Starting phenix.real_space_refine on Wed Aug 5 06:59:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8axa_15697/08_2026/8axa_15697.cif Found real_map, /net/cci-nas-00/data/ceres_data/8axa_15697/08_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_15697/08_2026/8axa_15697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8axa_15697/08_2026/8axa_15697.map" model { file = "/net/cci-nas-00/data/ceres_data/8axa_15697/08_2026/8axa_15697.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8axa_15697/08_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-2.2rc3-6140/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: 2.20, per 1000 atoms: 0.24 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: 1.02 Conformation dependent library (CDL) restraints added in 154.7 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: 1.30 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: 2.13 Time building geometry restraints manager: 1.29 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: 13684 1.88 - 3.76: 812 3.76 - 5.64: 18 5.64 - 7.52: 8 7.52 - 9.40: 2 Bond angle restraints: 14524 Sorted by residual: angle pdb=" O4' A B 139 " pdb=" C1' A B 139 " pdb=" N9 A B 139 " ideal model delta sigma weight residual 108.50 112.20 -3.70 7.00e-01 2.04e+00 2.79e+01 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=" C3' U B 190 " pdb=" O3' U B 190 " pdb=" P G B 191 " ideal model delta sigma weight residual 119.70 125.48 -5.78 1.20e+00 6.94e-01 2.32e+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 ... (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 - 0.039: 1220 0.039 - 0.078: 278 0.078 - 0.118: 101 0.118 - 0.157: 207 0.157 - 0.196: 4 Chirality restraints: 1810 Sorted by residual: 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 2.47 2.28 0.20 2.00e-01 2.50e+01 9.61e-01 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=" 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: 3.720 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.480 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:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.040 ------------------------------------------------------------------------------- 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= 0.306 Angle : 0.777 9.396 14524 Z= 0.636 Chirality : 0.057 0.196 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 0.00370 / 0.31 ( 9846) covalent geometry : angle 0.77657 / 0.64 (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 : 0.210 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 46 average time/residue: 0.5761 time to fit residues: 28.5171 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 : 0.204 ------------------------------------------------------------------------------- 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: 9.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 40.0000 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 20.0000 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 = 0.4172 r_free = 0.4172 target = 0.111511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.086773 restraints weight = 27084.819| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 1.88 r_work: 0.3533 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 9846 Z= 0.296 Angle : 0.691 8.899 14524 Z= 0.377 Chirality : 0.045 0.293 1810 Planarity : 0.007 0.087 923 Dihedral : 23.988 154.927 4347 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 7.04 % Allowed : 29.61 % 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: -0.61 (0.40), residues: 461 helix: 0.56 (0.31), residues: 245 sheet: -1.85 (0.58), residues: 78 loop : -1.02 (0.62), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 592 TYR 0.015 0.002 TYR A 91 PHE 0.017 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 0.00566 / 0.30 ( 9846) covalent geometry : angle 0.69064 / 0.38 (14524) hydrogen bonds : bond 0.07370 / 4.93 ( 420) hydrogen bonds : angle 4.36370 / 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 56 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 27 time to evaluate : 0.244 Fit side-chains REVERT: A 44 ASP cc_start: 0.9165 (OUTLIER) cc_final: 0.8509 (t0) REVERT: A 420 GLN cc_start: 0.6432 (OUTLIER) cc_final: 0.6121 (tm-30) REVERT: A 590 TYR cc_start: 0.8187 (OUTLIER) cc_final: 0.7924 (m-10) outliers start: 29 outliers final: 10 residues processed: 51 average time/residue: 0.3563 time to fit residues: 20.2325 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 : 0.252 ------------------------------------------------------------------------------- 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 302 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 590 TYR 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: 0.9980 chunk 67 optimal weight: 40.0000 chunk 5 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 40.0000 chunk 54 optimal weight: 8.9990 chunk 15 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 24 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 = 0.4205 r_free = 0.4205 target = 0.113358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.088793 restraints weight = 26994.422| |-----------------------------------------------------------------------------| r_work (start): 0.3727 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: 0.7893 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9846 Z= 0.155 Angle : 0.538 8.503 14524 Z= 0.306 Chirality : 0.036 0.295 1810 Planarity : 0.005 0.083 923 Dihedral : 23.975 154.491 4347 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 5.10 % Allowed : 31.55 % 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: -0.31 (0.40), residues: 461 helix: 0.79 (0.31), residues: 246 sheet: -1.82 (0.62), residues: 78 loop : -0.80 (0.60), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 435 TYR 0.017 0.002 TYR A 590 PHE 0.011 0.001 PHE A 433 TRP 0.010 0.001 TRP A 588 HIS 0.004 0.001 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.16 ( 9846) covalent geometry : angle 0.53778 / 0.31 (14524) hydrogen bonds : bond 0.05886 / 4.06 ( 420) hydrogen bonds : angle 4.07825 / 2.93 ( 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 51 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 30 time to evaluate : 0.209 Fit side-chains REVERT: A 44 ASP cc_start: 0.9140 (OUTLIER) cc_final: 0.8510 (t0) REVERT: A 455 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8763 (tp) REVERT: A 590 TYR cc_start: 0.8260 (OUTLIER) cc_final: 0.7996 (m-10) outliers start: 21 outliers final: 7 residues processed: 45 average time/residue: 0.3185 time to fit residues: 16.1557 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 : 0.192 ------------------------------------------------------------------------------- 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 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 590 TYR 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: 20.0000 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 18 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 = 0.4179 r_free = 0.4179 target = 0.111570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.086978 restraints weight = 27181.825| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 1.85 r_work: 0.3543 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9846 Z= 0.233 Angle : 0.617 8.826 14524 Z= 0.338 Chirality : 0.041 0.285 1810 Planarity : 0.006 0.085 923 Dihedral : 23.960 154.662 4347 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 8.50 % Allowed : 28.16 % 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: -0.56 (0.40), residues: 461 helix: 0.56 (0.31), residues: 251 sheet: -1.86 (0.61), residues: 74 loop : -1.01 (0.60), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 391 TYR 0.018 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 0.00442 / 0.23 ( 9846) covalent geometry : angle 0.61715 / 0.34 (14524) hydrogen bonds : bond 0.06557 / 4.45 ( 420) hydrogen bonds : angle 4.12747 / 2.98 ( 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 61 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 26 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 44 ASP cc_start: 0.9198 (OUTLIER) cc_final: 0.8567 (t0) REVERT: A 385 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7615 (mp0) REVERT: A 455 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8710 (tt) outliers start: 35 outliers final: 15 residues processed: 55 average time/residue: 0.2702 time to fit residues: 17.2595 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 : 0.218 ------------------------------------------------------------------------------- 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 58 VAL Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 348 THR 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 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: 0.9980 chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 33 optimal weight: 0.0050 chunk 47 optimal weight: 9.9990 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 26 optimal weight: 0.1980 chunk 6 optimal weight: 0.9980 chunk 58 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 overall best weight: 0.5794 ------------------------------------------------------------------------------- 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 = 0.4224 r_free = 0.4224 target = 0.114159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.089919 restraints weight = 26983.222| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 1.84 r_work: 0.3614 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9846 Z= 0.118 Angle : 0.503 8.471 14524 Z= 0.286 Chirality : 0.034 0.309 1810 Planarity : 0.005 0.082 923 Dihedral : 23.922 155.232 4347 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 5.58 % Allowed : 31.31 % Favored : 63.11 % 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: -0.08 (0.40), residues: 461 helix: 1.21 (0.31), residues: 243 sheet: -1.91 (0.57), residues: 82 loop : -0.99 (0.59), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 493 TYR 0.021 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 0.00215 / 0.12 ( 9846) covalent geometry : angle 0.50268 / 0.29 (14524) hydrogen bonds : bond 0.05213 / 3.65 ( 420) hydrogen bonds : angle 3.85011 / 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 54 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 31 time to evaluate : 0.131 Fit side-chains revert: symmetry clash REVERT: A 44 ASP cc_start: 0.9138 (OUTLIER) cc_final: 0.8497 (t0) REVERT: A 385 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7695 (mp0) REVERT: A 455 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8581 (tp) outliers start: 23 outliers final: 10 residues processed: 50 average time/residue: 0.3300 time to fit residues: 18.3796 Evaluate side-chains 38 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 25 time to evaluate : 0.226 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 28 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 64 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.4203 r_free = 0.4203 target = 0.112929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.088531 restraints weight = 27225.372| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 1.86 r_work: 0.3579 