8588 (m110) REVERT: A 549 ASP cc_start: 0.8058 (m-30) cc_final: 0.7713 (m-30) REVERT: A 585 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.8031 (ttp-170) REVERT: A 629 GLN cc_start: 0.7484 (tp40) cc_final: 0.7125 (tp40) outliers start: 11 outliers final: 6 residues processed: 102 average time/residue: 0.5913 time to fit residues: 63.1400 Evaluate side-chains 107 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 529 TYR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 585 ARG Chi-restraints excluded: chain A residue 631 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 31 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 24 optimal weight: 0.0270 chunk 1 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 3 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 29 optimal weight: 0.0570 chunk 13 optimal weight: 0.3980 overall best weight: 0.3156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN A 195 ASN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN A 632 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.172292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.133943 restraints weight = 8307.130| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 1.83 r_work: 0.3430 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6561 Z= 0.133 Angle : 0.550 6.043 9223 Z= 0.309 Chirality : 0.041 0.215 1048 Planarity : 0.006 0.061 908 Dihedral : 25.373 178.106 1685 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.15 % Favored : 95.68 % Rotamer: Outliers : 2.41 % Allowed : 17.87 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.37), residues: 579 helix: 1.96 (0.32), residues: 248 sheet: -0.57 (0.67), residues: 69 loop : 0.12 (0.42), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 111 TYR 0.016 0.002 TYR A 432 PHE 0.010 0.001 PHE A 137 TRP 0.020 0.002 TRP A 626 HIS 0.003 0.001 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 6561) covalent geometry : angle 0.54970 / 0.31 ( 9223) hydrogen bonds : bond 0.04388 / 4.13 ( 269) hydrogen bonds : angle 3.75077 / 4.39 ( 711) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7754 (mt-10) REVERT: A 86 GLU cc_start: 0.7758 (tt0) cc_final: 0.7459 (mt-10) REVERT: A 95 GLU cc_start: 0.7293 (mt-10) cc_final: 0.6855 (mt-10) REVERT: A 203 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7846 (mt0) REVERT: A 425 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7600 (tt) REVERT: A 427 LYS cc_start: 0.7734 (mtpt) cc_final: 0.7460 (tppt) REVERT: A 463 ASN cc_start: 0.8888 (m110) cc_final: 0.8607 (m110) REVERT: A 549 ASP cc_start: 0.8053 (m-30) cc_final: 0.7697 (m-30) REVERT: A 585 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7996 (ttp-170) REVERT: A 629 GLN cc_start: 0.7464 (tp40) cc_final: 0.7101 (tp40) outliers start: 12 outliers final: 7 residues processed: 102 average time/residue: 0.5728 time to fit residues: 61.2348 Evaluate side-chains 108 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 529 TYR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 585 ARG Chi-restraints excluded: chain A residue 631 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 24 optimal weight: 0.0070 chunk 30 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 17 optimal weight: 10.0000 chunk 28 optimal weight: 0.4980 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 ASN A 99 ASN A 195 ASN A 269 ASN A 632 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.170273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.132881 restraints weight = 8324.981| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.92 r_work: 0.3392 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 6561 Z= 0.166 Angle : 0.570 6.265 9223 Z= 0.320 Chirality : 0.043 0.212 1048 Planarity : 0.006 0.063 908 Dihedral : 25.308 177.826 1685 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.66 % Favored : 95.16 % Rotamer: Outliers : 2.61 % Allowed : 18.27 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.36), residues: 579 helix: 1.87 (0.32), residues: 249 sheet: -0.66 (0.64), residues: 71 loop : 0.15 (0.42), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 111 TYR 0.019 0.002 TYR A 529 PHE 0.009 0.001 PHE A 137 TRP 0.012 0.002 TRP A 249 HIS 0.003 0.001 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 ( 6561) covalent geometry : angle 0.56961 / 0.32 ( 9223) hydrogen bonds : bond 0.04554 / 4.29 ( 269) hydrogen bonds : angle 3.78434 / 4.40 ( 711) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.176 Fit side-chains revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7653 (mt-10) REVERT: A 86 GLU cc_start: 0.7824 (tt0) cc_final: 0.7500 (mt-10) REVERT: A 95 GLU cc_start: 0.7359 (mt-10) cc_final: 0.6957 (mt-10) REVERT: A 203 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7896 (mt0) REVERT: A 280 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8040 (tp) REVERT: A 425 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7695 (tt) REVERT: A 427 LYS cc_start: 0.7817 (mtpt) cc_final: 0.7549 (tppt) REVERT: A 463 ASN cc_start: 0.8851 (m110) cc_final: 0.8587 (m110) REVERT: A 549 ASP cc_start: 0.8098 (m-30) cc_final: 0.7751 (m-30) REVERT: A 585 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.8031 (ttp-170) REVERT: A 629 GLN cc_start: 0.7508 (tp40) cc_final: 0.7155 (tp40) outliers start: 13 outliers final: 6 residues processed: 100 average time/residue: 0.5766 time to fit residues: 60.2717 Evaluate side-chains 105 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 529 TYR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 585 ARG Chi-restraints excluded: chain A residue 631 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 51 optimal weight: 6.9990 chunk 6 optimal weight: 0.3980 chunk 7 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 26 optimal weight: 0.1980 chunk 31 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN A 632 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.170534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.132938 