Starting phenix.real_space_refine on Thu Jul 2 14:09:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8axa_15697/07_2026/8axa_15697.cif Found real_map, /net/cci-nas-00/data/ceres_data/8axa_15697/07_2026/8axa_15697.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8axa_15697/07_2026/8axa_15697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8axa_15697/07_2026/8axa_15697.map" model { file = "/net/cci-nas-00/data/ceres_data/8axa_15697/07_2026/8axa_15697.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8axa_15697/07_2026/8axa_15697.cif" } resolution = 2.96 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= -0.001 sd= 0.025 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 251 5.49 5 S 11 5.16 5 C 4801 2.51 5 N 1637 2.21 5 O 2442 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9142 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3774 Classifications: {'peptide': 465} Link IDs: {'PTRANS': 17, 'TRANS': 447} Chain breaks: 1 Chain: "B" Number of atoms: 5000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 5000 Inner-chain residues flagged as termini: ['pdbres=" U B 244 "'] Classifications: {'RNA': 235} Modifications used: {'5*END': 2, 'rna2p_pur': 18, 'rna2p_pyr': 20, 'rna3p_pur': 103, 'rna3p_pyr': 94} Link IDs: {'rna2p': 38, 'rna3p': 196} Chain: "C" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 261 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "D" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 104 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 1.96, per 1000 atoms: 0.21 Number of scatterers: 9142 At special positions: 0 Unit cell: (113.984, 94.016, 122.304, 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 11 16.00 P 251 15.00 O 2442 8.00 N 1637 7.00 C 4801 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: 0.78 Conformation dependent library (CDL) restraints added in 153.6 milliseconds 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 878 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 2 sheets defined 55.5% alpha, 10.1% beta 84 base pairs and 121 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 13 through 28 removed outlier: 3.711A pdb=" N ASP A 26 " --> pdb=" O LYS A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 42 Processing helix chain 'A' and resid 44 through 52 Processing helix chain 'A' and resid 57 through 62 Processing helix chain 'A' and resid 69 through 73 removed outlier: 3.831A pdb=" N ALA A 73 " --> pdb=" O PRO A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 98 Processing helix chain 'A' and resid 321 through 338 removed outlier: 3.675A pdb=" N PHE A 325 " --> pdb=" O GLN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 382 Processing helix chain 'A' and resid 384 through 406 Processing helix chain 'A' and resid 414 through 429 Processing helix chain 'A' and resid 476 through 482 Processing helix chain 'A' and resid 485 through 505 removed outlier: 3.874A pdb=" N ASN A 489 " --> pdb=" O TYR A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 538 Processing helix chain 'A' and resid 547 through 567 removed outlier: 3.535A pdb=" N MET A 551 " --> pdb=" O LYS A 547 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N GLU A 553 " --> pdb=" O GLY A 549 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 554 " --> pdb=" O ASP A 550 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN A 556 " --> pdb=" O ARG A 552 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 559 " --> pdb=" O VAL A 555 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLN A 560 " --> pdb=" O GLN A 556 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA A 561 " --> pdb=" O SER A 557 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN A 565 " --> pdb=" O ALA A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 585 Processing helix chain 'A' and resid 589 through 605 removed outlier: 3.671A pdb=" N ILE A 594 " --> pdb=" O TYR A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 637 removed outlier: 3.875A pdb=" N THR A 636 " --> pdb=" O ASN A 632 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG A 637 " --> pdb=" O LEU A 633 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 284 through 285 removed outlier: 3.541A pdb=" N GLY A 352 " --> pdb=" O PHE A 285 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN A 351 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LEU A 371 " --> pdb=" O LEU A 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 471 through 475 removed outlier: 6.638A pdb=" N VAL A 463 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N TYR A 474 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL A 461 " --> pdb=" O TYR A 474 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE A 447 " --> pdb=" O SER A 542 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N VAL A 544 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL A 449 " --> pdb=" O VAL A 544 " (cutoff:3.500A) removed outlier: 8.959A pdb=" N VAL A 451 " --> pdb=" O PRO A 546 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILE A 543 " --> pdb=" O GLU A 609 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N GLY A 611 " --> pdb=" O ILE A 543 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU A 545 " --> pdb=" O GLY A 611 " (cutoff:3.500A) 200 hydrogen bonds defined for protein. 