Starting phenix.real_space_refine on Sat Aug 23 01:26:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8axa_15697/08_2025/8axa_15697.cif Found real_map, /net/cci-nas-00/data/ceres_data/8axa_15697/08_2025/8axa_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_2025/8axa_15697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8axa_15697/08_2025/8axa_15697.map" model { file = "/net/cci-nas-00/data/ceres_data/8axa_15697/08_2025/8axa_15697.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8axa_15697/08_2025/8axa_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-2.0-5787/lib/python3.9/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: 2.34, per 1000 atoms: 0.26 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: 1.01 Conformation dependent library (CDL) restraints added in 164.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.42 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: 2.06 Time building geometry restraints manager: 1.27 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' U B 190 " pdb=" O3' U B 190 " ideal model delta sigma weight residual 1.427 1.444 -0.017 1.50e-02 4.44e+03 1.27e+00 bond pdb=" CG ARG A 493 " pdb=" CD ARG A 493 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.15e+00 bond pdb=" CB MET A 551 " pdb=" CG MET A 551 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.54e-01 bond pdb=" CB VAL A 377 " pdb=" CG1 VAL A 377 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.45e-01 bond pdb=" CB GLU A 358 " pdb=" CG GLU A 358 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.44e-01 ... (remaining 9841 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 14284 1.88 - 3.76: 212 3.76 - 5.64: 19 5.64 - 7.52: 7 7.52 - 9.40: 2 Bond angle restraints: 14524 Sorted by residual: 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 angle pdb=" C3' U B 190 " pdb=" O3' U B 190 " pdb=" P G B 191 " ideal model delta sigma weight residual 120.20 125.48 -5.28 1.50e+00 4.44e-01 1.24e+01 angle pdb=" C THR A 68 " pdb=" N ASP A 69 " pdb=" CA ASP A 69 " ideal model delta sigma weight residual 121.98 131.38 -9.40 3.11e+00 1.03e-01 9.13e+00 angle pdb=" O3' U B 190 " pdb=" P G B 191 " pdb=" OP1 G B 191 " ideal model delta sigma weight residual 108.00 116.20 -8.20 3.00e+00 1.11e-01 7.47e+00 angle pdb=" CA GLY A 52 " pdb=" C GLY A 52 " pdb=" O GLY A 52 " ideal model delta sigma weight residual 122.24 120.06 2.18 8.70e-01 1.32e+00 6.26e+00 ... (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: 1445 0.037 - 0.074: 287 0.074 - 0.110: 60 0.110 - 0.147: 13 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: 6.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.550 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:6.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 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 : 0.003 0.032 9846 Z= 0.160 Angle : 0.571 9.396 14524 Z= 0.294 Chirality : 0.033 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 aren 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 covalent geometry : bond 0.00328 ( 9846) covalent geometry : angle 0.57124 (14524) hydrogen bonds : bond 0.10297 ( 420) hydrogen bonds : angle 4.97477 ( 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 : 0.214 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 46 average time/residue: 0.5636 time to fit residues: 27.6499 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 : 0.213 ------------------------------------------------------------------------------- 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: 5.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN A 75 GLN A 367 ASN A 580 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.110639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.085914 restraints weight = 27201.732| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.01 r_work: 0.3519 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 9846 Z= 0.326 Angle : 0.696 8.953 14524 Z= 0.356 Chirality : 0.039 0.235 1810 Planarity : 0.006 0.087 923 Dihedral : 24.104 150.116 4347 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.90 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 aren not related in a simple way. whole: -0.72 (0.39), residues: 461 helix: 0.45 (0.31), residues: 254 sheet: -1.89 (0.61), residues: 74 loop : -1.19 (0.59), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 78 TYR 0.021 0.002 TYR A 590 PHE 0.016 0.002 PHE A 433 TRP 0.012 0.002 TRP A 366 HIS 0.006 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00664 ( 9846) covalent geometry : angle 0.69586 (14524) hydrogen bonds : bond 0.06412 ( 420) hydrogen bonds : angle 4.21787 ( 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 59 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 30 time to evaluate : 0.226 Fit side-chains REVERT: A 23 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7700 (tm) REVERT: A 44 ASP cc_start: 0.9139 (OUTLIER) cc_final: 0.8485 (t0) REVERT: A 397 GLU cc_start: 0.4466 (OUTLIER) cc_final: 0.3721 (tm-30) outliers start: 29 outliers final: 10 residues processed: 55 average time/residue: 0.3924 time to fit residues: 24.0379 Evaluate side-chains 36 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 23 time to evaluate : 0.228 ------------------------------------------------------------------------------- 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 23 LEU Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 464 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 40 optimal weight: 0.9980 chunk 67 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 62 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 288 ASN A 379 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.113579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.089125 restraints weight = 26989.412| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 1.86 r_work: 0.3596 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1549 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= 0.144 Angle : 0.559 8.916 14524 Z= 0.287 Chirality : 0.033 0.227 1810 Planarity : 0.005 0.085 923 Dihedral : 23.965 149.661 4347 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 5.34 % Allowed : 30.83 % Favored : 63.