Starting phenix.real_space_refine on Sat May 10 12:09:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wrp_37785/05_2025/8wrp_37785.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wrp_37785/05_2025/8wrp_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8wrp_37785/05_2025/8wrp_37785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wrp_37785/05_2025/8wrp_37785.map" model { file = "/net/cci-nas-00/data/ceres_data/8wrp_37785/05_2025/8wrp_37785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wrp_37785/05_2025/8wrp_37785.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.78, per 1000 atoms: 0.76 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: 1.77 Conformation dependent library (CDL) restraints added in 716.7 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: 2.24 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: 2.22 Time building geometry restraints manager: 2.03 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=" CA SER A 255 " pdb=" C SER A 255 " ideal model delta sigma weight residual 1.524 1.499 0.024 1.33e-02 5.65e+03 3.32e+00 bond pdb=" O3' G B -4 " pdb=" P A B -3 " ideal model delta sigma weight residual 1.607 1.634 -0.027 1.50e-02 4.44e+03 3.32e+00 bond pdb=" O3' DC C -11 " pdb=" P DA C -10 " ideal model delta sigma weight residual 1.607 1.634 -0.027 1.50e-02 4.44e+03 3.24e+00 bond pdb=" O3' C B 3 " pdb=" P C B 4 " ideal model delta sigma weight residual 1.607 1.631 -0.024 1.50e-02 4.44e+03 2.66e+00 bond pdb=" O3' DG C -12 " pdb=" P DC C -11 " ideal model delta sigma weight residual 1.607 1.631 -0.024 1.50e-02 4.44e+03 2.60e+00 ... (remaining 6556 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 8955 1.63 - 3.27: 228 3.27 - 4.90: 29 4.90 - 6.54: 10 6.54 - 8.17: 1 Bond angle restraints: 9223 Sorted by residual: angle pdb=" O LEU A 254 " pdb=" C LEU A 254 " pdb=" N SER A 255 " ideal model delta sigma weight residual 123.03 118.95 4.08 1.13e+00 7.83e-01 1.31e+01 angle pdb=" C4' G B -4 " pdb=" C3' G B -4 " pdb=" O3' G B -4 " ideal model delta sigma weight residual 113.00 118.33 -5.33 1.50e+00 4.44e-01 1.26e+01 angle pdb=" CA LEU A 254 " pdb=" C LEU A 254 " pdb=" N SER A 255 " ideal model delta sigma weight residual 115.23 119.41 -4.18 1.30e+00 5.92e-01 1.04e+01 angle pdb=" O4' C B 4 " pdb=" C4' C B 4 " pdb=" C3' C B 4 " ideal model delta sigma weight residual 104.00 106.96 -2.96 1.00e+00 1.00e+00 8.76e+00 angle pdb=" O2' C B 4 " pdb=" C2' C B 4 " pdb=" C1' C B 4 " ideal model delta sigma weight residual 108.40 112.74 -4.34 1.50e+00 4.44e-01 8.36e+00 ... (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: 901 0.055 - 0.109: 123 0.109 - 0.164: 21 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: 3.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 20.460 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:10.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 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= 0.175 Angle : 0.612 8.172 9223 Z= 0.345 Chirality : 0.041 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (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 TRP 0.014 0.002 TRP A 626 HIS 0.007 0.001 HIS A 641 PHE 0.012 0.001 PHE A 137 TYR 0.013 0.002 TYR A 432 ARG 0.008 0.001 ARG A 267 Details of bonding type rmsd hydrogen bonds : bond 0.20605 ( 269) hydrogen bonds : angle 7.21334 ( 711) covalent geometry : bond 0.00363 ( 6561) covalent geometry : angle 0.61167 ( 9223) *********************** 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 : 0.606 Fit side-chains revert: symmetry clash REVERT: A 95 GLU cc_start: 0.6636 (mt-10) cc_final: 0.6342 (mt-10) 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: 0.7870 (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: 1.3861 time to fit residues: 156.0129 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 : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 6.9990 chunk 48 optimal weight: 0.0470 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 0.0770 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 8.9990 chunk 19 optimal weight: 0.1980 chunk 30 optimal weight: 0.4980 chunk 37 optimal weight: 0.4980 chunk 58 optimal weight: 0.9990 overall best weight: 0.2636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN A 64 ASN A 99 ASN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN A 632 HIS ** A 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.173024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.135474 restraints weight = 8276.777| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 1.89 r_work: 0.3435 