Starting phenix.real_space_refine on Fri Aug 22 22:00:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8axb_15698/08_2025/8axb_15698.cif Found real_map, /net/cci-nas-00/data/ceres_data/8axb_15698/08_2025/8axb_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_2025/8axb_15698.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8axb_15698/08_2025/8axb_15698.map" model { file = "/net/cci-nas-00/data/ceres_data/8axb_15698/08_2025/8axb_15698.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8axb_15698/08_2025/8axb_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-2.0-5787/lib/python3.9/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: 2.19, per 1000 atoms: 0.26 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: 0.80 Conformation dependent library (CDL) restraints added in 143.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.30 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: 1.75 Time building geometry restraints manager: 1.05 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=" CB GLN A 41 " pdb=" CG GLN A 41 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.50e+00 bond pdb=" CG ARG A 17 " pdb=" CD ARG A 17 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 1.02e+00 bond pdb=" CA GLN A 64 " pdb=" C GLN A 64 " ideal model delta sigma weight residual 1.524 1.535 -0.011 1.26e-02 6.30e+03 7.55e-01 bond pdb=" CG1 ILE A 477 " pdb=" CD1 ILE A 477 " ideal model delta sigma weight residual 1.513 1.479 0.034 3.90e-02 6.57e+02 7.43e-01 bond pdb=" CB ASP A 465 " pdb=" CG ASP A 465 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 7.34e-01 ... (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=" CA GLN A 64 " pdb=" CB GLN A 64 " pdb=" CG GLN A 64 " ideal model delta sigma weight residual 114.10 121.45 -7.35 2.00e+00 2.50e-01 1.35e+01 angle pdb=" N GLN A 64 " pdb=" CA GLN A 64 " pdb=" C GLN A 64 " ideal model delta sigma weight residual 109.81 117.22 -7.41 2.21e+00 2.05e-01 1.13e+01 angle pdb=" CA GLN A 41 " pdb=" CB GLN A 41 " pdb=" CG GLN A 41 " ideal model delta sigma weight residual 114.10 119.24 -5.14 2.00e+00 2.50e-01 6.61e+00 angle pdb=" C LEU A 308 " pdb=" N SER A 309 " pdb=" CA SER A 309 " ideal model delta sigma weight residual 121.54 126.36 -4.82 1.91e+00 2.74e-01 6.37e+00 angle pdb=" CA LEU A 27 " pdb=" CB LEU A 27 " pdb=" CG LEU A 27 " ideal model delta sigma weight residual 116.30 125.00 -8.70 3.50e+00 8.16e-02 6.18e+00 ... (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: 3.730 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.480 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 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= 0.175 Angle : 0.620 8.704 13335 Z= 0.312 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 aren 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 covalent geometry : bond 0.00355 ( 9033) covalent geometry : angle 0.61964 (13335) hydrogen bonds : bond 0.15469 ( 340) hydrogen bonds : angle 6.34341 ( 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 : 0.209 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: 0.6588 time to fit residues: 41.1067 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 : 0.197 ------------------------------------------------------------------------------- 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: 8.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN A 49 GLN ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 GLN A 560 GLN A 580 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.131841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.104986 restraints weight = 22092.319| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 2.23 r_work: 0.3838 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 9033 Z= 0.341 Angle : 0.771 8.013 13335 Z= 0.389 Chirality : 0.041 0.202 1666 Planarity : 0.006 0.054 852 Dihedral : 23.855 120.662 4051 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 8.47 % Allowed : 29.37 % Favored : 62.17 % 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 aren not related in a simple way. whole: -1.30 (0.41), residues: 424 helix: -0.12 (0.34), residues: 205 sheet: -1.93 (0.57), residues: 78 loop : -1.05 (0.58), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 475 TYR 0.017 0.002 TYR A 581 PHE 0.020 0.003 PHE A 514 TRP 0.011 0.002 TRP A 366 HIS 0.007 0.002 HIS A 500 Details of bonding type rmsd covalent geometry : bond 0.00690 ( 9033) covalent geometry : angle 0.77127 (13335) hydrogen bonds : bond 0.08038 ( 340) hydrogen bonds : angle 4.62759 ( 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 69 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 37 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 71 ARG cc_start: 0.7304 (tpm170) cc_final: 0.6953 (tpm170) REVERT: A 509 PHE cc_start: 0.6487 (p90) cc_final: 0.6261 (p90) REVERT: A 565 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.6891 (mp10) REVERT: A 618 SER cc_start: 0.7867 (OUTLIER) cc_final: 0.7493 (p) outliers start: 32 outliers final: 8 residues processed: 64 average time/residue: 0.5098 time to fit residues: 35.0065 Evaluate side-chains 45 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 