Starting phenix.real_space_refine on Tue Aug 4 18:59:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wrp_37785/08_2026/8wrp_37785.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wrp_37785/08_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_37785/08_2026/8wrp_37785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wrp_37785/08_2026/8wrp_37785.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wrp_37785/08_2026/8wrp_37785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wrp_37785/08_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-2.2rc3-6140/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: 1.11, per 1000 atoms: 0.18 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: 0.35 Conformation dependent library (CDL) restraints added in 223.4 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: 0.51 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: 0.83 Time building geometry restraints manager: 0.48 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: 8807 1.63 - 3.27: 378 3.27 - 4.90: 27 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: 834 0.055 - 0.109: 160 0.109 - 0.164: 52 0.164 - 0.219: 1 0.219 - 0.273: 1 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=" 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 chirality pdb=" CA LEU A 564 " pdb=" N LEU A 564 " pdb=" C LEU A 564 " pdb=" CB LEU A 564 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.47e-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: 4.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.980 Find NCS groups from input model: 0.010 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:6.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.650 ------------------------------------------------------------------------------- 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= 0.295 Angle : 0.695 8.172 9223 Z= 0.485 Chirality : 0.049 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 0.00416 / 0.29 ( 6561) covalent geometry : angle 0.69494 / 0.49 ( 9223) hydrogen bonds : bond 0.20605 / 20.03 ( 269) hydrogen bonds : angle 7.21334 / 10.07 ( 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 : 0.114 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: 0.4855 time to fit residues: 54.6743 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 : 0.118 ------------------------------------------------------------------------------- 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: 2.9990 chunk 33 optimal weight: 0.0870 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: 0.6576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4125 r_free = 0.4125 target = 0.170560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.132099 restraints weight = 8306.802| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.93 r_work: 0.3387 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 6561 Z= 0.196 Angle : 0.661 7.767 9223 Z= 0.365 Chirality : 0.048 0.241 1048 Planarity : 0.007 0.068 908 Dihedral : 25.243 178.937 1685 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.41 % Allowed : 11.65 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.36), residues: 579 helix: 1.30 (0.32), residues: 252 sheet: -0.38 (0.68), residues: 66 loop : -0.07 (0.41), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 267 TYR 0.022 0.002 TYR A 529 PHE 0.012 0.001 PHE A 635 TRP 0.014 0.002 TRP A 249 HIS 0.008 0.002 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.20 ( 6561) covalent geometry : angle 0.66125 / 0.36 ( 9223) hydrogen bonds : bond 0.06489 / 6.66 ( 269) hydrogen bonds : angle 4.47348 / 5.69 ( 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 106 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.112 Fit side-chains revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7698 (mt-10) REVERT: A 86 GLU cc_start: 0.7785 (tt0) cc_final: 0.7437 (mt-10) REVERT: A 95 GLU cc_start: 0.7289 (mt-10) cc_final: 0.6913 (mt-10) REVERT: A 585 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.8052 (ttp-170) REVERT: A 629 GLN cc_start: 0.7552 (tp40) cc_final: 0.7262 (tp40) outliers start: 7 outliers final: 2 residues processed: 99 average time/residue: 0.3948 time to fit residues: 40.9974 Evaluate side-chains 100 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU 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: 2.9990 chunk 6 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 3 optimal weight: 9.9990 chunk 48 optimal weight: 0.0570 chunk 13 optimal weight: 0.4980 chunk 53 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 = 0.4127 r_free = 0.4127 target = 0.170712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.132067 restraints weight = 8212.911| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.80 r_work: 0.3400 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1623 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= 0.170 Angle : 0.603 6.735 9223 Z= 0.337 Chirality : 0.045 0.217 1048 Planarity : 0.006 0.067 908 Dihedral : 25.307 179.605 1685 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.01 % Allowed : 13.65 % Favored : 84.34 % 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: 0.88 (0.36), residues: 579 helix: 1.57 (0.32), residues: 249 sheet: -0.55 (0.67), residues: 68 loop : 0.05 (0.42), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 276 TYR 0.015 0.002 TYR A 432 PHE 0.010 0.001 PHE A 137 TRP 0.012 0.001 TRP A 249 HIS 0.007 0.001 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 ( 6561) covalent geometry : angle 0.60265 / 0.34 ( 9223) hydrogen bonds : bond 0.05386 / 5.61 ( 269) hydrogen bonds : angle 4.12916 / 5.21 ( 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 108 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7773 (mt-10) REVERT: A 95 GLU cc_start: 0.7295 (mt-10) cc_final: 0.6967 (mt-10) REVERT: A 425 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7582 (tt) REVERT: A 427 LYS cc_start: 0.7667 (mppt) cc_final: 0.7445 (mppt) REVERT: A 463 ASN cc_start: 0.8835 (m110) cc_final: 0.8544 (m110) REVERT: A 549 ASP cc_start: 0.8090 (m-30) cc_final: 0.7788 (m-30) REVERT: A 585 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.8037 (ttp-170) REVERT: A 629 GLN cc_start: 0.7520 (tp40) cc_final: 0.7183 (tp40) outliers start: 10 outliers final: 6 residues processed: 100 average time/residue: 0.4341 time to fit residues: 45.5049 Evaluate side-chains 99 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 3.9990 chunk 52 optimal weight: 0.0030 chunk 12 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 27 optimal weight: 0.0970 chunk 63 optimal weight: 0.9990 chunk 22 optimal weight: 0.0020 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 17 optimal weight: 8.9990 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN A 138 ASN A 195 ASN A 269 ASN A 541 GLN A 632 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.172760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.134417 restraints weight = 8285.641| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 1.78 r_work: 0.3433 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6561 Z= 0.132 Angle : 0.565 6.132 9223 Z= 0.316 Chirality : 0.042 0.240 1048 Planarity : 0.006 0.064 908 Dihedral : 25.315 179.990 1685 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.61 % Allowed : 14.26 % Favored : 83.13 % 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: 1.79 (0.32), residues: 249 sheet: -0.64 (0.65), residues: 71 loop : 0.11 (0.42), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 111 TYR 0.018 0.002 TYR A 529 PHE 0.009 0.001 PHE A 137 TRP 0.024 0.001 TRP A 436 HIS 0.004 0.001 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 ( 6561) covalent geometry : angle 0.56463 / 0.32 ( 9223) hydrogen bonds : bond 0.04718 / 4.90 ( 269) hydrogen bonds : angle 3.93147 / 4.90 ( 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 112 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7733 (mt-10) REVERT: A 95 GLU cc_start: 0.7247 (mt-10) cc_final: 0.6918 (mt-10) REVERT: A 292 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7840 (pt0) REVERT: A 425 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7503 (tt) REVERT: A 427 LYS cc_start: 0.7622 (mppt) cc_final: 0.7418 (mtpt) REVERT: A 463 ASN cc_start: 0.8847 (m110) cc_final: 0.8555 (m110) REVERT: A 549 ASP cc_start: 0.8042 (m-30) cc_final: 0.7722 (m-30) REVERT: A 585 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.8026 (ttp-170) REVERT: A 629 GLN cc_start: 0.7482 (tp40) cc_final: 0.7126 (tp40) outliers start: 13 outliers final: 6 residues processed: 105 average time/residue: 0.4392 time to fit residues: 48.4859 Evaluate side-chains 104 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 56 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 6 optimal weight: 0.0870 chunk 32 optimal weight: 0.1980 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.4137 r_free = 0.4137 target = 0.171671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.133965 restraints weight = 8349.404| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.87 r_work: 0.3403 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6561 Z= 0.163 Angle : 0.581 6.387 9223 Z= 0.324 Chirality : 0.043 0.228 1048 Planarity : 0.006 0.063 908 Dihedral : 25.285 179.677 1685 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.21 % Allowed : 15.46 % Favored : 82.33 % 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: 1.07 (0.36), residues: 579 helix: 1.83 (0.32), residues: 248 sheet: -0.60 (0.65), residues: 71 loop : 0.09 (0.42), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 111 TYR 0.018 0.002 TYR A 432 PHE 0.009 0.001 PHE A 635 TRP 0.013 0.001 TRP A 249 HIS 0.005 0.001 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 ( 6561) covalent geometry : angle 0.58079 / 0.32 ( 9223) hydrogen bonds : bond 0.04773 / 4.93 ( 269) hydrogen bonds : angle 3.84969 / 4.79 ( 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: 11 poor density : 100 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7609 (mt-10) REVERT: A 86 GLU cc_start: 0.7780 (tt0) cc_final: 0.7456 (mt-10) REVERT: A 95 GLU cc_start: 