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6561 Z= 0.142 Angle : 0.598 5.776 9223 Z= 0.321 Chirality : 0.040 0.142 1048 Planarity : 0.006 0.066 908 Dihedral : 25.161 179.414 1685 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.20 % Allowed : 10.84 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.37), residues: 579 helix: 1.65 (0.33), residues: 249 sheet: -0.59 (0.67), residues: 70 loop : 0.06 (0.42), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 249 HIS 0.004 0.001 HIS A 641 PHE 0.010 0.001 PHE A 137 TYR 0.024 0.002 TYR A 529 ARG 0.007 0.001 ARG A 111 Details of bonding type rmsd hydrogen bonds : bond 0.04731 ( 269) hydrogen bonds : angle 4.16767 ( 711) covalent geometry : bond 0.00308 ( 6561) covalent geometry : angle 0.59828 ( 9223) *********************** 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 108 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 102 time to evaluate : 0.600 Fit side-chains revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7696 (mt-10) REVERT: A 549 ASP cc_start: 0.8038 (m-30) cc_final: 0.7762 (m-30) REVERT: A 585 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.8038 (ttp-170) REVERT: A 629 GLN cc_start: 0.7498 (tp40) cc_final: 0.7163 (tp40) outliers start: 6 outliers final: 2 residues processed: 102 average time/residue: 1.2292 time to fit residues: 131.2534 Evaluate side-chains 101 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 97 time to evaluate : 0.544 ------------------------------------------------------------------------------- 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 27 optimal weight: 0.9980 chunk 33 optimal weight: 0.0870 chunk 48 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 39 optimal weight: 0.1980 chunk 45 optimal weight: 3.9990 chunk 38 optimal weight: 0.0020 chunk 25 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.3966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 541 GLN A 632 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.172745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.132037 restraints weight = 8264.670| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.69 r_work: 0.3431 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6561 Z= 0.152 Angle : 0.573 7.906 9223 Z= 0.304 Chirality : 0.040 0.139 1048 Planarity : 0.006 0.064 908 Dihedral : 25.109 179.294 1685 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.01 % Allowed : 12.45 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.37), residues: 579 helix: 1.75 (0.32), residues: 249 sheet: -0.53 (0.67), residues: 71 loop : 0.22 (0.43), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 249 HIS 0.006 0.001 HIS A 641 PHE 0.010 0.001 PHE A 137 TYR 0.014 0.002 TYR A 529 ARG 0.007 0.001 ARG A 111 Details of bonding type rmsd hydrogen bonds : bond 0.04307 ( 269) hydrogen bonds : angle 3.78854 ( 711) covalent geometry : bond 0.00335 ( 6561) covalent geometry : angle 0.57296 ( 9223) *********************** 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 113 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7806 (mt-10) REVERT: A 86 GLU cc_start: 0.7748 (tt0) cc_final: 0.7366 (mt-10) REVERT: A 95 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6914 (mt-10) REVERT: A 203 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7911 (mt0) REVERT: A 330 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7331 (pt0) REVERT: A 427 LYS cc_start: 0.7555 (mppt) cc_final: 0.7341 (mppt) REVERT: A 463 ASN cc_start: 0.8850 (m110) cc_final: 0.8536 (m110) REVERT: A 549 ASP cc_start: 0.8028 (m-30) cc_final: 0.7680 (m-30) REVERT: A 629 GLN cc_start: 0.7486 (tp40) cc_final: 0.7117 (tp40) outliers start: 10 outliers final: 5 residues processed: 105 average time/residue: 1.2278 time to fit residues: 135.1310 Evaluate side-chains 101 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.552 ------------------------------------------------------------------------------- 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 330 GLU 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 631 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 9 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 36 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.171064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.133745 restraints weight = 8363.578| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.89 r_work: 0.3394 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6561 Z= 0.192 Angle : 0.607 8.819 9223 Z= 0.321 Chirality : 0.042 0.142 1048 Planarity : 0.006 0.065 908 Dihedral : 25.159 179.517 1685 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.21 % Allowed : 14.