Starting phenix.real_space_refine on Thu Jul 2 09:48:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8axb_15698/07_2026/8axb_15698.cif Found real_map, /net/cci-nas-00/data/ceres_data/8axb_15698/07_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_15698/07_2026/8axb_15698.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8axb_15698/07_2026/8axb_15698.map" model { file = "/net/cci-nas-00/data/ceres_data/8axb_15698/07_2026/8axb_15698.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8axb_15698/07_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-dev-6108/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: 1.27, per 1000 atoms: 0.15 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: 0.40 Conformation dependent library (CDL) restraints added in 161.6 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: 0.85 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: 1.16 Time building geometry restraints manager: 0.57 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: 13035 1.74 - 3.48: 255 3.48 - 5.22: 35 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=" O2 C B 150 " pdb=" C2 C B 150 " pdb=" N3 C B 150 " ideal model delta sigma weight residual 121.90 118.76 3.14 7.00e-01 2.04e+00 2.02e+01 angle pdb=" C1' C B 150 " pdb=" N1 C B 150 " pdb=" C2 C B 150 " ideal model delta sigma weight residual 118.80 123.53 -4.73 1.10e+00 8.26e-01 1.85e+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: 1392 0.044 - 0.087: 226 0.087 - 0.131: 41 0.131 - 0.175: 6 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' C B 109 " pdb=" O4' C B 109 " pdb=" C2' C B 109 " pdb=" N1 C B 109 " both_signs ideal model delta sigma weight residual False 2.47 2.31 0.16 2.00e-01 2.50e+01 6.03e-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: 3.500 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 6.800 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.880 ------------------------------------------------------------------------------- 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= 0.280 Angle : 0.620 8.704 13335 Z= 0.519 Chirality : 0.034 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 0.00355 / 0.28 ( 9033) covalent geometry : angle 0.61982 / 0.52 (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 : 0.122 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: 0.4877 time to fit residues: 30.5102 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 : 0.114 ------------------------------------------------------------------------------- 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: 10.0000 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 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: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.131665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.104760 restraints weight = 21956.134| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 2.42 r_work: 0.3829 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 9033 Z= 0.388 Angle : 0.739 7.537 13335 Z= 0.423 Chirality : 0.046 0.219 1666 Planarity : 0.008 0.081 852 Dihedral : 23.873 120.635 4051 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 22.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 8.99 % Allowed : 28.57 % Favored : 62.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.40), residues: 424 helix: -0.63 (0.33), residues: 203 sheet: -2.12 (0.59), residues: 78 loop : -1.38 (0.57), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 71 TYR 0.021 0.003 TYR A 581 PHE 0.022 0.004 PHE A 514 TRP 0.012 0.003 TRP A 21 HIS 0.006 0.002 HIS A 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00757 / 0.39 ( 9033) covalent geometry : angle 0.73942 / 0.42 (13335) hydrogen bonds : bond 0.10142 / 6.99 ( 340) hydrogen bonds : angle 5.05544 / 3.89 ( 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 70 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 36 time to evaluate : 0.119 Fit side-chains revert: symmetry clash REVERT: A 330 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7491 (mm-30) REVERT: A 560 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7913 (tp40) REVERT: A 565 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7066 (mp10) outliers start: 34 outliers final: 11 residues processed: 64 average time/residue: 0.3507 time to fit residues: 24.1722 Evaluate side-chains 45 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 32 time to evaluate : 0.115 ------------------------------------------------------------------------------- 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 560 GLN Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 589 SER 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: 0.8980 chunk 41 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 40 optimal weight: 0.2980 chunk 44 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 chunk 12 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 16 ASN A 560 GLN A 584 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.136880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.110420 restraints weight = 21519.736| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 2.15 r_work: 0.3919 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9033 Z= 0.148 Angle : 0.538 7.646 13335 Z= 0.318 Chirality : 0.035 0.176 1666 Planarity : 0.005 0.062 852 Dihedral : 23.813 119.537 4051 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 5.82 % Allowed : 30.95 % Favored : 63.