Starting phenix.real_space_refine on Wed Feb 12 18:18:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8axb_15698/02_2025/8axb_15698.cif Found real_map, /net/cci-nas-00/data/ceres_data/8axb_15698/02_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_15698/02_2025/8axb_15698.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8axb_15698/02_2025/8axb_15698.map" model { file = "/net/cci-nas-00/data/ceres_data/8axb_15698/02_2025/8axb_15698.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8axb_15698/02_2025/8axb_15698.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 6.16, per 1000 atoms: 0.73 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: 2.27 Conformation dependent library (CDL) restraints added in 434.7 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: 3.95 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: 3.72 Time building geometry restraints manager: 2.65 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: 3.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 26.330 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.730 ------------------------------------------------------------------------------- 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= 0.225 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (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 TRP 0.011 0.001 TRP A 366 HIS 0.006 0.001 HIS A 42 PHE 0.016 0.002 PHE A 305 TYR 0.010 0.002 TYR A 89 ARG 0.005 0.001 ARG A 435 *********************** 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 : 0.522 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: 1.3512 time to fit residues: 84.8278 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 : 0.583 ------------------------------------------------------------------------------- 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 55 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 494 GLN A 560 GLN A 580 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.135244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.108704 restraints weight = 21400.123| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 2.16 r_work: 0.3897 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9033 Z= 0.294 Angle : 0.662 7.746 13335 Z= 0.334 Chirality : 0.036 0.193 1666 Planarity : 0.006 0.053 852 Dihedral : 23.655 119.747 4051 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 7.94 % Allowed : 28.57 % Favored : 63.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.42), residues: 424 helix: 0.22 (0.35), residues: 205 sheet: -1.74 (0.56), residues: 78 loop : -0.90 (0.59), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 366 HIS 0.004 0.001 HIS A 500 PHE 0.015 0.003 PHE A 514 TYR 0.015 0.002 TYR A 581 ARG 0.009 0.001 ARG A 71 *********************** 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: 30 poor density : 40 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: A 71 ARG cc_start: 0.7453 (tpm170) cc_final: 0.6594 (pmt170) REVERT: A 390 VAL cc_start: 0.7930 (OUTLIER) cc_final: 0.7713 (p) REVERT: A 560 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7762 (tp40) REVERT: A 565 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.6938 (mp10) REVERT: A 618 SER cc_start: 0.7795 (OUTLIER) cc_final: 0.7446 (p) REVERT: A 625 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7454 (tm-30) outliers start: 30 outliers final: 7 residues processed: 65 average time/residue: 1.0479 time to fit residues: 73.3376 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 : 0.886 ------------------------------------------------------------------------------- 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 331 ASP Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 390 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 618 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 27 optimal weight: 0.6980 chunk 6 optimal weight: 0.0970 chunk 55 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN ** A 321 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** 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 = 0.4504 r_free = 0.4504 target = 0.137915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.111524 restraints weight = 21973.327| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 2.20 r_work: 0.3935 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.1881 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= 0.200 Angle : 0.599 7.220 13335 Z= 0.300 Chirality : 0.033 0.171 1666 Planarity : 0.005 0.052 852 Dihedral : 23.554 119.278 4051 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 5.29 % Allowed : 30.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.42), residues: 424 helix: 0.49 (0.35), residues: 205 sheet: -1.44 (0.58), residues: 77 loop : -0.53 (0.58), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 366 HIS 0.005 0.001 HIS A 42 PHE 0.014 0.002 PHE A 433 TYR 0.018 0.002 TYR A 474 ARG 0.006 0.001 ARG A 502 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 41 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 560 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7692 (tp40) REVERT: A 565 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.6873 (mp10) REVERT: A 618 SER cc_start: 0.7660 (OUTLIER) cc_final: 0.7306 (p) REVERT: A 625 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7407 (tm-30) outliers start: 20 outliers final: 8 residues processed: 56 average time/residue: 1.0319 time to fit residues: 62.3552 Evaluate side-chains 50 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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 294 SER 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 589 SER 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 28 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 18 optimal weight: 0.0170 chunk 39 optimal weight: 0.2980 chunk 37 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 overall best weight: 1.0020 ------------------------------------------------------------------------------- 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 584 ASN 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 = 0.137326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.111111 restraints weight = 21630.604| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 2.19 r_work: 0.3938 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.2143 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= 0.218 Angle : 0.599 6.599 13335 Z= 0.301 Chirality : 0.033 0.220 1666 Planarity : 0.005 0.053 852 Dihedral : 23.526 119.417 4051 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 6.08 % Allowed : 27.25 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.41), residues: 424 helix: 0.55 (0.34), residues: 206 sheet: -1.48 (0.57), residues: 77 