588 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 220 hydrogen bonds 416 hydrogen bond angles 0 basepair planarities 84 basepair parallelities 121 stacking parallelities Total time for adding SS restraints: 1.87 Time building geometry restraints manager: 1.03 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: 1579 1.33 - 1.45: 3697 1.45 - 1.57: 4054 1.57 - 1.69: 500 1.69 - 1.80: 16 Bond restraints: 9846 Sorted by residual: bond pdb=" C3' DT C 37 " pdb=" C2' DT C 37 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DC C 45 " pdb=" C2' DC C 45 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.16e+00 bond pdb=" C3' DT C 38 " pdb=" C2' DT C 38 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.49e+00 bond pdb=" C3' DC C 44 " pdb=" C2' DC C 44 " ideal model delta sigma weight residual 1.516 1.534 -0.018 8.00e-03 1.56e+04 5.29e+00 bond pdb=" C3' DC C 41 " pdb=" C2' DC C 41 " ideal model delta sigma weight residual 1.516 1.534 -0.018 8.00e-03 1.56e+04 5.04e+00 ... (remaining 9841 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 14254 1.88 - 3.76: 242 3.76 - 5.64: 19 5.64 - 7.52: 7 7.52 - 9.40: 2 Bond angle restraints: 14524 Sorted by residual: angle pdb=" C1' C B 166 " pdb=" N1 C B 166 " pdb=" C2 C B 166 " ideal model delta sigma weight residual 118.80 124.53 -5.73 1.10e+00 8.26e-01 2.71e+01 angle pdb=" C1' C B 106 " pdb=" N1 C B 106 " pdb=" C2 C B 106 " ideal model delta sigma weight residual 118.80 124.28 -5.48 1.10e+00 8.26e-01 2.49e+01 angle pdb=" C1' U B 170 " pdb=" N1 U B 170 " pdb=" C2 U B 170 " ideal model delta sigma weight residual 117.70 123.42 -5.72 1.20e+00 6.94e-01 2.27e+01 angle pdb=" N1 U B 170 " pdb=" C2 U B 170 " pdb=" O2 U B 170 " ideal model delta sigma weight residual 122.80 126.04 -3.24 7.00e-01 2.04e+00 2.14e+01 angle pdb=" C CYS A 63 " pdb=" N GLN A 64 " pdb=" CA GLN A 64 " ideal model delta sigma weight residual 120.06 125.29 -5.23 1.19e+00 7.06e-01 1.93e+01 ... (remaining 14519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.46: 5252 30.46 - 60.92: 712 60.92 - 91.38: 210 91.38 - 121.84: 8 121.84 - 152.30: 3 Dihedral angle restraints: 6185 sinusoidal: 4829 harmonic: 1356 Sorted by residual: dihedral pdb=" CA LEU A 62 " pdb=" C LEU A 62 " pdb=" N CYS A 63 " pdb=" CA CYS A 63 " ideal model delta harmonic sigma weight residual 180.00 159.37 20.63 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" C4' U B 190 " pdb=" C3' U B 190 " pdb=" O3' U B 190 " pdb=" P G B 191 " ideal model delta sinusoidal sigma weight residual -110.00 42.30 -152.30 1 3.50e+01 8.16e-04 1.48e+01 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 180.00 160.98 19.02 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 6182 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1434 0.037 - 0.074: 288 0.074 - 0.110: 69 0.110 - 0.147: 14 0.147 - 0.184: 5 Chirality restraints: 1810 Sorted by residual: chirality pdb=" CB ILE A 4 " pdb=" CA ILE A 4 " pdb=" CG1 ILE A 4 " pdb=" CG2 ILE A 4 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.47e-01 chirality pdb=" C1' A B 139 " pdb=" O4' A B 139 " pdb=" C2' A B 139 " pdb=" N9 A B 139 " both_signs ideal model delta sigma weight residual False 2.46 2.28 0.18 2.00e-01 2.50e+01 8.35e-01 chirality pdb=" C3' G B 29 " pdb=" C4' G B 29 " pdb=" O3' G B 29 " pdb=" C2' G B 29 " both_signs ideal model delta sigma weight residual False -2.48 -2.30 -0.17 2.00e-01 2.50e+01 7.44e-01 ... (remaining 1807 not shown) Planarity restraints: 923 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 64 " 0.058 5.00e-02 4.00e+02 8.82e-02 1.25e+01 pdb=" N PRO A 65 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO A 65 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 65 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G B 49 " 0.029 2.00e-02 2.50e+03 1.25e-02 4.68e+00 pdb=" N9 G B 49 " -0.031 2.00e-02 2.50e+03 pdb=" C8 G B 49 " -0.001 2.00e-02 2.50e+03 pdb=" N7 G B 49 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G B 49 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G B 49 " 0.004 2.00e-02 2.50e+03 pdb=" O6 G B 49 " 0.006 2.00e-02 2.50e+03 pdb=" N1 G B 49 " 0.004 2.00e-02 2.50e+03 pdb=" C2 G B 49 " 0.000 2.00e-02 2.50e+03 pdb=" N2 G B 49 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G B 49 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G B 49 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 139 " -0.023 2.00e-02 2.50e+03 1.15e-02 3.63e+00 pdb=" N9 A B 139 " 0.030 2.00e-02 2.50e+03 pdb=" C8 A B 139 " -0.000 2.00e-02 2.50e+03 pdb=" N7 A B 139 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A B 139 " -0.003 2.00e-02 2.50e+03 pdb=" C6 A B 139 " -0.001 2.00e-02 2.50e+03 pdb=" N6 A B 139 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A B 139 " 0.000 2.00e-02 2.50e+03 pdb=" C2 A B 139 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A B 139 