0.7333 (mt-10) cc_final: 0.6970 (tt0) REVERT: A 203 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7914 (mt0) REVERT: A 425 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7589 (tt) REVERT: A 427 LYS cc_start: 0.7614 (mppt) cc_final: 0.7342 (mppt) REVERT: A 463 ASN cc_start: 0.8874 (m110) cc_final: 0.8578 (m110) REVERT: A 549 ASP cc_start: 0.8048 (m-30) cc_final: 0.7716 (m-30) REVERT: A 585 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.8032 (ttp-170) REVERT: A 629 GLN cc_start: 0.7533 (tp40) cc_final: 0.7174 (tp40) outliers start: 11 outliers final: 5 residues processed: 105 average time/residue: 0.4765 time to fit residues: 52.3182 Evaluate side-chains 105 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.144 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 24 optimal weight: 0.0970 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.0010 chunk 44 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- 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 = 0.4134 r_free = 0.4134 target = 0.171418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.133551 restraints weight = 8312.260| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 1.87 r_work: 0.3402 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6561 Z= 0.170 Angle : 0.603 8.783 9223 Z= 0.333 Chirality : 0.044 0.232 1048 Planarity : 0.006 0.063 908 Dihedral : 25.304 179.653 1685 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.21 % Allowed : 17.27 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.36), residues: 579 helix: 1.82 (0.32), residues: 248 sheet: -0.64 (0.64), residues: 71 loop : 0.06 (0.42), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 111 TYR 0.019 0.002 TYR A 432 PHE 0.010 0.001 PHE A 137 TRP 0.013 0.001 TRP A 249 HIS 0.004 0.001 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 ( 6561) covalent geometry : angle 0.60260 / 0.33 ( 9223) hydrogen bonds : bond 0.04749 / 4.87 ( 269) hydrogen bonds : angle 3.88051 / 4.81 ( 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 : 0.198 Fit side-chains revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7616 (mt-10) REVERT: A 86 GLU cc_start: 0.7783 (tt0) cc_final: 0.7459 (mt-10) REVERT: A 95 GLU cc_start: 0.7357 (mt-10) cc_final: 0.7002 (tt0) REVERT: A 203 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7937 (mt0) REVERT: A 280 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8017 (tp) REVERT: A 291 LYS cc_start: 0.8553 (ttmm) cc_final: 0.8322 (mttm) REVERT: A 425 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7623 (tt) REVERT: A 427 LYS cc_start: 0.7668 (mppt) cc_final: 0.7380 (mppt) REVERT: A 463 ASN cc_start: 0.8872 (m110) cc_final: 0.8587 (m110) REVERT: A 465 MET cc_start: 0.3799 (OUTLIER) cc_final: 0.3271 (mmm) REVERT: A 549 ASP cc_start: 0.8050 (m-30) cc_final: 0.7709 (m-30) REVERT: A 585 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.8057 (ttp-170) REVERT: A 629 GLN cc_start: 0.7507 (tp40) cc_final: 0.7154 (tp40) outliers start: 11 outliers final: 5 residues processed: 101 average time/residue: 0.4916 time to fit residues: 52.0574 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 : 0.123 ------------------------------------------------------------------------------- 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 465 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 31 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 24 optimal weight: 0.0270 chunk 1 optimal weight: 2.9990 chunk 15 optimal weight: 0.0770 chunk 3 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 overall best weight: 0.4396 ------------------------------------------------------------------------------- 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 = 0.4140 r_free = 0.4140 target = 0.171057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.132986 restraints weight = 8296.353| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 1.78 r_work: 0.3431 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2205 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= 0.146 Angle : 0.588 10.962 9223 Z= 0.324 Chirality : 0.043 0.233 1048 Planarity : 0.006 0.061 908 Dihedral : 25.269 179.019 1685 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.97 % Favored : 95.85 % Rotamer: Outliers : 2.21 % Allowed : 18.07 % 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: 1.06 (0.36), residues: 579 helix: 1.86 (0.32), residues: 248 sheet: -0.63 (0.65), residues: 71 loop : 0.05 (0.42), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 111 TYR 0.020 0.002 TYR A 432 PHE 0.010 0.001 PHE A 137 TRP 0.013 0.001 TRP A 249 HIS 0.004 0.001 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 ( 6561) covalent geometry : angle 0.58814 / 0.32 ( 9223) hydrogen bonds : bond 0.04462 / 4.58 ( 269) hydrogen bonds : angle 3.83146 / 4.68 ( 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: 11 poor density : 97 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7592 (mt-10) REVERT: A 86 GLU cc_start: 0.7780 (tt0) cc_final: 0.7447 (mt-10) REVERT: A 95 