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.42), residues: 424 helix: 0.01 (0.34), residues: 206 sheet: -1.83 (0.58), residues: 78 loop : -0.76 (0.60), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 350 TYR 0.011 0.002 TYR A 485 PHE 0.014 0.002 PHE A 325 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 0.00292 / 0.15 ( 9033) covalent geometry : angle 0.53819 / 0.32 (13335) hydrogen bonds : bond 0.07207 / 4.86 ( 340) hydrogen bonds : angle 4.42358 / 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 58 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 36 time to evaluate : 0.117 Fit side-chains revert: symmetry clash REVERT: A 560 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7654 (tp40) REVERT: A 565 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.6934 (mp10) outliers start: 22 outliers final: 6 residues processed: 54 average time/residue: 0.3725 time to fit residues: 21.7668 Evaluate side-chains 43 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 560 GLN Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 616 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 43 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 45 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 6 optimal weight: 0.0470 chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 48 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 overall best weight: 0.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 560 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.137564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.111258 restraints weight = 22183.603| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 2.20 r_work: 0.3927 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9033 Z= 0.148 Angle : 0.520 6.707 13335 Z= 0.306 Chirality : 0.034 0.240 1666 Planarity : 0.005 0.058 852 Dihedral : 23.722 118.805 4051 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 5.56 % Allowed : 29.10 % Favored : 65.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.42), residues: 424 helix: 0.33 (0.35), residues: 200 sheet: -1.77 (0.57), residues: 77 loop : -0.62 (0.58), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 502 TYR 0.016 0.002 TYR A 474 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 0.00290 / 0.15 ( 9033) covalent geometry : angle 0.51987 / 0.31 (13335) hydrogen bonds : bond 0.07077 / 4.83 ( 340) hydrogen bonds : angle 4.21820 / 3.28 ( 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 58 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 37 time to evaluate : 0.135 Fit side-chains revert: symmetry clash REVERT: A 298 LYS cc_start: 0.7316 (OUTLIER) cc_final: 0.7063 (tttt) REVERT: A 560 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7592 (tp40) REVERT: A 565 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.6917 (mp10) REVERT: A 625 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7479 (tm-30) outliers start: 21 outliers final: 9 residues processed: 55 average time/residue: 0.3216 time to fit residues: 19.3655 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 : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 589 SER 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: 0.0010 chunk 9 optimal weight: 0.7980 chunk 47 optimal weight: 9.9990 chunk 17 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 52 optimal weight: 10.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.138836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.112717 restraints weight = 21971.486| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 2.18 r_work: 0.3949 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.1872 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= 0.126 Angle : 0.494 6.838 13335 Z= 0.292 Chirality : 0.033 0.182 1666 Planarity : 0.004 0.057 852 Dihedral : 23.670 118.693 4050 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 5.82 % Allowed : 29.63 % 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: -0.60 (0.42), residues: 424 helix: 0.48 (0.35), residues: 204 sheet: -1.70 (0.57), residues: 76 loop : -0.68 (0.59), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 502 TYR 0.009 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 0.00247 / 0.13 ( 9033) covalent geometry : angle 0.49356 / 0.29 (13335) hydrogen bonds : bond 0.06761 / 4.62 ( 340) hydrogen bonds : angle 4.07026 / 3.18 ( 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 60 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 38 time to evaluate : 0.133 Fit side-chains revert: symmetry clash REVERT: A 298 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.7053 (tttt) REVERT: A 565 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.6903 (mp10) REVERT: A 625 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7364 (tm-30) outliers start: 22 outliers final: 7 residues processed: 56 average time/residue: 0.3612 time to fit residues: 21.8315 Evaluate side-chains 45 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.188 ------------------------------------------------------------------------------- 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 298 LYS Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 589 SER 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: 10.0000 chunk 16 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 8 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 21 optimal weight: 9.