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A B 139 " -0.001 2.00e-02 2.50e+03 ... (remaining 920 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 517 2.69 - 3.25: 8356 3.25 - 3.80: 17762 3.80 - 4.35: 22141 4.35 - 4.90: 30956 Nonbonded interactions: 79732 Sorted by model distance: nonbonded pdb=" O GLY A 454 " pdb=" OH TYR A 590 " model vdw 2.143 3.040 nonbonded pdb=" OE2 GLU A 34 " pdb=" O HOH A 701 " model vdw 2.176 3.040 nonbonded pdb=" O2' A B 63 " pdb=" O3' G B 88 " model vdw 2.193 3.040 nonbonded pdb=" O2' A B 169 " pdb=" N6 A B 173 " model vdw 2.232 3.120 nonbonded pdb=" O4 U B 144 " pdb=" N4 C B 148 " model vdw 2.234 3.120 ... (remaining 79727 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=0.00 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: 3.750 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.660 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 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 0.032 9846 Z= 0.288 Angle : 0.588 9.396 14524 Z= 0.492 Chirality : 0.034 0.184 1810 Planarity : 0.006 0.088 923 Dihedral : 23.946 152.304 5307 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.49 % Allowed : 32.28 % Favored : 67.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.41), residues: 461 helix: 1.25 (0.32), residues: 239 sheet: -1.71 (0.59), residues: 80 loop : -0.95 (0.59), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 493 TYR 0.026 0.002 TYR A 497 PHE 0.012 0.002 PHE A 401 TRP 0.008 0.001 TRP A 366 HIS 0.004 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.29 ( 9846) covalent geometry : angle 0.58761 / 0.49 (14524) hydrogen bonds : bond 0.10297 / 7.04 ( 420) hydrogen bonds : angle 4.97477 / 3.65 ( 1004) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.212 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 46 average time/residue: 0.5281 time to fit residues: 26.1240 Evaluate side-chains 27 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 30.0000 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 GLN A 75 GLN A 367 ASN A 420 GLN A 580 GLN A 598 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.111526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.086752 restraints weight = 27098.402| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.09 r_work: 0.3535 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 9846 Z= 0.310 Angle : 0.646 8.288 14524 Z= 0.368 Chirality : 0.041 0.240 1810 Planarity : 0.007 0.089 923 Dihedral : 24.051 152.683 4347 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 6.80 % Allowed : 29.85 % Favored : 63.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.40), residues: 461 helix: 0.58 (0.31), residues: 245 sheet: -1.84 (0.59), residues: 78 loop : -1.00 (0.62), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 592 TYR 0.015 0.002 TYR A 474 PHE 0.018 0.002 PHE A 433 TRP 0.011 0.002 TRP A 324 HIS 0.006 0.002 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.31 ( 9846) covalent geometry : angle 0.64553 / 0.37 (14524) hydrogen bonds : bond 0.07278 / 4.88 ( 420) hydrogen bonds : angle 4.36401 / 3.13 ( 1004) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 27 time to evaluate : 0.135 Fit side-chains REVERT: A 44 ASP cc_start: 0.9171 (OUTLIER) cc_final: 0.8516 (t0) REVERT: A 420 GLN cc_start: 0.6432 (OUTLIER) cc_final: 0.6123 (tm-30) outliers start: 28 outliers final: 9 residues processed: 49 average time/residue: 0.3880 time to fit residues: 21.1041 Evaluate side-chains 35 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 24 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 420 GLN Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 629 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 40 optimal weight: 0.7980 chunk 67 optimal weight: 40.0000 chunk 5 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 62 optimal weight: 30.0000 chunk 54 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN A 288 ASN A 379 ASN A 598 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.114065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.089496 restraints weight = 27030.389| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 1.87 r_work: 0.3601 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9846 Z= 0.134 Angle : 0.502 8.593 14524 Z= 0.296 Chirality : 0.034 0.229 1810 Planarity : 0.005 0.083 923 Dihedral : 24.054 151.037 4347 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 5.34 % Allowed : 32.28 % Favored : 62.