355 VAL 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 618 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 42 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 0.0980 chunk 62 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4516 r_free = 0.4516 target = 0.138223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.111943 restraints weight = 21813.726| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 2.17 r_work: 0.3961 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9033 Z= 0.135 Angle : 0.587 7.391 13335 Z= 0.295 Chirality : 0.033 0.174 1666 Planarity : 0.005 0.056 852 Dihedral : 23.591 119.233 4051 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 5.82 % Allowed : 30.42 % 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 aren not related in a simple way. whole: -0.39 (0.42), residues: 424 helix: 0.50 (0.35), residues: 206 sheet: -1.41 (0.59), residues: 76 loop : -0.47 (0.60), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 502 TYR 0.010 0.001 TYR A 497 PHE 0.014 0.002 PHE A 433 TRP 0.013 0.001 TRP A 366 HIS 0.005 0.001 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 9033) covalent geometry : angle 0.58673 (13335) hydrogen bonds : bond 0.06139 ( 340) hydrogen bonds : angle 4.01131 ( 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 63 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 41 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: A 89 TYR cc_start: 0.5050 (OUTLIER) cc_final: 0.4732 (t80) REVERT: A 279 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7229 (pt) REVERT: A 560 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7657 (tp40) REVERT: A 565 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.6841 (mp10) REVERT: A 618 SER cc_start: 0.7711 (OUTLIER) cc_final: 0.7359 (p) REVERT: A 625 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7395 (tm-30) outliers start: 22 outliers final: 5 residues processed: 59 average time/residue: 0.5103 time to fit residues: 32.1138 Evaluate side-chains 50 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.115 ------------------------------------------------------------------------------- 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 89 TYR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 331 ASP 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 618 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 43 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** 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 = 0.4485 r_free = 0.4485 target = 0.135898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.109187 restraints weight = 22273.459| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 2.19 r_work: 0.3919 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9033 Z= 0.186 Angle : 0.615 7.013 13335 Z= 0.308 Chirality : 0.034 0.231 1666 Planarity : 0.005 0.052 852 Dihedral : 23.581 119.623 4051 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 6.35 % Allowed : 29.37 % 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 aren not related in a simple way. whole: -0.43 (0.41), residues: 424 helix: 0.50 (0.34), residues: 206 sheet: -1.51 (0.57), residues: 77 loop : -0.46 (0.59), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 502 TYR 0.015 0.002 TYR A 590 PHE 0.013 0.002 PHE A 433 TRP 0.012 0.001 TRP A 366 HIS 0.006 0.001 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 9033) covalent geometry : angle 0.61500 (13335) hydrogen bonds : bond 0.06231 ( 340) hydrogen bonds : angle 4.03260 ( 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 66 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 42 time to evaluate : 0.225 Fit side-chains REVERT: A 48 TRP cc_start: 0.7930 (m-90) cc_final: 0.7576 (m100) REVERT: A 89 TYR cc_start: 0.5100 (OUTLIER) cc_final: 0.4722 (t80) REVERT: A 279 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7203 (pt) REVERT: A 298 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.7140 (ttmt) REVERT: A 552 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7450 (mmt180) REVERT: A 565 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.6908 (mp10) REVERT: A 618 SER cc_start: 0.7697 (OUTLIER) cc_final: 0.7380 (p) REVERT: A 625 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7404 (tm-30) outliers start: 24 outliers final: 6 residues processed: 60 average time/residue: 0.5621 time to fit residues: 36.0732 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 : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 89 TYR Chi-restraints excluded: chain A residue 279 LEU 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 460 THR Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 618 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 60 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN ** A 342 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.137681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.111217 restraints weight = 22227.782| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 2.19 r_work: 0.3938 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9033 Z= 0.151 Angle : 0.588 6.642 13335 Z= 0.295 Chirality : 0.032 