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6898 (tt0) REVERT: A 203 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7885 (mt0) REVERT: A 280 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.8028 (tp) REVERT: A 425 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7598 (tt) REVERT: A 427 LYS cc_start: 0.7675 (mppt) cc_final: 0.7379 (mppt) REVERT: A 463 ASN cc_start: 0.8874 (m110) cc_final: 0.8590 (m110) REVERT: A 549 ASP cc_start: 0.8058 (m-30) cc_final: 0.7703 (m-30) REVERT: A 585 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.8012 (ttp-170) REVERT: A 629 GLN cc_start: 0.7497 (tp40) cc_final: 0.7143 (tp40) outliers start: 11 outliers final: 5 residues processed: 101 average time/residue: 0.4836 time to fit residues: 51.0654 Evaluate side-chains 105 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.185 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 24 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 17 optimal weight: 0.0000 chunk 28 optimal weight: 0.4980 chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 overall best weight: 0.4584 ------------------------------------------------------------------------------- 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 = 0.4139 r_free = 0.4139 target = 0.171011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.134110 restraints weight = 8298.120| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.85 r_work: 0.3424 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6561 Z= 0.150 Angle : 0.590 11.421 9223 Z= 0.322 Chirality : 0.042 0.232 1048 Planarity : 0.006 0.061 908 Dihedral : 25.190 178.616 1685 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.32 % Favored : 95.51 % Rotamer: Outliers : 1.81 % Allowed : 18.47 % 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: 1.07 (0.36), residues: 579 helix: 1.84 (0.32), residues: 248 sheet: -0.58 (0.66), residues: 69 loop : 0.07 (0.42), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 111 TYR 0.021 0.002 TYR A 432 PHE 0.010 0.001 PHE A 137 TRP 0.011 0.001 TRP A 249 HIS 0.004 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 ( 6561) covalent geometry : angle 0.59041 / 0.32 ( 9223) hydrogen bonds : bond 0.04426 / 4.55 ( 269) hydrogen bonds : angle 3.85025 / 4.69 ( 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 104 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.128 Fit side-chains REVERT: A 74 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7756 (mt-10) REVERT: A 86 GLU cc_start: 0.7801 (tt0) cc_final: 0.7476 (mt-10) REVERT: A 95 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6994 (tt0) REVERT: A 203 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7910 (mt0) REVERT: A 280 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.8006 (tp) REVERT: A 425 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7619 (tt) REVERT: A 433 ARG cc_start: 0.7342 (mmp-170) cc_final: 0.6560 (mmp-170) REVERT: A 549 ASP cc_start: 0.8070 (m-30) cc_final: 0.7709 (m-30) REVERT: A 585 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.8021 (ttp-170) REVERT: A 629 GLN cc_start: 0.7499 (tp40) cc_final: 0.7144 (tp40) outliers start: 9 outliers final: 5 residues processed: 98 average time/residue: 0.5497 time to fit residues: 56.2729 Evaluate side-chains 107 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.156 ------------------------------------------------------------------------------- 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 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: 0.1980 chunk 7 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 27 optimal weight: 0.0980 chunk 48 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.4136 r_free = 0.4136 target = 0.170775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.134280 restraints weight = 8368.679| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.84 r_work: 0.3424 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6561 Z= 0.156 Angle : 0.598 9.381 9223 Z= 0.329 Chirality : 0.043 0.231 1048 Planarity : 0.006 0.063 908 Dihedral : 25.133 178.498 1685 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.32 % Favored : 95.51 % Rotamer: Outliers : 2.21 % Allowed : 18.67 % 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: 1.03 (0.36), residues: 579 helix: 1.81 (0.32), residues: 248 sheet: -0.64 (0.65), residues: 69 loop : 0.07 (0.42), residues: 262 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 0.010 0.001 PHE A 137 TRP 0.094 0.003 TRP A 626 HIS 0.003 0.001 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 ( 6561) covalent geometry : angle 0.59844 / 0.33 ( 9223) hydrogen bonds : bond 0.04527 / 4.65 ( 269) hydrogen bonds : angle 3.89725 / 4.70 ( 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: 11 poor density : 97 time to evaluate : 0.202 Fit side-chains REVERT: A 74 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7773 (mt-10) REVERT: A 86 GLU cc_start: 0.7812 (tt0) cc_final: 0.7484 (mt-10) REVERT: A 95 GLU cc_start: 0.7340 (mt-10) cc_final: 0.7013 (tt0) REVERT: A 203 