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9846 Z= 0.168 Angle : 0.549 10.935 14524 Z= 0.301 Chirality : 0.036 0.297 1810 Planarity : 0.005 0.083 923 Dihedral : 23.861 155.040 4347 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 6.80 % Allowed : 30.83 % 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: -0.30 (0.40), residues: 461 helix: 0.90 (0.31), residues: 254 sheet: -1.94 (0.61), residues: 76 loop : -1.07 (0.61), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 350 TYR 0.012 0.002 TYR A 590 PHE 0.014 0.001 PHE A 433 TRP 0.016 0.002 TRP A 588 HIS 0.004 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.17 ( 9846) covalent geometry : angle 0.54920 / 0.30 (14524) hydrogen bonds : bond 0.05468 / 3.76 ( 420) hydrogen bonds : angle 3.84702 / 2.79 ( 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 53 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 25 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: A 44 ASP cc_start: 0.9162 (OUTLIER) cc_final: 0.8522 (t0) REVERT: A 385 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7704 (mp0) REVERT: A 455 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8674 (tp) outliers start: 28 outliers final: 14 residues processed: 50 average time/residue: 0.3359 time to fit residues: 18.7971 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 : 0.127 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain A residue 629 SER 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: 0.9980 chunk 60 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 = 0.4189 r_free = 0.4189 target = 0.112066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.087342 restraints weight = 27194.701| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 1.86 r_work: 0.3563 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9846 Z= 0.199 Angle : 0.579 10.948 14524 Z= 0.315 Chirality : 0.038 0.298 1810 Planarity : 0.005 0.080 923 Dihedral : 23.899 154.922 4347 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 6.55 % Allowed : 31.55 % Favored : 61.89 % 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: -0.28 (0.40), residues: 461 helix: 0.95 (0.31), residues: 247 sheet: -1.93 (0.58), residues: 80 loop : -0.98 (0.62), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 350 TYR 0.015 0.002 TYR A 590 PHE 0.014 0.002 PHE A 433 TRP 0.015 0.002 TRP A 588 HIS 0.005 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.20 ( 9846) covalent geometry : angle 0.57924 / 0.32 (14524) hydrogen bonds : bond 0.05663 / 3.88 ( 420) hydrogen bonds : angle 3.93248 / 2.85 ( 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 49 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 22 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: A 44 ASP cc_start: 0.9161 (OUTLIER) cc_final: 0.8510 (t0) REVERT: A 385 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7625 (mp0) REVERT: A 455 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8543 (tt) outliers start: 27 outliers final: 16 residues processed: 46 average time/residue: 0.4231 time to fit residues: 21.2726 Evaluate side-chains 39 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 20 time to evaluate : 0.213 ------------------------------------------------------------------------------- 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 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 419 ILE 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 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: 0.5980 chunk 40 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 58 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4220 r_free = 0.4220 target = 0.113854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.089312 restraints weight = 27189.953| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.87 r_work: 0.3609 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9846 Z= 0.122 Angle : 0.507 8.616 14524 Z= 0.282 Chirality : 0.034 0.310 1810 Planarity : 0.005 0.081 923 Dihedral : 23.858 155.488 4347 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 4.13 % Allowed : 32.77 % Favored : 63.11 % 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: 0.11 (0.40), residues: 461 helix: 1.41 (0.31), residues: 242 sheet: -1.96 (0.56), residues: 82 loop : -0.89 (0.60), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 592 TYR 0.016 0.001 TYR A 590 PHE 0.011 0.001 PHE A 514 TRP 0.012 0.001 TRP A 588 HIS 0.003 0.001 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.12 ( 9846) covalent geometry : angle 0.50651 / 0.28 (14524) hydrogen bonds : bond 0.04867 / 3.41 ( 420) hydrogen bonds : angle 3.78844 / 2.76 ( 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 40 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 23 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: A 44 ASP cc_start: 0.9131 (OUTLIER) cc_final: 0.8474 (t0) REVERT: A 385 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7692 (mp0) REVERT: A 455 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8509 (tt) outliers start: 17 outliers final: 9 residues processed: 38 average time/residue: 0.3562 time to fit residues: 14.7506 Evaluate side-chains 32 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 20 time to evaluate : 0.146 ------------------------------------------------------------------------------- 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 349 LEU 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 44 optimal weight: 0.5980 chunk 34 optimal weight: 0.0040 chunk 24 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 60 optimal weight: 9.9990 chunk 62 optimal weight: 40.0000 chunk 61 optimal weight: 10.0000 overall best weight: 0.