restraints weight = 8374.635| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.94 r_work: 0.3393 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6561 Z= 0.157 Angle : 0.568 6.834 9223 Z= 0.317 Chirality : 0.042 0.213 1048 Planarity : 0.006 0.061 908 Dihedral : 25.267 177.962 1685 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.80 % Favored : 96.03 % Rotamer: Outliers : 3.01 % Allowed : 17.87 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.37), residues: 579 helix: 1.92 (0.32), residues: 249 sheet: -0.61 (0.64), residues: 71 loop : 0.16 (0.43), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 111 TYR 0.017 0.002 TYR A 432 PHE 0.010 0.001 PHE A 137 TRP 0.014 0.002 TRP A 249 HIS 0.003 0.001 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 ( 6561) covalent geometry : angle 0.56755 / 0.32 ( 9223) hydrogen bonds : bond 0.04440 / 4.18 ( 269) hydrogen bonds : angle 3.76943 / 4.35 ( 711) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7824 (mt-10) REVERT: A 86 GLU cc_start: 0.7853 (tt0) cc_final: 0.7546 (mt-10) REVERT: A 95 GLU cc_start: 0.7357 (mt-10) cc_final: 0.7044 (mt-10) REVERT: A 106 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7243 (tpm170) REVERT: A 203 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7915 (mt0) REVERT: A 280 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.8040 (tp) REVERT: A 425 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7699 (tt) REVERT: A 427 LYS cc_start: 0.7825 (mtpt) cc_final: 0.7557 (tppt) REVERT: A 463 ASN cc_start: 0.8876 (m110) cc_final: 0.8610 (m110) REVERT: A 549 ASP cc_start: 0.8114 (m-30) cc_final: 0.7759 (m-30) REVERT: A 585 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.8034 (ttp-170) REVERT: A 629 GLN cc_start: 0.7529 (tp40) cc_final: 0.7175 (tp40) outliers start: 15 outliers final: 8 residues processed: 99 average time/residue: 0.5741 time to fit residues: 59.5222 Evaluate side-chains 108 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 529 TYR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 585 ARG Chi-restraints excluded: chain A residue 626 TRP Chi-restraints excluded: chain A residue 631 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 28 optimal weight: 0.0770 chunk 42 optimal weight: 0.9980 chunk 6 optimal weight: 0.1980 chunk 23 optimal weight: 0.2980 chunk 17 optimal weight: 7.9990 chunk 10 optimal weight: 0.3980 chunk 4 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 26 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 overall best weight: 0.2938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.171923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.134279 restraints weight = 8271.865| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 1.77 r_work: 0.3449 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6561 Z= 0.130 Angle : 0.546 7.477 9223 Z= 0.306 Chirality : 0.041 0.214 1048 Planarity : 0.006 0.061 908 Dihedral : 25.152 177.899 1685 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.15 % Favored : 95.68 % Rotamer: Outliers : 1.81 % Allowed : 19.28 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.37), residues: 579 helix: 2.00 (0.32), residues: 249 sheet: -0.44 (0.67), residues: 69 loop : 0.20 (0.43), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 111 TYR 0.018 0.002 TYR A 432 PHE 0.009 0.001 PHE A 137 TRP 0.017 0.001 TRP A 249 HIS 0.003 0.001 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 ( 6561) covalent geometry : angle 0.54590 / 0.31 ( 9223) hydrogen bonds : bond 0.04150 / 3.89 ( 269) hydrogen bonds : angle 3.71002 / 4.26 ( 711) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7809 (mt-10) REVERT: A 95 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6884 (mt-10) REVERT: A 106 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7152 (tpm170) REVERT: A 203 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7862 (mt0) REVERT: A 425 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7589 (tt) REVERT: A 427 LYS cc_start: 0.7734 (mtpt) cc_final: 0.7459 (tppt) REVERT: A 463 ASN cc_start: 0.8867 (m110) cc_final: 0.8586 (m110) REVERT: A 549 ASP cc_start: 0.8045 (m-30) cc_final: 0.7698 (m-30) REVERT: A 629 GLN cc_start: 0.7414 (tp40) cc_final: 0.7059 (tp40) outliers start: 9 outliers final: 5 residues processed: 100 average time/residue: 0.6158 time to fit residues: 64.2943 Evaluate side-chains 106 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 529 TYR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 631 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 2 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 24 optimal weight: 0.0770 chunk 33 optimal weight: 0.0370 chunk 41 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 49 optimal weight: 0.1980 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.171805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.134775 restraints weight = 8346.032| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.84 r_work: 0.3424 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6561 Z= 0.138 Angle : 0.559 9.442 9223 Z= 0.311 Chirality : 0.041 0.212 1048 Planarity : 0.006 0.060 908 Dihedral : 25.086 177.746 1685 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.80 % Favored : 96.03 % Rotamer: Outliers : 2.41 % Allowed : 19.08 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.37), residues: 579 helix: 1.95 (0.32), residues: 253 sheet: -0.48 (0.65), residues: 71 loop : 0.27 (0.43), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 111 TYR 0.019 0.002 TYR A 432 PHE 0.009 0.001 PHE A 137 TRP 0.015 0.002 TRP A 249 HIS 0.003 0.001 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 ( 6561) covalent geometry : angle 0.55852 / 0.31 ( 9223) hydrogen bonds : bond 0.04161 / 3.94 ( 269) hydrogen bonds : angle 3.73532 / 4.25 ( 711) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2724.27 seconds wall clock time: 47 minutes 8.93 seconds (2828.93 seconds total)