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.41), residues: 461 helix: 1.18 (0.31), residues: 243 sheet: -1.80 (0.61), residues: 82 loop : -0.87 (0.60), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 435 TYR 0.031 0.002 TYR A 590 PHE 0.011 0.001 PHE A 433 TRP 0.006 0.001 TRP A 366 HIS 0.003 0.001 HIS A 342 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9846) covalent geometry : angle 0.55948 (14524) hydrogen bonds : bond 0.04645 ( 420) hydrogen bonds : angle 3.79173 ( 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 52 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 30 time to evaluate : 0.225 Fit side-chains REVERT: A 23 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7586 (tm) REVERT: A 44 ASP cc_start: 0.9181 (OUTLIER) cc_final: 0.8573 (t0) REVERT: A 385 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7722 (mp0) REVERT: A 455 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8505 (tt) outliers start: 22 outliers final: 4 residues processed: 46 average time/residue: 0.3959 time to fit residues: 20.2806 Evaluate side-chains 32 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 385 GLU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 48 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 379 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.110489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.085566 restraints weight = 27305.361| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.88 r_work: 0.3526 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1912 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= 0.285 Angle : 0.667 9.320 14524 Z= 0.338 Chirality : 0.037 0.229 1810 Planarity : 0.006 0.084 923 Dihedral : 24.055 148.583 4347 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % 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 aren not related in a simple way. whole: -0.49 (0.40), residues: 461 helix: 0.67 (0.31), residues: 254 sheet: -1.82 (0.63), residues: 74 loop : -1.14 (0.61), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 350 TYR 0.022 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 covalent geometry : bond 0.00583 ( 9846) covalent geometry : angle 0.66705 (14524) hydrogen bonds : bond 0.05697 ( 420) hydrogen bonds : angle 4.01256 ( 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 54 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 26 time to evaluate : 0.219 Fit side-chains REVERT: A 23 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7719 (tm) REVERT: A 44 ASP cc_start: 0.9147 (OUTLIER) cc_final: 0.8506 (t0) REVERT: A 385 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7714 (mp0) REVERT: A 388 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7886 (mp0) outliers start: 28 outliers final: 10 residues processed: 49 average time/residue: 0.3525 time to fit residues: 19.4786 Evaluate side-chains 39 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 25 time to evaluate : 0.212 ------------------------------------------------------------------------------- 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 23 LEU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 388 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 464 VAL Chi-restraints excluded: chain A residue 471 VAL 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: 0.6980 chunk 45 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 33 optimal weight: 0.0040 chunk 47 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 0.0010 chunk 26 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 75 GLN A 379 ASN A 613 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.114962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.091166 restraints weight = 27279.173| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 1.74 r_work: 0.3656 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 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 0.039 9846 Z= 0.115 Angle : 0.554 10.155 14524 Z= 0.281 Chirality : 0.032 0.218 1810 Planarity : 0.005 0.080 923 Dihedral : 23.879 148.656 4347 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 6.55 % Allowed : 30.34 % 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 aren not related in a simple way. whole: 0.21 (0.41), residues: 461 helix: 1.49 (0.32), residues: 242 sheet: -1.92 (0.57), residues: 82 loop : -0.84 (0.60), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 435 TYR 0.011 0.001 TYR A 474 PHE 0.011 0.001 PHE A 433 TRP 0.021 0.001 TRP A 588 HIS 0.003 0.001 HIS A 342 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 9846) covalent geometry : angle 0.55442 (14524) hydrogen bonds : bond 0.04220 ( 420) hydrogen bonds : angle 3.63605 ( 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 58 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 31 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 23 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7579 (tm) REVERT: A 44 ASP cc_start: 0.9135 (OUTLIER) cc_final: 0.8472 (t0) REVERT: A 335 LYS cc_start: 0.7150 (tttt) cc_final: 0.6529 (tmtt) REVERT: A 455 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8464 (tt) outliers start: 27 outliers final: 11 residues processed: 54 average time/residue: 0.3584 time to fit residues: 21.6978 Evaluate side-chains 37 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 23 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 59 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 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 548 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 28 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 13 optimal weight: 0.0470 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 overall best weight: 1.