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 ASN A 75 GLN A 288 ASN A 379 ASN A 598 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.113918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.089556 restraints weight = 26915.236| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 1.85 r_work: 0.3614 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9846 Z= 0.125 Angle : 0.507 8.747 14524 Z= 0.281 Chirality : 0.033 0.307 1810 Planarity : 0.005 0.079 923 Dihedral : 23.789 155.505 4347 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 4.61 % Allowed : 32.28 % Favored : 63.11 % 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: 0.25 (0.41), residues: 461 helix: 1.55 (0.31), residues: 242 sheet: -1.93 (0.57), residues: 77 loop : -0.91 (0.59), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 592 TYR 0.014 0.001 TYR A 590 PHE 0.011 0.001 PHE A 433 TRP 0.013 0.001 TRP A 588 HIS 0.003 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.12 ( 9846) covalent geometry : angle 0.50689 / 0.28 (14524) hydrogen bonds : bond 0.04730 / 3.29 ( 420) hydrogen bonds : angle 3.75962 / 2.73 ( 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 41 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 22 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: A 44 ASP cc_start: 0.9148 (OUTLIER) cc_final: 0.8505 (t0) REVERT: A 385 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7633 (mp0) REVERT: A 455 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8664 (tp) outliers start: 19 outliers final: 12 residues processed: 38 average time/residue: 0.3733 time to fit residues: 15.7237 Evaluate side-chains 34 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 19 time to evaluate : 0.196 ------------------------------------------------------------------------------- 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 330 GLU Chi-restraints excluded: chain A residue 349 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 54 optimal weight: 8.9990 chunk 48 optimal weight: 20.0000 chunk 24 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 19 optimal weight: 0.2980 chunk 4 optimal weight: 4.9990 chunk 66 optimal weight: 20.0000 chunk 39 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 31 optimal weight: 0.6980 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 = 0.4188 r_free = 0.4188 target = 0.111913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.087207 restraints weight = 27198.245| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 1.87 r_work: 0.3561 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9846 Z= 0.202 Angle : 0.583 9.004 14524 Z= 0.315 Chirality : 0.038 0.300 1810 Planarity : 0.005 0.079 923 Dihedral : 23.814 154.768 4347 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 4.85 % Allowed : 32.77 % 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: 0.16 (0.41), residues: 461 helix: 1.38 (0.31), residues: 240 sheet: -1.83 (0.59), residues: 82 loop : -0.74 (0.62), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 592 TYR 0.040 0.002 TYR A 590 PHE 0.015 0.002 PHE A 433 TRP 0.011 0.002 TRP A 588 HIS 0.006 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.20 ( 9846) covalent geometry : angle 0.58285 / 0.31 (14524) hydrogen bonds : bond 0.05444 / 3.72 ( 420) hydrogen bonds : angle 3.92793 / 2.84 ( 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 40 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 20 time to evaluate : 0.150 Fit side-chains revert: symmetry clash REVERT: A 44 ASP cc_start: 0.9151 (OUTLIER) cc_final: 0.8513 (t0) REVERT: A 385 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7781 (mp0) REVERT: A 455 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8557 (tt) outliers start: 20 outliers final: 12 residues processed: 37 average time/residue: 0.3365 time to fit residues: 13.6998 Evaluate side-chains 35 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 20 time to evaluate : 0.154 ------------------------------------------------------------------------------- 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 330 GLU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 385 GLU 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 628 LEU Chi-restraints excluded: chain A residue 629 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 60 optimal weight: 9.9990 chunk 6 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 57 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.112682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.088039 restraints weight = 26868.114| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 1.84 r_work: 0.3584 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9846 Z= 0.153 Angle : 0.533 9.090 14524 Z= 0.293 Chirality : 0.035 0.307 1810 Planarity : 0.005 0.078 923 Dihedral : 23.838 154.905 4347 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.90 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: 0.16 (0.41), residues: 461 helix: 1.40 (0.31), residues: 242 sheet: -1.82 (0.59), residues: 82 loop : -0.85 (0.61), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 350 TYR 0.013 0.002 TYR A 590 PHE 0.011 0.001 PHE A 433 TRP 0.009 0.001 TRP A 588 HIS 0.004 0.001 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.15 ( 9846) covalent geometry : angle 0.53319 / 0.29 (14524) hydrogen bonds : bond 0.05024 / 3.47 ( 420) hydrogen bonds : angle 3.86194 / 2.80 ( 1004) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2356.77 seconds wall clock time: 41 minutes 0.28 seconds (2460.28 seconds total)