0.189 1666 Planarity : 0.004 0.055 852 Dihedral : 23.540 119.403 4050 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 7.94 % Allowed : 27.51 % 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 aren not related in a simple way. whole: -0.23 (0.42), residues: 424 helix: 0.68 (0.34), residues: 205 sheet: -1.44 (0.57), residues: 77 loop : -0.39 (0.60), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 502 TYR 0.009 0.001 TYR A 590 PHE 0.013 0.002 PHE A 433 TRP 0.012 0.001 TRP A 366 HIS 0.005 0.001 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 9033) covalent geometry : angle 0.58764 (13335) hydrogen bonds : bond 0.05985 ( 340) hydrogen bonds : angle 3.90724 ( 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 70 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 40 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 TYR cc_start: 0.4997 (OUTLIER) cc_final: 0.4677 (t80) REVERT: A 279 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7247 (pt) REVERT: A 298 LYS cc_start: 0.7335 (OUTLIER) cc_final: 0.7098 (ttmt) REVERT: A 552 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7439 (mmt180) REVERT: A 565 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.6914 (mp10) REVERT: A 618 SER cc_start: 0.7752 (OUTLIER) cc_final: 0.7339 (p) REVERT: A 625 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7360 (tm-30) outliers start: 30 outliers final: 12 residues processed: 65 average time/residue: 0.4842 time to fit residues: 34.0181 Evaluate side-chains 57 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 39 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 28 ASN 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 91 TYR Chi-restraints excluded: chain A residue 279 LEU 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 451 VAL Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 595 GLN Chi-restraints excluded: chain A residue 618 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 40 optimal weight: 0.6980 chunk 58 optimal weight: 7.9990 chunk 16 optimal weight: 0.2980 chunk 33 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 36 optimal weight: 0.3980 chunk 19 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.139976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.113906 restraints weight = 22033.440| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 2.17 r_work: 0.3980 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9033 Z= 0.124 Angle : 0.566 6.948 13335 Z= 0.283 Chirality : 0.031 0.170 1666 Planarity : 0.004 0.055 852 Dihedral : 23.455 119.006 4050 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 13.52 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 aren not related in a simple way. whole: 0.12 (0.43), residues: 424 helix: 0.92 (0.34), residues: 205 sheet: -1.28 (0.56), residues: 77 loop : -0.11 (0.63), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 502 TYR 0.031 0.002 TYR A 474 PHE 0.012 0.002 PHE A 13 TRP 0.013 0.001 TRP A 366 HIS 0.005 0.001 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 9033) covalent geometry : angle 0.56586 (13335) hydrogen bonds : bond 0.05739 ( 340) hydrogen bonds : angle 3.77040 ( 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: 20 poor density : 42 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 TYR cc_start: 0.5028 (OUTLIER) cc_final: 0.4708 (t80) REVERT: A 279 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7267 (pt) REVERT: A 298 LYS cc_start: 0.7340 (OUTLIER) cc_final: 0.7100 (tptt) REVERT: A 565 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7007 (mp10) REVERT: A 618 SER cc_start: 0.7766 (OUTLIER) cc_final: 0.7366 (p) REVERT: A 625 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7427 (tm-30) outliers start: 20 outliers final: 8 residues processed: 59 average time/residue: 0.5242 time to fit residues: 33.2638 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 : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 89 TYR Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 279 LEU 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 460 THR Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 595 GLN Chi-restraints excluded: chain A residue 618 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 22 optimal weight: 0.0370 chunk 2 optimal weight: 0.8980 chunk 36 optimal weight: 0.0670 chunk 62 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 59 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 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 = 0.4546 r_free = 0.4546 target = 0.139935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.113744 restraints weight = 22234.960| |-----------------------------------------------------------------------------| r_work (start): 0.4116 rms_B_bonded: 2.20 r_work: 0.3976 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9033 Z= 0.128 Angle : 0.568 9.704 13335 Z= 0.280 Chirality : 0.031 0.170 1666 Planarity : 0.004 0.055 852 Dihedral : 23.428 118.739 4050 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 5.03 % Allowed : 30.16 % 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 aren not related in a simple way. whole: 0.31 (0.43), residues: 424 helix: 1.12 (0.35), residues: 205 sheet: -1.12 (0.57), residues: 77 loop : -0.15 (0.63), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 502 TYR 0.024 0.002 TYR A 590 PHE 0.011 0.001 PHE A 433 TRP 0.013 0.001 TRP A 366 HIS 0.003 0.001 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9033) covalent geometry : angle 0.56834 (13335) hydrogen bonds : bond 0.05679 ( 340) hydrogen bonds : angle 3.67097 ( 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 59 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 40 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 TYR cc_start: 0.5038 (OUTLIER) cc_final: 0.4720 (t80) REVERT: A 279 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7272 (pt) REVERT: A 362 LYS cc_start: 0.8097 (mmtt) cc_final: 0.7382 (mptm) REVERT: A 552 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.7338 (mmt180) REVERT: A 565 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7044 (mp10) REVERT: A 618 SER cc_start: 0.7811 (OUTLIER) cc_final: 0.7405 (p) REVERT: A 625 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7420 (tm-30) outliers start: 19 outliers final: 10 residues processed: 55 average time/residue: 0.4900 time to fit residues: 29.1467 Evaluate side-chains 51 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 36 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 28 ASN 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 91 TYR Chi-restraints excluded: chain A residue 279 LEU 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 460 THR Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 595 GLN Chi-restraints excluded: chain A residue 618 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 56 optimal weight: 3.9990 chunk 30 optimal weight: 0.0050 chunk 27 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 0.0670 chunk 20 optimal weight: 0.2980 overall best weight: 0.3532 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 HIS ** 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 = 0.4583 r_free = 0.4583 target = 0.142402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.116469 restraints weight = 21863.431| |-----------------------------------------------------------------------------| r_work (start): 0.4193 rms_B_bonded: 2.18 r_work: 0.4056 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9033 Z= 0.110 Angle : 0.561 11.988 13335 Z= 0.275 Chirality : 0.030 0.167 1666 Planarity : 0.004 0.054 852 Dihedral : 23.382 118.442 4050 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % 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 aren not related in a simple way. whole: 0.49 (0.43), residues: 424 helix: 1.23 (0.35), residues: 203 sheet: -0.99 (0.57), residues: 77 loop : -0.02 (0.63), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 435 TYR 0.031 0.002 TYR A 590 PHE 0.015 0.001 PHE A 13 TRP 0.014 0.001 TRP A 366 HIS 0.004 0.001 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 9033) covalent geometry : angle 0.56079 (13335) hydrogen bonds : bond 0.05638 ( 340) hydrogen bonds : angle 3.61823 ( 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: 16 poor density : 42 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: A 89 TYR cc_start: 0.5082 (OUTLIER) cc_final: 0.4756 (t80) REVERT: A 279 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7307 (pt) REVERT: A 362 LYS cc_start: 0.7983 (mmtt) cc_final: 0.7335 (mptm) REVERT: A 437 SER cc_start: 0.8448 (t) cc_final: 0.8219 (p) REVERT: A 565 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7102 (mp10) REVERT: A 618 SER cc_start: 0.7721 (OUTLIER) cc_final: 0.7331 (p) REVERT: A 625 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7331 (tm-30) outliers start: 16 outliers final: 7 residues processed: 55 average time/residue: 0.3928 time to fit residues: 23.7518 Evaluate side-chains 48 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.162 ------------------------------------------------------------------------------- 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 91 TYR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 595 GLN Chi-restraints excluded: chain A residue 618 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 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 = 0.4527 r_free = 0.4527 target = 0.138439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.111974 restraints weight = 21915.619| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 2.18 r_work: 0.3956 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9033 Z= 0.176 Angle : 0.607 12.537 13335 Z= 0.300 Chirality : 0.032 0.204 1666 Planarity : 0.004 0.052 852 Dihedral : 23.443 118.597 4050 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.97 % Allowed : 31.75 % 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 aren not related in a simple way. whole: 0.19 (0.43), residues: 424 helix: 1.02 (0.35), residues: 205 sheet: -1.13 (0.58), residues: 77 loop : -0.24 (0.61), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 435 TYR 0.030 0.002 TYR A 590 PHE 0.013 0.002 PHE A 325 TRP 0.010 0.001 TRP A 366 HIS 0.005 0.001 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 9033) covalent geometry : angle 0.60709 (13335) hydrogen bonds : bond 0.05863 ( 340) hydrogen bonds : angle 3.77328 ( 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 54 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: A 89 TYR cc_start: 0.5132 (OUTLIER) cc_final: 0.4780 (t80) REVERT: A 279 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7264 (pt) REVERT: A 362 LYS cc_start: 0.8225 (mmtt) cc_final: 0.7568 (mptm) REVERT: A 437 SER cc_start: 0.8479 (t) cc_final: 0.8251 (p) REVERT: A 565 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7031 (mp10) REVERT: A 618 SER cc_start: 0.7830 (OUTLIER) cc_final: 0.7444 (p) REVERT: A 625 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7398 (tm-30) outliers start: 15 outliers final: 7 residues processed: 51 average time/residue: 0.5351 time to fit residues: 29.2939 Evaluate side-chains 48 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.219 ------------------------------------------------------------------------------- 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 91 TYR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 595 GLN Chi-restraints excluded: chain A residue 618 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 6 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 46 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 HIS ** 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 = 0.4530 r_free = 0.4530 target = 0.138790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.112430 restraints weight = 21711.472| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 2.18 r_work: 0.3962 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9033 Z= 0.163 Angle : 0.613 13.366 13335 Z= 0.302 Chirality : 0.032 0.224 1666 Planarity : 0.004 0.053 852 Dihedral : 23.458 117.486 4050 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.97 % Allowed : 33.07 % Favored : 62.96 % 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 aren not related in a simple way. whole: 0.12 (0.42), residues: 424 helix: 0.97 (0.35), residues: 205 sheet: -1.27 (0.57), residues: 79 loop : -0.18 (0.61), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 435 TYR 0.023 0.002 TYR A 590 PHE 0.012 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 covalent geometry : bond 0.00337 ( 9033) covalent geometry : angle 0.61307 (13335) hydrogen bonds : bond 0.05838 ( 340) hydrogen bonds : angle 3.77732 ( 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 52 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 37 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 24 MET cc_start: 0.8005 (mmm) cc_final: 0.7792 (mmm) REVERT: A 89 TYR cc_start: 0.5061 (OUTLIER) cc_final: 0.4704 (t80) REVERT: A 362 LYS cc_start: 0.8204 (mmtt) cc_final: 0.7552 (mptm) REVERT: A 565 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7087 (mp10) REVERT: A 618 SER cc_start: 0.7842 (OUTLIER) cc_final: 0.7390 (p) REVERT: A 625 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7381 (tm-30) outliers start: 15 outliers final: 8 residues processed: 49 average time/residue: 0.4823 time to fit residues: 25.5366 Evaluate side-chains 47 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.190 ------------------------------------------------------------------------------- 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 91 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 460 THR Chi-restraints excluded: chain A residue 565 GLN Chi-restraints excluded: chain A residue 595 GLN Chi-restraints excluded: chain A residue 618 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 56 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 8 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 3 optimal weight: 0.3980 chunk 14 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 0.0470 chunk 32 optimal weight: 1.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 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 = 0.4552 r_free = 0.4552 target = 0.140062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.113777 restraints weight = 21977.724| |-----------------------------------------------------------------------------| r_work (start): 0.4153 rms_B_bonded: 2.17 r_work: 0.4015 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.3241 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= 0.131 Angle : 0.590 12.931 13335 Z= 0.291 Chirality : 0.031 0.232 1666 Planarity : 0.004 0.054 852 Dihedral : 23.405 116.517 4050 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.23 % Allowed : 33.33 % 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 aren not related in a simple way. whole: 0.27 (0.43), residues: 424 helix: 1.08 (0.35), residues: 203 sheet: -1.20 (0.57), residues: 79 loop : -0.08 (0.62), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 502 TYR 0.032 0.002 TYR A 590 PHE 0.022 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 covalent geometry : bond 0.00273 ( 9033) covalent geometry : angle 0.59040 (13335) hydrogen bonds : bond 0.05649 ( 340) hydrogen bonds : angle 3.73471 ( 803) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3177.95 seconds wall clock time: 55 minutes 4.28 seconds (3304.28 seconds total)