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 288 ASN A 613 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.112104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.087912 restraints weight = 27471.614| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 1.76 r_work: 0.3582 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9846 Z= 0.220 Angle : 0.609 9.582 14524 Z= 0.306 Chirality : 0.034 0.222 1810 Planarity : 0.005 0.079 923 Dihedral : 23.905 147.015 4347 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % 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 aren not related in a simple way. whole: -0.00 (0.41), residues: 461 helix: 1.20 (0.31), residues: 248 sheet: -1.97 (0.60), residues: 78 loop : -0.84 (0.61), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 350 TYR 0.012 0.002 TYR A 474 PHE 0.013 0.002 PHE A 433 TRP 0.010 0.002 TRP A 588 HIS 0.005 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 9846) covalent geometry : angle 0.60916 (14524) hydrogen bonds : bond 0.04771 ( 420) hydrogen bonds : angle 3.76472 ( 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 : 0.242 Fit side-chains revert: symmetry clash REVERT: A 23 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7681 (tm) REVERT: A 44 ASP cc_start: 0.9147 (OUTLIER) cc_final: 0.8495 (t0) REVERT: A 397 GLU cc_start: 0.4483 (OUTLIER) cc_final: 0.3796 (tm-30) REVERT: A 455 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8548 (tt) REVERT: A 514 PHE cc_start: 0.6173 (OUTLIER) cc_final: 0.5689 (p90) outliers start: 28 outliers final: 13 residues processed: 49 average time/residue: 0.3923 time to fit residues: 21.4856 Evaluate side-chains 39 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 21 time to evaluate : 0.254 ------------------------------------------------------------------------------- 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 23 LEU 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 373 LEU Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 427 THR 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 629 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 39 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 29 optimal weight: 0.0670 chunk 12 optimal weight: 0.7980 chunk 9 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 overall best weight: 1.3522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 379 ASN A 420 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.112718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.088575 restraints weight = 27438.773| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 1.73 r_work: 0.3601 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9846 Z= 0.180 Angle : 0.593 11.511 14524 Z= 0.297 Chirality : 0.034 0.219 1810 Planarity : 0.005 0.078 923 Dihedral : 23.895 145.689 4347 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 7.04 % Allowed : 30.10 % 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 aren not related in a simple way. whole: 0.13 (0.41), residues: 461 helix: 1.40 (0.32), residues: 242 sheet: -1.92 (0.58), residues: 82 loop : -0.82 (0.61), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 435 TYR 0.012 0.001 TYR A 474 PHE 0.013 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 covalent geometry : bond 0.00371 ( 9846) covalent geometry : angle 0.59302 (14524) hydrogen bonds : bond 0.04523 ( 420) hydrogen bonds : angle 3.75699 ( 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 52 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 23 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 23 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7668 (tm) REVERT: A 44 ASP cc_start: 0.9152 (OUTLIER) cc_final: 0.8508 (t0) REVERT: A 397 GLU cc_start: 0.4475 (OUTLIER) cc_final: 0.3782 (tm-30) REVERT: A 420 GLN cc_start: 0.6343 (OUTLIER) cc_final: 0.6061 (tm-30) REVERT: A 455 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8498 (tt) REVERT: A 514 PHE cc_start: 0.6169 (OUTLIER) cc_final: 0.5640 (p90) outliers start: 29 outliers final: 14 residues processed: 49 average time/residue: 0.3884 time to fit residues: 21.1878 Evaluate side-chains 42 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 22 time to evaluate : 0.224 ------------------------------------------------------------------------------- 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 23 LEU 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 373 LEU Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 420 GLN Chi-restraints excluded: chain A residue 427 THR 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 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: 0.7980 chunk 40 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 44 optimal weight: 0.0770 chunk 1 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 overall best weight: 1.0940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 420 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 = 0.113108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.088781 restraints weight = 27299.196| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 1.82 r_work: 0.3606 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9846 Z= 0.160 Angle : 0.589 13.661 14524 Z= 0.292 Chirality : 0.033 0.249 1810 Planarity : 0.005 0.077 923 Dihedral : 23.859 143.504 4347 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 6.07 % Allowed : 31.31 % 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 aren not related in a simple way. whole: 0.23 (0.41), residues: 461 helix: 1.50 (0.32), residues: 242 sheet: -1.83 (0.58), residues: 82 loop : -0.86 (0.61), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 350 TYR 0.025 0.002 TYR A 497 PHE 0.011 0.001 PHE A 433 TRP 0.012 0.001 TRP A 588 HIS 0.003 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 9846) covalent geometry : angle 0.58873 (14524) hydrogen bonds : bond 0.04333 ( 420) hydrogen bonds : angle 3.73459 ( 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 49 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 24 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: A 23 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7686 (tm) REVERT: A 44 ASP cc_start: 0.9162 (OUTLIER) cc_final: 0.8521 (t0) REVERT: A 397 GLU cc_start: 0.4490 (OUTLIER) cc_final: 0.3806 (tm-30) REVERT: A 420 GLN cc_start: 0.6348 (OUTLIER) cc_final: 0.6096 (tm-30) REVERT: A 455 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8522 (tt) REVERT: A 514 PHE cc_start: 0.6232 (OUTLIER) cc_final: 0.5729 (p90) outliers start: 25 outliers final: 13 residues processed: 47 average time/residue: 0.4109 time to fit residues: 21.4986 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 : 0.218 ------------------------------------------------------------------------------- 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 23 LEU 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 373 LEU Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 420 GLN Chi-restraints excluded: chain A residue 427 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 44 optimal weight: 0.0030 chunk 34 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 2 optimal weight: 0.3980 chunk 6 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 overall best weight: 1.