Starting phenix.real_space_refine on Wed Aug 5 02:18:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8axb_15698/08_2026/8axb_15698.cif Found real_map, /net/cci-nas-00/data/ceres_data/8axb_15698/08_2026/8axb_15698.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8axb_15698/08_2026/8axb_15698.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8axb_15698/08_2026/8axb_15698.map" model { file = "/net/cci-nas-00/data/ceres_data/8axb_15698/08_2026/8axb_15698.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8axb_15698/08_2026/8axb_15698.cif" } resolution = 2.87 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= 0.000 sd= 0.024 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 229 5.49 5 S 10 5.16 5 C 4397 2.51 5 N 1501 2.21 5 O 2246 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: 8383 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3485 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 17, 'TRANS': 412} Chain breaks: 2 Chain: "B" Number of atoms: 4896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 4896 Classifications: {'RNA': 230} Modifications used: {'5*END': 1, 'rna2p_pur': 21, 'rna2p_pyr': 17, 'rna3p_pur': 97, 'rna3p_pyr': 95} Link IDs: {'rna2p': 38, 'rna3p': 191} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 1.48, per 1000 atoms: 0.18 Number of scatterers: 8383 At special positions: 0 Unit cell: (104, 94.016, 121.472, 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 10 16.00 P 229 15.00 O 2246 8.00 N 1501 7.00 C 4397 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: 0.65 Conformation dependent library (CDL) restraints added in 253.4 milliseconds 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 808 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 3 sheets defined 54.4% alpha, 11.9% beta 64 base pairs and 115 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 13 through 26 Processing helix chain 'A' and resid 28 through 41 Processing helix chain 'A' and resid 44 through 50 removed outlier: 3.843A pdb=" N TRP A 48 " --> pdb=" O ASP A 44 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN A 49 " --> pdb=" O PHE A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 64 removed outlier: 4.570A pdb=" N GLN A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 67 No H-bonds generated for 'chain 'A' and resid 65 through 67' Processing helix chain 'A' and resid 69 through 73 Processing helix chain 'A' and resid 76 through 95 Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 318 through 338 removed outlier: 3.905A pdb=" N HIS A 323 " --> pdb=" O ASN A 319 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N TRP A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG A 336 " --> pdb=" O GLN A 332 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS A 337 " --> pdb=" O GLN A 333 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 383 through 395 removed outlier: 3.795A pdb=" N ARG A 391 " --> pdb=" O THR A 387 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLN A 392 " --> pdb=" O GLU A 388 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLU A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 482 Processing helix chain 'A' and resid 484 through 505 removed outlier: 3.966A pdb=" N LEU A 488 " --> pdb=" O ASN A 484 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN A 489 " --> pdb=" O TYR A 485 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG A 490 " --> pdb=" O GLU A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 538 removed outlier: 3.573A pdb=" N TYR A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 550 Processing helix chain 'A' and resid 551 through 567 removed outlier: 3.658A pdb=" N GLN A 556 " --> pdb=" O ARG A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 585 removed outlier: 3.933A pdb=" N LYS A 576 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 605 Processing helix chain 'A' and resid 618 through 635 removed outlier: 3.691A pdb=" N LEU A 635 " --> pdb=" O TYR A 631 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 283 through 285 removed outlier: 6.820A pdb=" N LEU A 349 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASP A 378 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 291 through 295 Processing sheet with id=AA3, first strand: chain 'A' and resid 470 through 473 removed outlier: 6.421A pdb=" N VAL A 463 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY A 450 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N VAL A 544 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL A 449 " --> pdb=" O VAL A 544 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU A 609 " --> pdb=" O ILE A 543 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 545 " --> pdb=" O GLU A 609 " (cutoff:3.500A) 176 hydrogen bonds defined for protein. 