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.36), residues: 579 helix: 1.81 (0.32), residues: 248 sheet: -0.55 (0.66), residues: 74 loop : 0.24 (0.42), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 249 HIS 0.007 0.002 HIS A 214 PHE 0.011 0.002 PHE A 635 TYR 0.018 0.002 TYR A 432 ARG 0.009 0.001 ARG A 111 Details of bonding type rmsd hydrogen bonds : bond 0.04348 ( 269) hydrogen bonds : angle 3.78579 ( 711) covalent geometry : bond 0.00428 ( 6561) covalent geometry : angle 0.60724 ( 9223) *********************** 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: 16 poor density : 97 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7789 (mt-10) REVERT: A 86 GLU cc_start: 0.7780 (tt0) cc_final: 0.7404 (mt-10) REVERT: A 95 GLU cc_start: 0.7325 (mt-10) cc_final: 0.6969 (mt-10) REVERT: A 203 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7924 (mt0) REVERT: A 330 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7345 (pt0) REVERT: A 427 LYS cc_start: 0.7670 (mppt) cc_final: 0.7347 (mppt) REVERT: A 463 ASN cc_start: 0.8878 (m110) cc_final: 0.8584 (m110) REVERT: A 465 MET cc_start: 0.3671 (OUTLIER) cc_final: 0.3122 (mmm) REVERT: A 549 ASP cc_start: 0.8042 (m-30) cc_final: 0.7707 (m-30) REVERT: A 629 GLN cc_start: 0.7536 (tp40) cc_final: 0.7177 (tp40) outliers start: 16 outliers final: 9 residues processed: 103 average time/residue: 1.2132 time to fit residues: 130.8522 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 : 0.546 ------------------------------------------------------------------------------- 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 291 LYS Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 453 GLU 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 631 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 34 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 0.0070 chunk 45 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 36 optimal weight: 0.0980 chunk 52 optimal weight: 0.0770 chunk 33 optimal weight: 0.0980 chunk 50 optimal weight: 1.9990 overall best weight: 0.1756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4165 r_free = 0.4165 target = 0.173960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.136231 restraints weight = 8379.782| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.87 r_work: 0.3466 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6561 Z= 0.117 Angle : 0.537 5.608 9223 Z= 0.285 Chirality : 0.038 0.133 1048 Planarity : 0.005 0.061 908 Dihedral : 25.044 178.482 1685 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.41 % Allowed : 16.27 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.37), residues: 579 helix: 1.99 (0.33), residues: 252 sheet: -0.38 (0.68), residues: 69 loop : 0.24 (0.43), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 249 HIS 0.004 0.001 HIS A 214 PHE 0.007 0.001 PHE A 137 TYR 0.017 0.001 TYR A 432 ARG 0.009 0.000 ARG A 111 Details of bonding type rmsd hydrogen bonds : bond 0.03680 ( 269) hydrogen bonds : angle 3.55171 ( 711) covalent geometry : bond 0.00252 ( 6561) covalent geometry : angle 0.53745 ( 9223) *********************** 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 114 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7541 (mt-10) REVERT: A 86 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7541 (mt-10) REVERT: A 95 GLU cc_start: 0.7261 (mt-10) cc_final: 0.6839 (mt-10) REVERT: A 203 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7818 (mt0) REVERT: A 330 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7119 (pt0) REVERT: A 402 SER cc_start: 0.7993 (m) cc_final: 0.7753 (m) REVERT: A 463 ASN cc_start: 0.8841 (m110) cc_final: 0.8549 (m110) REVERT: A 549 ASP cc_start: 0.8024 (m-30) cc_final: 0.7664 (m-30) REVERT: A 629 GLN cc_start: 0.7457 (tp40) cc_final: 0.7092 (tp40) outliers start: 12 outliers final: 3 residues processed: 106 average time/residue: 1.2728 time to fit residues: 140.9059 Evaluate side-chains 105 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 529 TYR Chi-restraints excluded: chain A residue 547 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 0.0970 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 10 optimal weight: 0.0970 chunk 35 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 23 optimal weight: 0.0870 chunk 22 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 0.0370 chunk 19 optimal weight: 1.9990 overall best weight: 0.1832 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 