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.40), residues: 461 helix: 0.92 (0.31), residues: 246 sheet: -1.79 (0.61), residues: 78 loop : -0.75 (0.60), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 78 TYR 0.029 0.002 TYR A 590 PHE 0.009 0.001 PHE A 433 TRP 0.011 0.001 TRP A 588 HIS 0.004 0.001 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.13 ( 9846) covalent geometry : angle 0.50217 / 0.30 (14524) hydrogen bonds : bond 0.05544 / 3.84 ( 420) hydrogen bonds : angle 3.97440 / 2.87 ( 1004) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 28 time to evaluate : 0.200 Fit side-chains REVERT: A 44 ASP cc_start: 0.9135 (OUTLIER) cc_final: 0.8501 (t0) REVERT: A 455 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8768 (tp) outliers start: 22 outliers final: 8 residues processed: 45 average time/residue: 0.3634 time to fit residues: 18.3064 Evaluate side-chains 32 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 22 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 446 HIS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 628 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 48 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 0.0000 chunk 37 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN A 379 ASN A 598 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.112113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.087459 restraints weight = 27407.413| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 1.93 r_work: 0.3550 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9846 Z= 0.227 Angle : 0.555 8.864 14524 Z= 0.321 Chirality : 0.037 0.232 1810 Planarity : 0.005 0.085 923 Dihedral : 24.009 150.449 4347 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 7.77 % Allowed : 30.10 % Favored : 62.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.40), residues: 461 helix: 0.72 (0.31), residues: 251 sheet: -1.96 (0.61), residues: 76 loop : -0.92 (0.61), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 350 TYR 0.024 0.002 TYR A 590 PHE 0.015 0.002 PHE A 433 TRP 0.011 0.002 TRP A 588 HIS 0.005 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.23 ( 9846) covalent geometry : angle 0.55478 / 0.32 (14524) hydrogen bonds : bond 0.06163 / 4.20 ( 420) hydrogen bonds : angle 4.02783 / 2.91 ( 1004) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 26 time to evaluate : 0.225 Fit side-chains REVERT: A 44 ASP cc_start: 0.9174 (OUTLIER) cc_final: 0.8565 (t0) REVERT: A 385 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7641 (mp0) REVERT: A 455 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8690 (tt) REVERT: A 514 PHE cc_start: 0.6303 (OUTLIER) cc_final: 0.5925 (p90) outliers start: 32 outliers final: 14 residues processed: 52 average time/residue: 0.2956 time to fit residues: 17.4857 Evaluate side-chains 41 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 23 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 446 HIS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 484 ASN Chi-restraints excluded: chain A residue 514 PHE Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 629 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 42 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 58 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN A 379 ASN A 598 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.113815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.089367 restraints weight = 27194.855| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 1.88 r_work: 0.3598 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9846 Z= 0.133 Angle : 0.492 8.832 14524 Z= 0.287 Chirality : 0.033 0.230 1810 Planarity : 0.005 0.082 923 Dihedral : 23.991 150.188 4347 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 5.58 % Allowed : 31.55 % Favored : 62.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.40), residues: 461 helix: 1.18 (0.31), residues: 243 sheet: -1.90 (0.57), residues: 82 loop : -0.97 (0.60), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 350 TYR 0.020 0.002 TYR A 590 PHE 0.012 0.001 PHE A 514 TRP 0.007 0.001 TRP A 588 HIS 0.003 0.001 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.13 ( 9846) covalent geometry : angle 0.49214 / 0.29 (14524) hydrogen bonds : bond 0.05162 / 3.59 ( 420) hydrogen bonds : angle 3.85093 / 2.80 ( 1004) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 30 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 44 ASP cc_start: 0.9141 (OUTLIER) cc_final: 0.8502 (t0) REVERT: A 385 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7715 (mp0) REVERT: A 455 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8571 (tt) outliers start: 23 outliers final: 10 residues processed: 49 average time/residue: 0.3350 time to fit residues: 18.3443 Evaluate side-chains 37 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 24 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 446 HIS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 628 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 64 optimal weight: 9.9990 chunk 34 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN A 288 ASN A 379 ASN A 598 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.113293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.088941 restraints weight = 27313.711| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 1.86 r_work: 0.3583 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9846 Z= 0.158 Angle : 0.502 8.982 14524 Z= 0.290 Chirality : 0.034 0.228 1810 Planarity : 0.005 0.082 923 Dihedral : 23.948 149.954 4347 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 6.07 % Allowed : 31.55 % Favored : 62.