loop : -0.47 (0.58), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 366 HIS 0.005 0.001 HIS A 42 PHE 0.013 0.002 PHE A 433 TYR 0.014 0.002 TYR A 590 ARG 0.004 0.000 ARG A 502 *********************** 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 63 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 40 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 TYR cc_start: 0.5164 (OUTLIER) cc_final: 0.4853 (t80) REVERT: A 565 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.6893 (mp10) REVERT: A 618 SER cc_start: 0.7735 (OUTLIER) cc_final: 0.7439 (p) REVERT: A 625 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7376 (tm-30) outliers start: 23 outliers final: 9 residues processed: 58 average time/residue: 0.9871 time to fit residues: 62.1468 Evaluate side-chains 50 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 89 TYR Chi-restraints excluded: chain A residue 294 SER 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 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 50 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 22 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 560 GLN A 584 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.137326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.110559 restraints weight = 21849.091| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 2.21 r_work: 0.3941 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.2378 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= 0.201 Angle : 0.582 6.815 13335 Z= 0.292 Chirality : 0.032 0.194 1666 Planarity : 0.004 0.054 852 Dihedral : 23.512 119.266 4050 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 7.14 % Allowed : 26.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.41), residues: 424 helix: 0.66 (0.34), residues: 206 sheet: -1.41 (0.57), residues: 77 loop : -0.32 (0.59), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 366 HIS 0.004 0.001 HIS A 42 PHE 0.013 0.002 PHE A 433 TYR 0.020 0.002 TYR A 474 ARG 0.003 0.000 ARG A 502 *********************** 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 68 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 41 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 TYR cc_start: 0.5030 (OUTLIER) cc_final: 0.4705 (t80) REVERT: A 560 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7659 (tp40) REVERT: A 565 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.6842 (mp10) REVERT: A 618 SER cc_start: 0.7751 (OUTLIER) cc_final: 0.7390 (p) REVERT: A 625 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7364 (tm-30) outliers start: 27 outliers final: 11 residues processed: 63 average time/residue: 1.0395 time to fit residues: 70.9696 Evaluate side-chains 53 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 38 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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 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 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 0 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 0.0270 chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 15 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 overall best weight: 1.1042 ------------------------------------------------------------------------------- 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 = 0.4502 r_free = 0.4502 target = 0.136859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.110301 restraints weight = 21887.314| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 2.17 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: 0.7248 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9033 Z= 0.227 Angle : 0.594 6.042 13335 Z= 0.297 Chirality : 0.033 0.169 1666 Planarity : 0.004 0.053 852 Dihedral : 23.527 119.287 4050 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 7.14 % Allowed : 28.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.42), residues: 424 helix: 0.73 (0.34), residues: 206 sheet: -1.38 (0.58), residues: 77 loop : -0.27 (0.61), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 366 HIS 0.004 0.001 HIS A 42 PHE 0.013 0.002 PHE A 325 TYR 0.020 0.002 TYR A 590 ARG 0.003 0.000 ARG A 502 *********************** 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 68 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 41 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 TYR cc_start: 0.5014 (OUTLIER) cc_final: 0.4670 (t80) REVERT: A 298 LYS cc_start: 0.7357 (OUTLIER) cc_final: 0.7108 (tptt) REVERT: A 560 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7705 (tp40) REVERT: A 565 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.6875 (mp10) REVERT: A 618 SER cc_start: 0.7802 (OUTLIER) cc_final: 0.7433 (p) REVERT: A 625 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7357 (tm-30) outliers start: 27 outliers final: 13 residues processed: 63 average time/residue: 0.9740 time to fit residues: 66.5354 Evaluate side-chains 55 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 37 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 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 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 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 618 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 6 optimal weight: 0.7980 chunk 18 optimal weight: 0.0050 chunk 19 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 61 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 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 = 0.4550 r_free = 0.4550 target = 0.140239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.113841 restraints weight = 22274.314| |-----------------------------------------------------------------------------| r_work (start): 0.4123 rms_B_bonded: 2.22 r_work: 0.3982 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9033 Z= 0.161 Angle : 0.562 7.298 13335 Z= 0.280 Chirality : 0.031 0.169 1666 Planarity : 0.004 0.055 852 Dihedral : 23.455 118.795 4050 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 5.03 % Allowed : 30.42 % Favored : 64.