99 ASN A 250 GLN 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 = 0.4171 r_free = 0.4171 target = 0.174490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.137087 restraints weight = 8418.409| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 1.86 r_work: 0.3473 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6561 Z= 0.115 Angle : 0.530 5.815 9223 Z= 0.279 Chirality : 0.037 0.132 1048 Planarity : 0.005 0.059 908 Dihedral : 24.935 178.379 1685 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.41 % Allowed : 17.47 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.37), residues: 579 helix: 2.16 (0.33), residues: 248 sheet: -0.29 (0.68), residues: 69 loop : 0.30 (0.43), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 249 HIS 0.004 0.001 HIS A 214 PHE 0.008 0.001 PHE A 137 TYR 0.017 0.001 TYR A 432 ARG 0.010 0.000 ARG A 111 Details of bonding type rmsd hydrogen bonds : bond 0.03517 ( 269) hydrogen bonds : angle 3.51261 ( 711) covalent geometry : bond 0.00251 ( 6561) covalent geometry : angle 0.52998 ( 9223) *********************** 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 107 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.592 Fit side-chains revert: symmetry clash REVERT: A 74 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7576 (mt-10) REVERT: A 95 GLU cc_start: 0.7263 (mt-10) cc_final: 0.6862 (mt-10) REVERT: A 106 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.7202 (tpm170) REVERT: A 203 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7832 (mt0) REVERT: A 330 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.7137 (pt0) REVERT: A 463 ASN cc_start: 0.8899 (m110) cc_final: 0.8596 (m110) REVERT: A 549 ASP cc_start: 0.8025 (m-30) cc_final: 0.7650 (m-30) REVERT: A 629 GLN cc_start: 0.7474 (tp40) cc_final: 0.7095 (tp40) outliers start: 12 outliers final: 7 residues processed: 100 average time/residue: 1.3336 time to fit residues: 139.2353 Evaluate side-chains 100 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLU 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 287 GLU Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 529 TYR Chi-restraints excluded: chain A residue 547 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 52 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 99 ASN A 195 ASN A 250 GLN A 269 ASN A 632 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.169952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.124756 restraints weight = 8288.227| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.71 r_work: 0.3387 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 6561 Z= 0.248 Angle : 0.633 6.832 9223 Z= 0.332 Chirality : 0.043 0.144 1048 Planarity : 0.006 0.062 908 Dihedral : 25.009 178.662 1685 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.84 % Favored : 94.99 % Rotamer: Outliers : 3.01 % Allowed : 16.87 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.37), residues: 579 helix: 1.90 (0.32), residues: 249 sheet: -0.54 (0.65), residues: 74 loop : 0.19 (0.43), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 626 HIS 0.008 0.002 HIS A 641 PHE 0.013 0.002 PHE A 635 TYR 0.019 0.002 TYR A 432 ARG 0.012 0.001 ARG A 111 Details of bonding type rmsd hydrogen bonds : bond 0.04498 ( 269) hydrogen bonds : angle 3.78975 ( 711) covalent geometry : bond 0.00560 ( 6561) covalent geometry : angle 0.63284 ( 9223) *********************** 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 111 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7792 (mt-10) REVERT: A 95 GLU cc_start: 0.7443 (mt-10) cc_final: 0.7231 (mt-10) REVERT: A 203 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7955 (mt0) REVERT: A 292 GLU cc_start: 0.8045 (pt0) cc_final: 0.7738 (pt0) REVERT: A 330 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7360 (pt0) REVERT: A 425 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7695 (tt) REVERT: A 427 LYS cc_start: 0.7716 (OUTLIER) cc_final: 0.7418 (tppt) REVERT: A 463 ASN cc_start: 0.8934 (m110) cc_final: 0.8626 (m110) REVERT: A 549 ASP cc_start: 0.7985 (m-30) cc_final: 0.7599 (m-30) REVERT: A 629 GLN cc_start: 0.7458 (tp40) cc_final: 0.7080 (tp40) outliers start: 15 outliers final: 10 residues processed: 102 average time/residue: 1.2260 time to fit residues: 131.0293 Evaluate side-chains 110 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLU 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 291 LYS Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 427 LYS 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 