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.40), residues: 461 helix: 0.94 (0.31), residues: 254 sheet: -1.98 (0.59), residues: 76 loop : -1.10 (0.60), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 350 TYR 0.015 0.002 TYR A 590 PHE 0.013 0.001 PHE A 433 TRP 0.008 0.001 TRP A 366 HIS 0.004 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.16 ( 9846) covalent geometry : angle 0.50187 / 0.29 (14524) hydrogen bonds : bond 0.05245 / 3.62 ( 420) hydrogen bonds : angle 3.81257 / 2.78 ( 1004) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 25 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 44 ASP cc_start: 0.9172 (OUTLIER) cc_final: 0.8523 (t0) REVERT: A 385 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7704 (mp0) REVERT: A 455 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8623 (tt) outliers start: 25 outliers final: 12 residues processed: 47 average time/residue: 0.3559 time to fit residues: 18.8303 Evaluate side-chains 38 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 23 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 446 HIS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 628 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 39 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 26 optimal weight: 0.6980 chunk 60 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN A 379 ASN A 598 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.110693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.085852 restraints weight = 27265.205| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.02 r_work: 0.3527 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9846 Z= 0.269 Angle : 0.601 9.126 14524 Z= 0.341 Chirality : 0.039 0.229 1810 Planarity : 0.006 0.081 923 Dihedral : 24.011 149.176 4347 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 7.04 % Allowed : 30.34 % Favored : 62.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.40), residues: 461 helix: 0.58 (0.31), residues: 254 sheet: -1.95 (0.62), residues: 74 loop : -1.14 (0.60), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 350 TYR 0.015 0.002 TYR A 91 PHE 0.017 0.002 PHE A 433 TRP 0.013 0.002 TRP A 366 HIS 0.006 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.27 ( 9846) covalent geometry : angle 0.60122 / 0.34 (14524) hydrogen bonds : bond 0.06433 / 4.37 ( 420) hydrogen bonds : angle 4.08623 / 2.96 ( 1004) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 25 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.9170 (OUTLIER) cc_final: 0.8535 (t0) REVERT: A 455 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8594 (tt) REVERT: A 514 PHE cc_start: 0.6288 (OUTLIER) cc_final: 0.5840 (p90) outliers start: 29 outliers final: 15 residues processed: 50 average time/residue: 0.3587 time to fit residues: 20.0265 Evaluate side-chains 42 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 24 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 446 HIS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 484 ASN Chi-restraints excluded: chain A residue 514 PHE Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 629 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 21 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN A 598 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.112829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.088124 restraints weight = 27202.320| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 1.87 r_work: 0.3579 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9846 Z= 0.138 Angle : 0.511 9.157 14524 Z= 0.294 Chirality : 0.034 0.227 1810 Planarity : 0.005 0.078 923 Dihedral : 24.012 149.251 4347 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 4.13 % Allowed : 33.25 % Favored : 62.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.40), residues: 461 helix: 1.19 (0.31), residues: 242 sheet: -1.93 (0.58), residues: 82 loop : -1.03 (0.60), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 435 TYR 0.017 0.002 TYR A 590 PHE 0.012 0.001 PHE A 514 TRP 0.005 0.001 TRP A 588 HIS 0.003 0.001 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.14 ( 9846) covalent geometry : angle 0.51076 / 0.29 (14524) hydrogen bonds : bond 0.05088 / 3.54 ( 420) hydrogen bonds : angle 3.87961 / 2.83 ( 1004) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 25 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 44 ASP cc_start: 0.9141 (OUTLIER) cc_final: 0.8497 (t0) REVERT: A 455 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8533 (tt) REVERT: A 514 PHE cc_start: 0.6138 (OUTLIER) cc_final: 0.5706 (p90) outliers start: 17 outliers final: 10 residues processed: 40 average time/residue: 0.3400 time to fit residues: 15.3633 Evaluate side-chains 37 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 24 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 446 HIS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 514 PHE Chi-restraints excluded: chain A residue 628 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 44 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 6 optimal weight: 0.0980 chunk 60 optimal weight: 8.9990 chunk 62 optimal weight: 30.0000 chunk 61 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN A 379 ASN A 598 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.112878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.088192 restraints weight = 27090.562| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 1.87 r_work: 0.3585 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9846 Z= 0.147 Angle : 0.507 9.256 14524 Z= 0.291 Chirality : 0.034 0.224 1810 Planarity : 0.005 0.081 923 Dihedral : 23.962 148.766 4347 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 4.61 % Allowed : 33.01 % Favored : 62.