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.43), residues: 424 helix: 0.98 (0.35), residues: 205 sheet: -1.06 (0.58), residues: 76 loop : -0.25 (0.62), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 366 HIS 0.005 0.001 HIS A 42 PHE 0.012 0.001 PHE A 433 TYR 0.029 0.002 TYR A 474 ARG 0.003 0.000 ARG A 502 *********************** 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 60 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 41 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 TYR cc_start: 0.5030 (OUTLIER) cc_final: 0.4719 (t80) REVERT: A 362 LYS cc_start: 0.7935 (mmtt) cc_final: 0.7162 (mmtm) REVERT: A 552 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.7336 (mmt180) REVERT: A 560 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.7541 (tp40) REVERT: A 565 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.6906 (mp10) REVERT: A 618 SER cc_start: 0.7667 (OUTLIER) cc_final: 0.7321 (p) REVERT: A 625 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7466 (tm-30) outliers start: 19 outliers final: 8 residues processed: 57 average time/residue: 0.9828 time to fit residues: 60.7835 Evaluate side-chains 51 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 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 560 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 9 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 GLN A 560 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.131800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.104682 restraints weight = 22283.813| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 2.23 r_work: 0.3838 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 9033 Z= 0.416 Angle : 0.742 9.818 13335 Z= 0.370 Chirality : 0.039 0.211 1666 Planarity : 0.005 0.049 852 Dihedral : 23.725 119.783 4050 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 5.29 % Allowed : 29.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.41), residues: 424 helix: 0.38 (0.34), residues: 206 sheet: -1.53 (0.57), residues: 77 loop : -0.50 (0.59), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 21 HIS 0.007 0.002 HIS A 500 PHE 0.020 0.003 PHE A 325 TYR 0.040 0.003 TYR A 590 ARG 0.005 0.001 ARG A 492 *********************** 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 60 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 40 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 TYR cc_start: 0.4900 (OUTLIER) cc_final: 0.4579 (t80) REVERT: A 298 LYS cc_start: 0.7411 (OUTLIER) cc_final: 0.7197 (ttmt) REVERT: A 362 LYS cc_start: 0.8280 (mmtt) cc_final: 0.7534 (mmtm) REVERT: A 560 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7711 (tp40) REVERT: A 565 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.6903 (mp10) outliers start: 20 outliers final: 10 residues processed: 56 average time/residue: 1.0806 time to fit residues: 65.3584 Evaluate side-chains 48 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 34 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 44 optimal weight: 4.9990 chunk 27 optimal weight: 0.0570 chunk 22 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 4 optimal weight: 0.4980 chunk 18 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.138346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.112016 restraints weight = 22257.140| |-----------------------------------------------------------------------------| r_work (start): 0.4089 rms_B_bonded: 2.19 r_work: 0.3946 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9033 Z= 0.186 Angle : 0.620 12.329 13335 Z= 0.307 Chirality : 0.032 0.173 1666 Planarity : 0.004 0.059 852 Dihedral : 23.567 118.797 4050 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.50 % Allowed : 32.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.42), residues: 424 helix: 0.73 (0.34), residues: 205 sheet: -1.25 (0.58), residues: 77 loop : -0.24 (0.61), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 366 HIS 0.005 0.001 HIS A 42 PHE 0.012 0.002 PHE A 514 TYR 0.026 0.002 TYR A 590 ARG 0.005 0.000 ARG A 71 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: A 24 MET cc_start: 0.7976 (mmm) cc_final: 0.7719 (mmm) REVERT: A 89 TYR cc_start: 0.4950 (OUTLIER) cc_final: 0.4592 (t80) REVERT: A 362 LYS cc_start: 0.8034 (mmtt) cc_final: 0.7254 (mmtm) REVERT: A 560 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7537 (tp40) REVERT: A 565 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7066 (mp10) REVERT: A 625 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7290 (tm-30) outliers start: 17 outliers final: 8 residues processed: 57 average time/residue: 0.8716 time to fit residues: 54.3555 Evaluate side-chains 51 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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 560 GLN 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 3 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 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 = 0.4519 r_free = 0.4519 target = 0.137829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.111578 restraints weight = 21741.505| |-----------------------------------------------------------------------------| r_work (start): 0.4095 rms_B_bonded: 2.15 r_work: 0.3952 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9033 Z= 0.215 Angle : 0.628 12.066 13335 Z= 0.312 Chirality : 0.033 0.170 1666 Planarity : 0.004 0.055 852 Dihedral : 23.541 119.155 4050 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.97 % Allowed : 33.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.42), residues: 424 helix: 0.70 (0.35), residues: 205 sheet: -1.21 (0.58), residues: 77 loop : -0.35 (0.59), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 366 HIS 0.006 0.001 HIS A 42 PHE 0.020 0.002 PHE A 13 TYR 0.034 0.002 TYR A 590 ARG 0.004 0.000 ARG A 435 ********************** 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 56 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: A 89 TYR cc_start: 0.5028 (OUTLIER) cc_final: 0.4670 (t80) REVERT: A 362 LYS cc_start: 0.8128 (mmtt) cc_final: 0.7341 (mmtm) REVERT: A 565 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7044 (mp10) REVERT: A 625 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7290 (tm-30) outliers start: 15 outliers final: 8 residues processed: 54 average time/residue: 0.9452 time to fit residues: 55.5567 Evaluate side-chains 47 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 589 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 23 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.137349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.110856 restraints weight = 21974.102| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 2.19 r_work: 0.3939 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9033 Z= 0.229 Angle : 0.636 12.246 13335 Z= 0.316 Chirality : 0.033 0.190 1666 Planarity : 0.004 0.053 852 Dihedral : 23.543 118.869 4050 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.44 % Allowed : 33.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.42), residues: 424 helix: 0.67 (0.34), residues: 205 sheet: -1.21 (0.58), residues: 77 loop : -0.40 (0.59), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 366 HIS 0.005 0.001 HIS A 42 PHE 0.013 0.002 PHE A 514 TYR 0.026 0.002 TYR A 590 ARG 0.003 0.000 ARG A 492 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6295.09 seconds wall clock time: 111 minutes 47.90 seconds (6707.90 seconds total)