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 420 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.112444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.088304 restraints weight = 27335.351| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 1.72 r_work: 0.3601 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9846 Z= 0.192 Angle : 0.607 12.764 14524 Z= 0.300 Chirality : 0.033 0.219 1810 Planarity : 0.005 0.077 923 Dihedral : 23.849 141.092 4347 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 5.83 % Allowed : 31.55 % 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 aren not related in a simple way. whole: 0.17 (0.41), residues: 461 helix: 1.42 (0.31), residues: 242 sheet: -1.80 (0.59), residues: 82 loop : -0.86 (0.60), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 350 TYR 0.027 0.002 TYR A 497 PHE 0.012 0.001 PHE A 433 TRP 0.013 0.002 TRP A 588 HIS 0.004 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 9846) covalent geometry : angle 0.60704 (14524) hydrogen bonds : bond 0.04516 ( 420) hydrogen bonds : angle 3.75687 ( 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 45 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 21 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: A 23 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7708 (tm) REVERT: A 44 ASP cc_start: 0.9173 (OUTLIER) cc_final: 0.8535 (t0) REVERT: A 397 GLU cc_start: 0.4492 (OUTLIER) cc_final: 0.3796 (tm-30) REVERT: A 420 GLN cc_start: 0.6318 (OUTLIER) cc_final: 0.6060 (tm-30) REVERT: A 455 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8527 (tt) REVERT: A 514 PHE cc_start: 0.6174 (OUTLIER) cc_final: 0.5613 (p90) outliers start: 24 outliers final: 15 residues processed: 43 average time/residue: 0.4267 time to fit residues: 20.3114 Evaluate side-chains 42 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 21 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 23 LEU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 420 GLN Chi-restraints excluded: chain A residue 427 THR 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 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 54 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.110764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.086342 restraints weight = 27456.853| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 1.79 r_work: 0.3563 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 9846 Z= 0.258 Angle : 0.657 12.554 14524 Z= 0.328 Chirality : 0.036 0.219 1810 Planarity : 0.005 0.077 923 Dihedral : 23.916 140.424 4347 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % 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 aren not related in a simple way. whole: -0.13 (0.41), residues: 461 helix: 1.03 (0.31), residues: 248 sheet: -1.83 (0.62), residues: 78 loop : -0.91 (0.61), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 350 TYR 0.025 0.002 TYR A 497 PHE 0.014 0.002 PHE A 433 TRP 0.014 0.002 TRP A 588 HIS 0.005 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00530 ( 9846) covalent geometry : angle 0.65700 (14524) hydrogen bonds : bond 0.05190 ( 420) hydrogen bonds : angle 3.90685 ( 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 47 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 22 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 23 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7801 (tm) REVERT: A 44 ASP cc_start: 0.9180 (OUTLIER) cc_final: 0.8563 (t0) REVERT: A 397 GLU cc_start: 0.4613 (OUTLIER) cc_final: 0.3850 (tm-30) REVERT: A 455 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8551 (tt) REVERT: A 514 PHE cc_start: 0.6168 (OUTLIER) cc_final: 0.5623 (p90) outliers start: 25 outliers final: 15 residues processed: 44 average time/residue: 0.3464 time to fit residues: 17.2289 Evaluate side-chains 41 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 21 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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 23 LEU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 427 THR 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 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: 3.9990 chunk 6 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.111818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.087921 restraints weight = 26942.424| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 1.70 r_work: 0.3617 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9846 Z= 0.202 Angle : 0.618 12.586 14524 Z= 0.309 Chirality : 0.034 0.217 1810 Planarity : 0.005 0.077 923 Dihedral : 23.897 140.288 4347 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 5.10 % Allowed : 32.28 % 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 aren not related in a simple way. whole: 0.08 (0.41), residues: 461 helix: 1.28 (0.31), residues: 242 sheet: -1.76 (0.60), residues: 82 loop : -0.83 (0.61), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 350 TYR 0.025 0.002 TYR A 497 PHE 0.013 0.002 PHE A 433 TRP 0.013 0.002 TRP A 588 HIS 0.004 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 9846) covalent geometry : angle 0.61793 (14524) hydrogen bonds : bond 0.04717 ( 420) hydrogen bonds : angle 3.83312 ( 1004) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2704.09 seconds wall clock time: 47 minutes 3.55 seconds (2823.55 seconds total)