507 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 164 hydrogen bonds 296 hydrogen bond angles 0 basepair planarities 64 basepair parallelities 115 stacking parallelities Total time for adding SS restraints: 1.34 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1490 1.33 - 1.45: 3396 1.45 - 1.57: 3675 1.57 - 1.69: 458 1.69 - 1.81: 14 Bond restraints: 9033 Sorted by residual: bond pdb=" N9 A B 24 " pdb=" C4 A B 24 " ideal model delta sigma weight residual 1.374 1.362 0.012 6.00e-03 2.78e+04 4.09e+00 bond pdb=" N3 G B 88 " pdb=" C4 G B 88 " ideal model delta sigma weight residual 1.350 1.337 0.013 7.00e-03 2.04e+04 3.65e+00 bond pdb=" N9 G B 59 " pdb=" C8 G B 59 " ideal model delta sigma weight residual 1.374 1.361 0.013 7.00e-03 2.04e+04 3.42e+00 bond pdb=" N9 G B 88 " pdb=" C4 G B 88 " ideal model delta sigma weight residual 1.375 1.361 0.014 8.00e-03 1.56e+04 3.21e+00 bond pdb=" C5 G B 88 " pdb=" C4 G B 88 " ideal model delta sigma weight residual 1.379 1.367 0.012 7.00e-03 2.04e+04 2.89e+00 ... (remaining 9028 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 12466 1.74 - 3.48: 821 3.48 - 5.22: 38 5.22 - 6.96: 7 6.96 - 8.70: 3 Bond angle restraints: 13335 Sorted by residual: angle pdb=" C1' C B 216 " pdb=" N1 C B 216 " pdb=" C2 C B 216 " ideal model delta sigma weight residual 118.80 124.39 -5.59 1.10e+00 8.26e-01 2.59e+01 angle pdb=" N1 C B 150 " pdb=" C2 C B 150 " pdb=" O2 C B 150 " ideal model delta sigma weight residual 118.90 121.82 -2.92 6.00e-01 2.78e+00 2.36e+01 angle pdb=" C1' C B 114 " pdb=" N1 C B 114 " pdb=" C2 C B 114 " ideal model delta sigma weight residual 118.80 124.12 -5.32 1.10e+00 8.26e-01 2.34e+01 angle pdb=" O5' G B 238 " pdb=" C5' G B 238 " pdb=" C4' G B 238 " ideal model delta sigma weight residual 109.40 113.07 -3.67 8.00e-01 1.56e+00 2.11e+01 angle pdb=" O5' G B 59 " pdb=" C5' G B 59 " pdb=" C4' G B 59 " ideal model delta sigma weight residual 109.40 113.00 -3.60 8.00e-01 1.56e+00 2.03e+01 ... (remaining 13330 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.37: 4609 23.37 - 46.73: 674 46.73 - 70.10: 368 70.10 - 93.47: 80 93.47 - 116.83: 4 Dihedral angle restraints: 5735 sinusoidal: 4485 harmonic: 1250 Sorted by residual: dihedral pdb=" CA PHE A 433 " pdb=" C PHE A 433 " pdb=" N GLU A 434 " pdb=" CA GLU A 434 " ideal model delta harmonic sigma weight residual 180.00 157.51 22.49 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" O4' A B 160 " pdb=" C1' A B 160 " pdb=" N9 A B 160 " pdb=" C4 A B 160 " ideal model delta sinusoidal sigma weight residual -90.00 -16.96 -73.04 1 2.00e+01 2.50e-03 1.70e+01 dihedral pdb=" CA LEU A 308 " pdb=" C LEU A 308 " pdb=" N SER A 309 " pdb=" CA SER A 309 " ideal model delta harmonic sigma weight residual 180.00 160.37 19.63 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 5732 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1139 0.044 - 0.087: 270 0.087 - 0.131: 168 0.131 - 0.175: 88 0.175 - 0.218: 1 Chirality restraints: 1666 Sorted by residual: chirality pdb=" CA GLN A 64 " pdb=" N GLN A 64 " pdb=" C GLN A 64 " pdb=" CB GLN A 64 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB ILE A 312 " pdb=" CA ILE A 312 " pdb=" CG1 ILE A 312 " pdb=" CG2 ILE A 312 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.61e-01 chirality pdb=" C1' G B 101 " pdb=" O4' G B 101 " pdb=" C2' G B 101 " pdb=" N9 G B 101 " both_signs ideal model delta sigma weight residual False 2.47 2.31 0.16 2.00e-01 2.50e+01 6.75e-01 ... (remaining 1663 not shown) Planarity restraints: 852 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 524 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.56e+00 pdb=" CG ASP A 524 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASP A 524 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP A 524 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 157 " -0.027 2.00e-02 2.50e+03 1.39e-02 5.31e+00 pdb=" N9 A B 157 " 0.037 2.00e-02 2.50e+03 pdb=" C8 A B 157 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A B 157 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A B 157 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A B 157 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A B 157 " -0.005 2.00e-02 2.50e+03 pdb=" N1 A B 157 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A B 157 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A B 157 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A B 157 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 281 " -0.037 5.00e-02 4.00e+02 5.71e-02 5.23e+00 pdb=" N PRO A 282 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 282 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 282 " -0.031 5.00e-02 4.00e+02 ... (remaining 849 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 190 2.61 - 3.18: 6955 3.18 - 3.75: 16618 3.75 - 4.33: 20953 4.33 - 4.90: 29103 Nonbonded interactions: 73819 Sorted by model distance: nonbonded pdb=" O LEU A 54 " pdb=" OH TYR A 91 " model vdw 2.036 3.040 nonbonded pdb=" O6 G B 108 " pdb=" O2 U B 183 " model vdw 2.046 2.432 nonbonded pdb=" N2 G B 168 " pdb=" O2 C B 174 " model vdw 2.067 2.496 nonbonded pdb=" NE2 GLN A 580 " pdb=" O2' G B 12 " model vdw 2.140 3.120 nonbonded pdb=" N2 G B 105 " pdb=" O2 C B 186 " model vdw 2.163 2.496 ... (remaining 73814 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: 4.