631 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 56 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 30 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 34 optimal weight: 0.4980 chunk 0 optimal weight: 0.9990 chunk 25 optimal weight: 0.2980 chunk 3 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4123 r_free = 0.4123 target = 0.169899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.131758 restraints weight = 8210.257| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.86 r_work: 0.3406 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6561 Z= 0.181 Angle : 0.596 6.514 9223 Z= 0.314 Chirality : 0.040 0.137 1048 Planarity : 0.006 0.061 908 Dihedral : 24.944 178.232 1685 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.32 % Favored : 95.51 % Rotamer: Outliers : 2.61 % Allowed : 18.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.37), residues: 579 helix: 1.91 (0.32), residues: 249 sheet: -0.48 (0.66), residues: 74 loop : 0.23 (0.43), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 249 HIS 0.006 0.001 HIS A 214 PHE 0.010 0.001 PHE A 635 TYR 0.024 0.002 TYR A 432 ARG 0.013 0.000 ARG A 111 Details of bonding type rmsd hydrogen bonds : bond 0.04084 ( 269) hydrogen bonds : angle 3.67909 ( 711) covalent geometry : bond 0.00407 ( 6561) covalent geometry : angle 0.59599 ( 9223) *********************** 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 111 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7762 (mt-10) REVERT: A 86 GLU cc_start: 0.7801 (tt0) cc_final: 0.7413 (mt-10) REVERT: A 95 GLU cc_start: 0.7343 (mt-10) cc_final: 0.6849 (mt-10) REVERT: A 203 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7889 (mt0) REVERT: A 292 GLU cc_start: 0.8014 (pt0) cc_final: 0.7746 (pt0) REVERT: A 330 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7274 (pt0) REVERT: A 425 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7730 (tt) REVERT: A 427 LYS cc_start: 0.7763 (mtpt) cc_final: 0.7483 (tppt) REVERT: A 463 ASN cc_start: 0.8874 (m110) cc_final: 0.8593 (m110) REVERT: A 549 ASP cc_start: 0.8019 (m-30) cc_final: 0.7661 (m-30) REVERT: A 629 GLN cc_start: 0.7510 (tp40) cc_final: 0.7144 (tp40) outliers start: 13 outliers final: 9 residues processed: 103 average time/residue: 1.2406 time to fit residues: 133.7437 Evaluate side-chains 113 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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 291 LYS Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 351 THR 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 631 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 46 optimal weight: 4.9990 chunk 32 optimal weight: 0.4980 chunk 2 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 26 optimal weight: 0.2980 chunk 36 optimal weight: 0.0870 chunk 27 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 28 optimal weight: 0.1980 chunk 11 optimal weight: 0.7980 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 250 GLN A 632 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.172580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.135617 restraints weight = 8425.758| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.92 r_work: 0.3422 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6561 Z= 0.141 Angle : 0.570 7.625 9223 Z= 0.300 Chirality : 0.038 0.135 1048 Planarity : 0.006 0.065 908 Dihedral : 24.796 177.538 1685 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.97 % Favored : 95.85 % Rotamer: Outliers : 2.21 % Allowed : 19.68 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.37), residues: 579 helix: 1.97 (0.32), residues: 250 sheet: -0.30 (0.68), residues: 71 loop : 0.34 (0.43), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 249 HIS 0.004 0.001 HIS A 214 PHE 0.008 0.001 PHE A 137 TYR 0.022 0.002 TYR A 432 ARG 0.014 0.001 ARG A 111 Details of bonding type rmsd hydrogen bonds : bond 0.03817 ( 269) hydrogen bonds : angle 3.59260 ( 711) covalent geometry : bond 0.00311 ( 6561) covalent geometry : angle 0.56985 ( 9223) *********************** 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 110 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7760 (mt-10) REVERT: A 86 GLU cc_start: 0.7855 (tt0) cc_final: 0.7571 (mt-10) REVERT: A 95 GLU cc_start: 0.7333 (mt-10) cc_final: 0.6898 (mt-10) REVERT: A 203 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7881 (mt0) REVERT: A 330 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7234 (pt0) REVERT: A 425 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7656 (tt) REVERT: A 427 LYS cc_start: 0.7710 (mtpt) cc_final: 0.7429 (tppt) REVERT: A 463 ASN cc_start: 0.8845 (m110) cc_final: 0.8504 (m110) REVERT: A 549 ASP cc_start: 0.8053 (m-30) cc_final: 0.7716 (m-30) REVERT: A 629 GLN cc_start: 0.7559 (tp40) cc_final: 0.7193 (tp40) outliers start: 11 outliers final: 6 residues processed: 104 average time/residue: 1.2289 time to fit residues: 134.1734 Evaluate side-chains 110 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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 330 GLU Chi-restraints excluded: chain A residue 351 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 62 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 12 optimal weight: 0.8980 chunk 37 optimal weight: 0.0870 chunk 56 optimal weight: 0.8980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 250 GLN A 632 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.170585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.133191 restraints weight = 8429.714| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.95 r_work: 0.3387 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6561 Z= 0.190 Angle : 0.623 7.821 9223 Z= 0.325 Chirality : 0.041 0.159 1048 Planarity : 0.006 0.060 908 Dihedral : 24.775 177.734 1685 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.32 % Favored : 95.51 % Rotamer: Outliers : 2.41 % Allowed : 19.88 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.37), residues: 579 helix: 1.85 (0.32), residues: 252 sheet: -0.49 (0.66), residues: 74 loop : 0.27 (0.43), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 304 HIS 0.005 0.001 HIS A 641 PHE 0.012 0.001 PHE A 137 TYR 0.021 0.002 TYR A 432 ARG 0.015 0.001 ARG A 111 Details of bonding type rmsd hydrogen bonds : bond 0.04195 ( 269) hydrogen bonds : angle 3.69673 ( 711) covalent geometry : bond 0.00428 ( 6561) covalent geometry : angle 0.62260 ( 9223) ********************** 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 110 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7755 (mt-10) REVERT: A 86 GLU cc_start: 0.7864 (tt0) cc_final: 0.7583 (mt-10) REVERT: A 95 GLU cc_start: 0.7419 (mt-10) cc_final: 0.6995 (mt-10) REVERT: A 203 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7936 (mt0) REVERT: A 330 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7332 (pt0) REVERT: A 425 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7742 (tt) REVERT: A 427 LYS cc_start: 0.7739 (mtpt) cc_final: 0.7463 (tppt) REVERT: A 442 GLN cc_start: 0.7673 (tm-30) cc_final: 0.7141 (tm-30) REVERT: A 463 ASN cc_start: 0.8856 (m110) cc_final: 0.8526 (m110) REVERT: A 549 ASP cc_start: 0.8067 (m-30) cc_final: 0.7719 (m-30) REVERT: A 551 THR cc_start: 0.7932 (t) cc_final: 0.7666 (p) REVERT: A 629 GLN cc_start: 0.7592 (tp40) cc_final: 0.7250 (tp40) outliers start: 12 outliers final: 8 residues processed: 104 average time/residue: 1.2569 time to fit residues: 136.8117 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 : 0.582 ------------------------------------------------------------------------------- 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 330 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 372 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 6 optimal weight: 0.0970 chunk 60 optimal weight: 0.0970 chunk 34 optimal weight: 0.4980 chunk 39 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 GLN A 632 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.171341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.130836 restraints weight = 8533.659| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.79 r_work: 0.3413 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6561 Z= 0.168 Angle : 0.616 10.563 9223 Z= 0.318 Chirality : 0.040 0.174 1048 Planarity : 0.006 0.062 908 Dihedral : 24.689 177.308 1685 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.32 % Favored : 95.51 % Rotamer: Outliers : 2.41 % Allowed : 20.08 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.37), residues: 579 helix: 1.87 (0.32), residues: 252 sheet: -0.41 (0.67), residues: 71 loop : 0.26 (0.43), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 249 HIS 0.004 0.001 HIS A 641 PHE 0.010 0.001 PHE A 635 TYR 0.020 0.002 TYR A 432 ARG 0.014 0.001 ARG A 111 Details of bonding type rmsd hydrogen bonds : bond 0.04014 ( 269) hydrogen bonds : angle 3.65320 ( 711) covalent geometry : bond 0.00376 ( 6561) covalent geometry : angle 0.61551 ( 9223) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5814.15 seconds wall clock time: 100 minutes 32.63 seconds (6032.63 seconds total)