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 560 GLN A 584 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.137312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.110808 restraints weight = 21932.837| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 2.21 r_work: 0.3937 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9033 Z= 0.155 Angle : 0.511 8.455 13335 Z= 0.297 Chirality : 0.034 0.209 1666 Planarity : 0.005 0.055 852 Dihedral : 23.626 118.635 4050 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 6.61 % Allowed : 28.57 % Favored : 64.81 % 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: -0.56 (0.42), residues: 424 helix: 0.53 (0.35), residues: 205 sheet: -1.71 (0.56), residues: 77 loop : -0.70 (0.59), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 502 TYR 0.032 0.002 TYR A 474 PHE 0.014 0.002 PHE A 514 TRP 0.011 0.001 TRP A 366 HIS 0.005 0.001 HIS A 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 ( 9033) covalent geometry : angle 0.51056 / 0.30 (13335) hydrogen bonds : bond 0.06857 / 4.71 ( 340) hydrogen bonds : angle 4.05720 / 3.16 ( 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 62 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 37 time to evaluate : 0.172 Fit side-chains revert: symmetry clash REVERT: A 89 TYR cc_start: 0.5108 (OUTLIER) cc_final: 0.4814 (t80) REVERT: A 298 LYS cc_start: 0.7334 (OUTLIER) cc_final: 0.7126 (ttmt) REVERT: A 560 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7483 (tp40) REVERT: A 565 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.6888 (mp10) REVERT: A 625 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7413 (tm-30) outliers start: 25 outliers final: 9 residues processed: 57 average time/residue: 0.3288 time to fit residues: 20.4519 Evaluate side-chains 50 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.130 ------------------------------------------------------------------------------- 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 89 TYR Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 560 GLN 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: 6.9990 chunk 2 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 59 optimal weight: 20.0000 chunk 33 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 37 optimal weight: 0.0170 chunk 61 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 560 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.138536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.112341 restraints weight = 21881.970| |-----------------------------------------------------------------------------| r_work (start): 0.4100 rms_B_bonded: 2.20 r_work: 0.3958 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9033 Z= 0.125 Angle : 0.502 9.946 13335 Z= 0.292 Chirality : 0.033 0.182 1666 Planarity : 0.004 0.056 852 Dihedral : 23.596 118.619 4050 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 5.29 % Allowed : 30.42 % 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: -0.47 (0.42), residues: 424 helix: 0.55 (0.35), residues: 205 sheet: -1.62 (0.56), residues: 77 loop : -0.58 (0.59), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 327 TYR 0.020 0.002 TYR A 474 PHE 0.014 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 0.00252 / 0.13 ( 9033) covalent geometry : angle 0.50230 / 0.29 (13335) hydrogen bonds : bond 0.06575 / 4.49 ( 340) hydrogen bonds : angle 4.01432 / 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 58 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 38 time to evaluate : 0.128 Fit side-chains revert: symmetry clash REVERT: A 89 TYR cc_start: 0.5089 (OUTLIER) cc_final: 0.4788 (t80) REVERT: A 298 LYS cc_start: 0.7332 (OUTLIER) cc_final: 0.7118 (ttmt) REVERT: A 560 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.7410 (tp40) REVERT: A 565 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.6968 (mp10) REVERT: A 625 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7412 (tm-30) outliers start: 20 outliers final: 9 residues processed: 54 average time/residue: 0.3652 time to fit residues: 21.3921 Evaluate side-chains 48 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.201 ------------------------------------------------------------------------------- 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 298 LYS 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 560 GLN Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 589 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 56 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 27 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 chunk 28 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN A 584 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.138688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.112393 restraints weight = 21834.855| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 2.18 r_work: 0.3961 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 9033 Z= 0.134 Angle : 0.513 11.322 13335 Z= 0.295 Chirality : 0.033 0.200 1666 Planarity : 0.004 0.055 852 Dihedral : 23.552 118.535 4050 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.50 % Allowed : 31.22 % 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: -0.44 (0.41), residues: 424 helix: 0.57 (0.34), residues: 204 sheet: -1.59 (0.56), residues: 77 loop : -0.54 (0.58), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 435 TYR 0.017 0.002 TYR A 474 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 0.00281 / 0.13 ( 9033) covalent geometry : angle 0.51294 / 0.30 (13335) hydrogen bonds : bond 0.06558 / 4.49 ( 340) hydrogen bonds : angle 4.01200 / 3.13 ( 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 53 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 36 time to evaluate : 0.193 Fit side-chains revert: symmetry clash REVERT: A 89 TYR cc_start: 0.5091 (OUTLIER) cc_final: 0.4793 (t80) REVERT: A 560 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.7295 (tp40) REVERT: A 565 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.6990 (mp10) REVERT: A 625 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7393 (tm-30) outliers start: 17 outliers final: 9 residues processed: 49 average time/residue: 0.3712 time to fit