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.080 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 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 0.037 9033 Z= 0.303 Angle : 0.807 8.704 13335 Z= 0.662 Chirality : 0.058 0.218 1666 Planarity : 0.005 0.057 852 Dihedral : 23.868 116.831 4927 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.53 % Allowed : 33.60 % Favored : 65.87 % 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: -0.94 (0.42), residues: 424 helix: 0.28 (0.37), residues: 191 sheet: -1.70 (0.58), residues: 77 loop : -1.00 (0.55), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 435 TYR 0.010 0.002 TYR A 89 PHE 0.016 0.002 PHE A 305 TRP 0.011 0.001 TRP A 366 HIS 0.006 0.001 HIS A 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.30 ( 9033) covalent geometry : angle 0.80699 / 0.66 (13335) hydrogen bonds : bond 0.15469 / 10.07 ( 340) hydrogen bonds : angle 6.34341 / 5.03 ( 803) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 0.112 Fit side-chains revert: symmetry clash REVERT: A 64 GLN cc_start: 0.6799 (pm20) cc_final: 0.6588 (pm20) REVERT: A 625 GLU cc_start: 0.7291 (tm-30) cc_final: 0.7062 (tm-30) outliers start: 2 outliers final: 1 residues processed: 59 average time/residue: 0.5166 time to fit residues: 32.2706 Evaluate side-chains 38 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 16 ASN A 49 GLN ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN A 580 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.130786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.104144 restraints weight = 22014.675| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 2.24 r_work: 0.3816 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.073 9033 Z= 0.448 Angle : 0.876 8.639 13335 Z= 0.468 Chirality : 0.056 0.334 1666 Planarity : 0.008 0.091 852 Dihedral : 23.920 119.427 4051 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 24.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 10.32 % Allowed : 28.31 % Favored : 61.38 % 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: -2.19 (0.40), residues: 424 helix: -0.94 (0.32), residues: 204 sheet: -2.23 (0.58), residues: 78 loop : -1.40 (0.57), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 475 TYR 0.023 0.004 TYR A 581 PHE 0.024 0.005 PHE A 514 TRP 0.012 0.003 TRP A 366 HIS 0.009 0.003 HIS A 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00878 / 0.45 ( 9033) covalent geometry : angle 0.87617 / 0.47 (13335) hydrogen bonds : bond 0.10947 / 7.52 ( 340) hydrogen bonds : angle 5.24327 / 4.03 ( 803) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 35 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: A 565 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7075 (mp10) outliers start: 39 outliers final: 12 residues processed: 67 average time/residue: 0.3857 time to fit residues: 27.8344 Evaluate side-chains 47 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 616 ARG Chi-restraints excluded: chain A residue 626 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 42 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 0.2980 chunk 62 optimal weight: 6.9990 chunk 40 optimal weight: 0.2980 chunk 44 optimal weight: 9.9990 chunk 55 optimal weight: 20.0000 chunk 12 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 584 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.137468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.111094 restraints weight = 21465.142| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 2.15 r_work: 0.3936 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9033 Z= 0.138 Angle : 0.564 7.706 13335 Z= 0.324 Chirality : 0.036 0.176 1666 Planarity : 0.005 0.062 852 Dihedral : 23.780 118.665 4051 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 6.08 % Allowed : 30.16 % Favored : 63.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.42), residues: 424 helix: 0.07 (0.34), residues: 205 sheet: -1.71 (0.59), residues: 76 loop : -0.82 (0.60), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 502 TYR 0.014 0.002 TYR A 485 PHE 0.014 0.002 PHE A 433 TRP 0.013 0.001 TRP A 366 HIS 0.004 0.001 HIS A 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.14 ( 9033) covalent geometry : angle 0.56388 / 0.32 (13335) hydrogen bonds : bond 0.07434 / 4.99 ( 340) hydrogen bonds : angle 4.42499 / 3.43 ( 803) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 38 time to evaluate : 0.129 Fit side-chains revert: symmetry clash REVERT: A 89 TYR cc_start: 0.5075 (OUTLIER) cc_final: 0.4773 (t80) REVERT: A 565 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.6953 (mp10) outliers start: 23 outliers final: 5 residues processed: 56 average