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7925 (mt0) REVERT: A 280 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.8001 (tp) REVERT: A 425 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7623 (tt) REVERT: A 463 ASN cc_start: 0.8901 (m110) cc_final: 0.8616 (m110) REVERT: A 549 ASP cc_start: 0.8054 (m-30) cc_final: 0.7690 (m-30) REVERT: A 585 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.8008 (ttp-170) REVERT: A 629 GLN cc_start: 0.7479 (tp40) cc_final: 0.7103 (tp40) outliers start: 11 outliers final: 6 residues processed: 102 average time/residue: 0.5993 time to fit residues: 63.9833 Evaluate side-chains 106 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.188 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 28 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 6 optimal weight: 0.1980 chunk 23 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 0.0970 chunk 4 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 29 optimal weight: 0.4980 chunk 26 optimal weight: 0.6980 chunk 49 optimal weight: 0.0060 overall best weight: 0.2794 ------------------------------------------------------------------------------- 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 = 0.4149 r_free = 0.4149 target = 0.171843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.134922 restraints weight = 8251.080| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 1.81 r_work: 0.3448 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6561 Z= 0.129 Angle : 0.584 11.482 9223 Z= 0.320 Chirality : 0.041 0.232 1048 Planarity : 0.006 0.064 908 Dihedral : 25.048 178.252 1685 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.66 % Favored : 95.16 % Rotamer: Outliers : 1.61 % Allowed : 20.08 % Favored : 78.31 % 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 (0.37), residues: 579 helix: 1.92 (0.32), residues: 247 sheet: -0.55 (0.66), residues: 69 loop : 0.08 (0.42), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 111 TYR 0.022 0.002 TYR A 432 PHE 0.009 0.001 PHE A 137 TRP 0.045 0.002 TRP A 626 HIS 0.003 0.001 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 ( 6561) covalent geometry : angle 0.58355 / 0.32 ( 9223) hydrogen bonds : bond 0.04219 / 4.34 ( 269) hydrogen bonds : angle 3.83317 / 4.61 ( 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: 8 poor density : 98 time to evaluate : 0.111 Fit side-chains REVERT: A 74 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7764 (mt-10) REVERT: A 95 GLU cc_start: 0.7291 (mt-10) cc_final: 0.6985 (tt0) REVERT: A 203 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7890 (mt0) REVERT: A 425 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7597 (tt) REVERT: A 463 ASN cc_start: 0.8904 (m110) cc_final: 0.8616 (m110) REVERT: A 465 MET cc_start: 0.3911 (mmm) cc_final: 0.3155 (mmm) REVERT: A 549 ASP cc_start: 0.8032 (m-30) cc_final: 0.7672 (m-30) REVERT: A 629 GLN cc_start: 0.7445 (tp40) cc_final: 0.7080 (tp40) outliers start: 8 outliers final: 4 residues processed: 101 average time/residue: 0.4908 time to fit residues: 51.7948 Evaluate side-chains 103 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 97 time to evaluate : 0.111 ------------------------------------------------------------------------------- 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 425 LEU Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 562 VAL 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: 2.9990 chunk 27 optimal weight: 0.3980 chunk 54 optimal weight: 0.8980 chunk 24 optimal weight: 0.0010 chunk 33 optimal weight: 0.0570 chunk 41 optimal weight: 0.2980 chunk 28 optimal weight: 0.8980 chunk 23 optimal weight: 0.1980 chunk 5 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 overall best weight: 0.1904 ------------------------------------------------------------------------------- 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 = 0.4163 r_free = 0.4163 target = 0.173097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.136983 restraints weight = 8363.680| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 1.77 r_work: 0.3450 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6561 Z= 0.119 Angle : 0.564 11.252 9223 Z= 0.310 Chirality : 0.040 0.231 1048 Planarity : 0.006 0.063 908 Dihedral : 24.923 178.651 1685 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.15 % Favored : 95.68 % Rotamer: Outliers : 1.41 % Allowed : 20.08 % 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: 1.22 (0.37), residues: 579 helix: 1.91 (0.32), residues: 249 sheet: -0.43 (0.66), residues: 69 loop : 0.18 (0.42), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 111 TYR 0.027 0.001 TYR A 432 PHE 0.008 0.001 PHE A 137 TRP 0.018 0.002 TRP A 270 HIS 0.002 0.001 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 ( 6561) covalent geometry : angle 0.56399 / 0.31 ( 9223) hydrogen bonds : bond 0.03971 / 4.11 ( 269) hydrogen bonds : angle 3.77147 / 4.50 ( 711) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2341.95 seconds wall clock time: 40 minutes 25.15 seconds (2425.15 seconds total)