residues: 19.8506 Evaluate side-chains 48 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.170 ------------------------------------------------------------------------------- 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 377 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 560 GLN 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: 5.9990 chunk 45 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 chunk 27 optimal weight: 0.0770 chunk 34 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 25 optimal weight: 0.0050 overall best weight: 0.8156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.138346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.111814 restraints weight = 22070.563| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 2.23 r_work: 0.3953 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9033 Z= 0.139 Angle : 0.512 12.575 13335 Z= 0.294 Chirality : 0.033 0.171 1666 Planarity : 0.004 0.055 852 Dihedral : 23.511 118.535 4050 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.44 % Allowed : 32.28 % 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: -0.44 (0.41), residues: 424 helix: 0.58 (0.35), residues: 204 sheet: -1.57 (0.56), residues: 77 loop : -0.58 (0.58), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 435 TYR 0.027 0.002 TYR A 474 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 0.00283 / 0.14 ( 9033) covalent geometry : angle 0.51229 / 0.29 (13335) hydrogen bonds : bond 0.06540 / 4.48 ( 340) hydrogen bonds : angle 4.02289 / 3.13 ( 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 49 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.189 Fit side-chains revert: symmetry clash REVERT: A 89 TYR cc_start: 0.5099 (OUTLIER) cc_final: 0.4804 (t80) REVERT: A 565 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7053 (mp10) REVERT: A 625 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7393 (tm-30) outliers start: 13 outliers final: 10 residues processed: 46 average time/residue: 0.3701 time to fit residues: 18.5095 Evaluate side-chains 46 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.118 ------------------------------------------------------------------------------- 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 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: 0.0170 chunk 47 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 46 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.138933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.112536 restraints weight = 21893.167| |-----------------------------------------------------------------------------| r_work (start): 0.4105 rms_B_bonded: 2.20 r_work: 0.3963 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9033 Z= 0.128 Angle : 0.515 13.382 13335 Z= 0.294 Chirality : 0.032 0.188 1666 Planarity : 0.004 0.055 852 Dihedral : 23.470 118.494 4050 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % 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: -0.26 (0.42), residues: 424 helix: 0.73 (0.35), residues: 204 sheet: -1.52 (0.56), residues: 77 loop : -0.50 (0.58), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 435 TYR 0.032 0.002 TYR A 590 PHE 0.021 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 0.00262 / 0.13 ( 9033) covalent geometry : angle 0.51468 / 0.29 (13335) hydrogen bonds : bond 0.06384 / 4.36 ( 340) hydrogen bonds : angle 3.93152 / 3.06 ( 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 51 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 37 time to evaluate : 0.128 Fit side-chains revert: symmetry clash REVERT: A 89 TYR cc_start: 0.5046 (OUTLIER) cc_final: 0.4758 (t80) REVERT: A 565 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7021 (mp10) REVERT: A 625 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7385 (tm-30) outliers start: 14 outliers final: 9 residues processed: 48 average time/residue: 0.3601 time to fit residues: 18.7302 Evaluate side-chains 45 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.143 ------------------------------------------------------------------------------- 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 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 498 LEU Chi-restraints excluded: chain A residue 554 VAL 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: 7.9990 chunk 48 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 0.0670 chunk 32 optimal weight: 0.6980 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN A 560 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.138821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.112341 restraints weight = 22144.228| |-----------------------------------------------------------------------------| r_work (start): 0.4110 rms_B_bonded: 2.24 r_work: 0.3969 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9033 Z= 0.132 Angle : 0.515 13.314 13335 Z= 0.294 Chirality : 0.032 0.235 1666 Planarity : 0.004 0.055 852 Dihedral : 23.439 118.465 4050 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.17 % Allowed : 32.80 % Favored : 64.02 % 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: -0.14 (0.42), residues: 424 helix: 0.86 (0.35), residues: 204 sheet: -1.47 (0.56), residues: 77 loop : -0.46 (0.58), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 502 TYR 0.022 0.002 TYR A 474 PHE 0.013 0.002 PHE A 514 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 0.00272 / 0.13 ( 9033) covalent geometry : angle 0.51523 / 0.29 (13335) hydrogen bonds : bond 0.06354 / 4.34 ( 340) hydrogen bonds : angle 3.87374 / 3.03 ( 803) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2382.23 seconds wall clock time: 41 minutes 18.52 seconds (2478.52 seconds total)