time/residue: 0.2920 time to fit residues: 17.9228 Evaluate side-chains 43 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 TYR Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 565 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 43 optimal weight: 9.9990 chunk 10 optimal weight: 0.2980 chunk 38 optimal weight: 0.6980 chunk 45 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 6 optimal weight: 0.4980 chunk 21 optimal weight: 0.0980 chunk 20 optimal weight: 0.1980 chunk 48 optimal weight: 10.0000 chunk 5 optimal weight: 0.3980 chunk 36 optimal weight: 4.9990 overall best weight: 0.2980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.139724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.113715 restraints weight = 21997.790| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 2.20 r_work: 0.3970 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9033 Z= 0.115 Angle : 0.515 6.664 13335 Z= 0.297 Chirality : 0.034 0.255 1666 Planarity : 0.005 0.058 852 Dihedral : 23.624 117.716 4051 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.76 % Allowed : 30.16 % Favored : 65.08 % 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: -0.65 (0.42), residues: 424 helix: 0.36 (0.35), residues: 205 sheet: -1.61 (0.57), residues: 76 loop : -0.66 (0.60), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 502 TYR 0.024 0.002 TYR A 474 PHE 0.013 0.002 PHE A 433 TRP 0.012 0.001 TRP A 366 HIS 0.004 0.001 HIS A 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.12 ( 9033) covalent geometry : angle 0.51468 / 0.30 (13335) hydrogen bonds : bond 0.06972 / 4.77 ( 340) hydrogen bonds : angle 4.13024 / 3.23 ( 803) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 41 time to evaluate : 0.131 Fit side-chains revert: symmetry clash REVERT: A 565 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.6913 (mp10) REVERT: A 625 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7397 (tm-30) outliers start: 18 outliers final: 4 residues processed: 54 average time/residue: 0.3675 time to fit residues: 21.5319 Evaluate side-chains 44 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 565 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 0.0980 chunk 9 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 17 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 60 optimal weight: 20.0000 chunk 52 optimal weight: 9.9990 chunk 39 optimal weight: 0.6980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.136533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.110284 restraints weight = 21865.122| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 2.15 r_work: 0.3927 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9033 Z= 0.167 Angle : 0.542 7.698 13335 Z= 0.305 Chirality : 0.036 0.209 1666 Planarity : 0.005 0.055 852 Dihedral : 23.583 118.182 4050 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.70 % Allowed : 32.01 % Favored : 64.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.42), residues: 424 helix: 0.39 (0.34), residues: 206 sheet: -1.72 (0.58), residues: 77 loop : -0.64 (0.59), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 492 TYR 0.022 0.002 TYR A 497 PHE 0.016 0.002 PHE A 313 TRP 0.011 0.001 TRP A 366 HIS 0.005 0.001 HIS A 500 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.17 ( 9033) covalent geometry : angle 0.54170 / 0.31 (13335) hydrogen bonds : bond 0.07168 / 4.92 ( 340) hydrogen bonds : angle 4.11619 / 3.22 ( 803) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: A 565 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.6972 (mp10) REVERT: A 625 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7374 (tm-30) outliers start: 14 outliers final: 4 residues processed: 49 average time/residue: 0.3929 time to fit residues: 20.8996 Evaluate side-chains 42 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 565 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 40 optimal weight: 1.9990 chunk 58 optimal weight: 20.0000 chunk 16 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 42 optimal weight: 0.4980 chunk 38 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.138375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.111957 restraints weight = 21925.228| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 2.20 r_work: 0.3950 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9033 Z= 0.123 Angle : 0.506 7.621 13335 Z= 0.289 Chirality : 0.033 0.173 1666 Planarity : 0.004 0.055 852 Dihedral : 23.531 118.117 4050 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.23 % Allowed : 31.22 % Favored : 64.55 % 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: -0.49 (0.42), residues: 424 helix: 0.57 (0.35), residues: 205 sheet: -1.59 (0.57), residues: 76 loop : -0.69 (0.59), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 502 TYR 0.023 0.002 TYR A 497 PHE 0.013 0.002 PHE A 514 TRP 0.012 0.001 TRP A 366 HIS 0.007 0.001 HIS A 