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.40), residues: 461 helix: 1.26 (0.31), residues: 242 sheet: -1.90 (0.57), residues: 82 loop : -1.04 (0.60), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 435 TYR 0.014 0.002 TYR A 590 PHE 0.012 0.001 PHE A 433 TRP 0.006 0.001 TRP A 366 HIS 0.003 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.15 ( 9846) covalent geometry : angle 0.50691 / 0.29 (14524) hydrogen bonds : bond 0.05006 / 3.47 ( 420) hydrogen bonds : angle 3.87307 / 2.82 ( 1004) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 25 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 44 ASP cc_start: 0.9143 (OUTLIER) cc_final: 0.8491 (t0) REVERT: A 455 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8540 (tt) REVERT: A 514 PHE cc_start: 0.6188 (OUTLIER) cc_final: 0.5760 (p90) outliers start: 19 outliers final: 11 residues processed: 42 average time/residue: 0.4145 time to fit residues: 19.2377 Evaluate side-chains 35 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 21 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 446 HIS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 514 PHE Chi-restraints excluded: chain A residue 628 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 54 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 69 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN A 288 ASN A 598 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.111528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.086716 restraints weight = 27148.844| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 1.90 r_work: 0.3548 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9846 Z= 0.208 Angle : 0.554 9.419 14524 Z= 0.314 Chirality : 0.036 0.224 1810 Planarity : 0.005 0.077 923 Dihedral : 23.976 147.905 4347 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 4.13 % Allowed : 33.74 % Favored : 62.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.40), residues: 461 helix: 0.80 (0.31), residues: 253 sheet: -1.95 (0.61), residues: 76 loop : -1.02 (0.61), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 350 TYR 0.016 0.002 TYR A 91 PHE 0.015 0.002 PHE A 433 TRP 0.009 0.002 TRP A 588 HIS 0.006 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.21 ( 9846) covalent geometry : angle 0.55417 / 0.31 (14524) hydrogen bonds : bond 0.05585 / 3.83 ( 420) hydrogen bonds : angle 3.97552 / 2.88 ( 1004) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 22 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 44 ASP cc_start: 0.9150 (OUTLIER) cc_final: 0.8520 (t0) REVERT: A 455 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8562 (tt) REVERT: A 514 PHE cc_start: 0.6225 (OUTLIER) cc_final: 0.5676 (p90) outliers start: 17 outliers final: 9 residues processed: 37 average time/residue: 0.3699 time to fit residues: 15.3052 Evaluate side-chains 33 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 21 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 514 PHE Chi-restraints excluded: chain A residue 628 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 60 optimal weight: 8.9990 chunk 6 optimal weight: 0.0570 chunk 42 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 45 optimal weight: 0.5980 overall best weight: 1.0902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN A 598 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.112885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.088733 restraints weight = 26891.181| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.68 r_work: 0.3612 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9846 Z= 0.142 Angle : 0.509 9.398 14524 Z= 0.289 Chirality : 0.033 0.222 1810 Planarity : 0.005 0.081 923 Dihedral : 23.968 147.736 4347 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.88 % Allowed : 33.50 % Favored : 62.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.40), residues: 461 helix: 1.28 (0.31), residues: 242 sheet: -1.85 (0.59), residues: 77 loop : -1.07 (0.58), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 435 TYR 0.014 0.002 TYR A 590 PHE 0.011 0.001 PHE A 433 TRP 0.005 0.001 TRP A 382 HIS 0.007 0.001 HIS A 446 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.14 ( 9846) covalent geometry : angle 0.50852 / 0.29 (14524) hydrogen bonds : bond 0.04882 / 3.40 ( 420) hydrogen bonds : angle 3.86885 / 2.82 ( 1004) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2574.06 seconds wall clock time: 44 minutes 50.39 seconds (2690.39 seconds total)