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 ( 9033) covalent geometry : angle 0.50643 / 0.29 (13335) hydrogen bonds : bond 0.06716 / 4.58 ( 340) hydrogen bonds : angle 4.01738 / 3.15 ( 803) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 38 time to evaluate : 0.187 Fit side-chains revert: symmetry clash REVERT: A 11 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.8110 (mp) REVERT: A 89 TYR cc_start: 0.5083 (OUTLIER) cc_final: 0.4783 (t80) REVERT: A 565 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.6912 (mp10) REVERT: A 625 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7419 (tm-30) outliers start: 16 outliers final: 7 residues processed: 51 average time/residue: 0.3727 time to fit residues: 20.7042 Evaluate side-chains 47 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 89 TYR Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 589 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 22 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 59 optimal weight: 30.0000 chunk 33 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.137927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.111416 restraints weight = 22011.280| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 2.20 r_work: 0.3933 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9033 Z= 0.143 Angle : 0.524 8.969 13335 Z= 0.296 Chirality : 0.034 0.175 1666 Planarity : 0.004 0.054 852 Dihedral : 23.469 118.188 4050 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 5.03 % Allowed : 30.42 % Favored : 64.55 % 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: -0.51 (0.41), residues: 424 helix: 0.54 (0.34), residues: 205 sheet: -1.61 (0.57), residues: 77 loop : -0.65 (0.58), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 435 TYR 0.025 0.002 TYR A 590 PHE 0.014 0.002 PHE A 514 TRP 0.011 0.001 TRP A 366 HIS 0.004 0.001 HIS A 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 ( 9033) covalent geometry : angle 0.52417 / 0.30 (13335) hydrogen bonds : bond 0.06798 / 4.66 ( 340) hydrogen bonds : angle 4.01228 / 3.13 ( 803) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 38 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: A 89 TYR cc_start: 0.5074 (OUTLIER) cc_final: 0.4714 (t80) REVERT: A 565 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.6918 (mp10) REVERT: A 625 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7440 (tm-30) outliers start: 19 outliers final: 6 residues processed: 53 average time/residue: 0.3409 time to fit residues: 19.7990 Evaluate side-chains 46 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 89 TYR Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 565 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 56 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 50 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 0.0470 chunk 20 optimal weight: 0.8980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN A 584 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.139207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.112912 restraints weight = 21744.964| |-----------------------------------------------------------------------------| r_work (start): 0.4105 rms_B_bonded: 2.19 r_work: 0.3963 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9033 Z= 0.124 Angle : 0.520 11.060 13335 Z= 0.291 Chirality : 0.033 0.205 1666 Planarity : 0.004 0.056 852 Dihedral : 23.429 118.186 4050 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.97 % Allowed : 30.95 % Favored : 65.08 % 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: -0.29 (0.42), residues: 424 helix: 0.74 (0.35), residues: 205 sheet: -1.52 (0.57), residues: 76 loop : -0.59 (0.58), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 502 TYR 0.029 0.003 TYR A 590 PHE 0.018 0.002 PHE A 13 TRP 0.012 0.001 TRP A 366 HIS 0.005 0.001 HIS A 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 ( 9033) covalent geometry : angle 0.51952 / 0.29 (13335) hydrogen bonds : bond 0.06509 / 4.44 ( 340) hydrogen bonds : angle 3.91546 / 3.07 ( 803) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: A 89 TYR cc_start: 0.5067 (OUTLIER) cc_final: 0.4722 (t80) REVERT: A 565 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.6964 (mp10) REVERT: A 625 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7374 (tm-30) outliers start: 15 outliers final: 8 residues processed: 56 average time/residue: 0.3784 time to fit residues: 22.7968 Evaluate side-chains 47 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 89 TYR Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 589 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 15 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 61 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 chunk 27 optimal weight: 0.0570 chunk 34 optimal weight: 0.0980 chunk 53 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.139354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.113135 restraints weight = 22021.360| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 2.22 r_work: 0.3981 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9033 Z= 0.124 Angle : 0.523 12.343 13335 Z= 0.292 Chirality : 0.033 0.156 1666 Planarity : 0.004 0.055 852 Dihedral : 23.403 118.116 4050 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.76 % Allowed : 30.69 % Favored : 64.55 % 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: -0.26 (0.42), residues: 424 helix: 0.73 (0.35), residues: 205 sheet: -1.42 (0.57), residues: 76 loop : -0.56 (0.59), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 492 TYR 0.034 0.002 TYR A 590 PHE 0.013 0.002 PHE A 514 TRP 0.012 0.001 TRP A 366 HIS 0.005 0.001 HIS A 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 9033) covalent geometry : angle 0.52315 / 0.29 (13335) hydrogen bonds : bond 0.06411 / 4.39 ( 340) hydrogen bonds : angle 3.92050 / 3.06 ( 803) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 41 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: A 89 TYR cc_start: 0.5080 (OUTLIER) cc_final: 0.4677 (t80) REVERT: A 362 LYS cc_start: 0.8051 (mmmt) cc_final: 0.7753 (mmmm) REVERT: A 565 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7012 (mp10) REVERT: A 625 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7351 (tm-30) outliers start: 18 outliers final: 10 residues processed: 56 average time/residue: 0.3526 time to fit residues: 21.4759 Evaluate side-chains 51 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 89 TYR Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 589 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 6 optimal weight: 0.5980 chunk 47 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 56 optimal weight: 8.9990 chunk 30 optimal weight: 0.0980 chunk 38 optimal weight: 0.0870 chunk 4 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.139019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.112631 restraints weight = 21899.409| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 2.21 r_work: 0.3974 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9033 Z= 0.131 Angle : 0.537 13.256 13335 Z= 0.297 Chirality : 0.033 0.205 1666 Planarity : 0.004 0.053 852 Dihedral : 23.383 118.173 4050 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.23 % Allowed : 31.48 % Favored : 64.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.42), residues: 424 helix: 0.76 (0.35), residues: 205 sheet: -1.45 (0.57), residues: 77 loop : -0.44 (0.59), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 391 TYR 0.023 0.002 TYR A 497 PHE 0.013 0.002 PHE A 514 TRP 0.012 0.001 TRP A 366 HIS 0.004 0.001 HIS A 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 ( 9033) covalent geometry : angle 0.53658 / 0.30 (13335) hydrogen bonds : bond 0.06367 / 4.35 ( 340) hydrogen bonds : angle 3.90578 / 3.05 ( 803) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 39 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: A 89 TYR cc_start: 0.5062 (OUTLIER) cc_final: 0.4626 (t80) REVERT: A 362 LYS cc_start: 0.8041 (mmmt) cc_final: 0.7745 (mmmm) REVERT: A 565 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7089 (mp10) REVERT: A 625 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7348 (tm-30) outliers start: 16 outliers final: 10 residues processed: 51 average time/residue: 0.3639 time to fit residues: 20.4140 Evaluate side-chains 49 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 89 TYR Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 589 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 56 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 8 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 0.0670 chunk 32 optimal weight: 0.7980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.140021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.113802 restraints weight = 22260.028| |-----------------------------------------------------------------------------| r_work (start): 0.4122 rms_B_bonded: 2.23 r_work: 0.3982 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 9033 Z= 0.121 Angle : 0.524 13.165 13335 Z= 0.291 Chirality : 0.032 0.240 1666 Planarity : 0.004 0.055 852 Dihedral : 23.365 118.082 4050 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.17 % Allowed : 32.54 % Favored : 64.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.42), residues: 424 helix: 0.70 (0.35), residues: 205 sheet: -1.34 (0.57), residues: 77 loop : -0.45 (0.58), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 391 TYR 0.024 0.002 TYR A 497 PHE 0.024 0.002 PHE A 13 TRP 0.014 0.001 TRP A 588 HIS 0.006 0.001 HIS A 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 ( 9033) covalent geometry : angle 0.52426 / 0.29 (13335) hydrogen bonds : bond 0.06232 / 4.26 ( 340) hydrogen bonds : angle 3.81666 / 2.98 ( 803) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2595.81 seconds wall clock time: 44 minutes 54.23 seconds (2694.23 seconds total)