Starting phenix.real_space_refine on Wed Aug 5 17:04:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xjw_38408/08_2026/8xjw_38408.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xjw_38408/08_2026/8xjw_38408.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xjw_38408/08_2026/8xjw_38408.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xjw_38408/08_2026/8xjw_38408.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xjw_38408/08_2026/8xjw_38408.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xjw_38408/08_2026/8xjw_38408.map" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5737 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 P 31 5.49 5 S 29 5.16 5 C 3882 2.51 5 N 1108 2.21 5 O 1197 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 6248 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5595 Classifications: {'peptide': 690} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 23, 'TRANS': 666} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 338 Classifications: {'DNA': 16} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 15} Chain: "C" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 308 Classifications: {'RNA': 15} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 8} Link IDs: {'rna3p': 14} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1, 'water': 3} Link IDs: {None: 3} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 1.36, per 1000 atoms: 0.22 Number of scatterers: 6248 At special positions: 0 Unit cell: (73.186, 91.057, 107.226, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 1 24.99 S 29 16.00 P 31 15.00 O 1197 8.00 N 1108 7.00 C 3882 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.36 Conformation dependent library (CDL) restraints added in 296.5 milliseconds 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1316 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 9 sheets defined 35.7% alpha, 21.3% beta 9 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 13 through 17 removed outlier: 3.789A pdb=" N LEU A 17 " --> pdb=" O ALA A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 48 Processing helix chain 'A' and resid 84 through 107 Processing helix chain 'A' and resid 159 through 166 removed outlier: 3.557A pdb=" N MET A 163 " --> pdb=" O THR A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 269 removed outlier: 3.693A pdb=" N LYS A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 288 removed outlier: 3.561A pdb=" N THR A 279 " --> pdb=" O ARG A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 331 Processing helix chain 'A' and resid 349 through 354 Processing helix chain 'A' and resid 358 through 375 removed outlier: 3.519A pdb=" N ILE A 362 " --> pdb=" O THR A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 399 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 408 through 413 removed outlier: 3.643A pdb=" N PHE A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 428 Processing helix chain 'A' and resid 432 through 442 Processing helix chain 'A' and resid 453 through 467 removed outlier: 3.761A pdb=" N ILE A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE A 463 " --> pdb=" O ALA A 459 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 464 " --> pdb=" O PHE A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 488 Processing helix chain 'A' and resid 491 through 507 removed outlier: 3.763A pdb=" N THR A 495 " --> pdb=" O SER A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 585 removed outlier: 3.696A pdb=" N LEU A 573 " --> pdb=" O LEU A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 611 removed outlier: 4.363A pdb=" N VAL A 606 " --> pdb=" O HIS A 602 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU A 607 " --> pdb=" O THR A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 692 removed outlier: 3.730A pdb=" N ILE A 685 " --> pdb=" O PRO A 681 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 686 " --> pdb=" O PHE A 682 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU A 687 " --> pdb=" O SER A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 695 No H-bonds generated for 'chain 'A' and resid 693 through 695' Processing helix chain 'A' and resid 709 through 722 removed outlier: 3.935A pdb=" N LEU A 714 " --> pdb=" O HIS A 710 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5 removed outlier: 3.817A pdb=" N THR A 639 " --> pdb=" O ASN A 634 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 7 through 9 removed outlier: 3.738A pdb=" N GLN A 153 " --> pdb=" O TYR A 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 7 through 9 removed outlier: 3.738A pdb=" N GLN A 153 " --> pdb=" O TYR A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 54 Processing sheet with id=AA5, first strand: chain 'A' and resid 176 through 178 Processing sheet with id=AA6, first strand: chain 'A' and resid 231 through 233 Processing sheet with id=AA7, first strand: chain 'A' and resid 308 through 311 removed outlier: 3.666A pdb=" N THR A 646 " --> pdb=" O CYS A 657 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ILE A 591 " --> pdb=" O ASP A 618 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL A 620 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE A 593 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ILE A 622 " --> pdb=" O ILE A 593 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ARG A 595 " --> pdb=" O ILE A 622 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N VAL A 528 " --> pdb=" O ASP A 596 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A 535 " --> pdb=" O LEU A 559 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 322 through 323 Processing sheet with id=AA9, first strand: chain 'A' and resid 379 through 382 removed outlier: 8.956A pdb=" N THR A 416 " --> pdb=" O ASN A 340 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LYS A 342 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N LEU A 418 " --> pdb=" O LYS A 342 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N SER A 344 " --> pdb=" O LEU A 418 " (cutoff:3.500A) 246 hydrogen bonds defined for protein. 687 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 21 hydrogen bonds 38 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 1.55 Time building geometry restraints manager: 0.48 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: 1727 1.33 - 1.45: 1318 1.45 - 1.57: 3290 1.57 - 1.69: 60 1.69 - 1.81: 51 Bond restraints: 6446 Sorted by residual: bond pdb=" P DT B 1 " pdb=" OP3 DT B 1 " ideal model delta sigma weight residual 1.480 1.571 -0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" C3' DT B 13 " pdb=" C2' DT B 13 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.83e+00 bond pdb=" C3' DG B 15 " pdb=" C2' DG B 15 " ideal model delta sigma weight residual 1.516 1.532 -0.016 8.00e-03 1.56e+04 3.92e+00 bond pdb=" C1' DT B 6 " pdb=" N1 DT B 6 " ideal model delta sigma weight residual 1.468 1.494 -0.026 1.40e-02 5.10e+03 3.44e+00 bond pdb=" C3' DT B 16 " pdb=" C2' DT B 16 " ideal model delta sigma weight residual 1.516 1.531 -0.015 8.00e-03 1.56e+04 3.40e+00 ... (remaining 6441 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 8539 1.53 - 3.06: 270 3.06 - 4.59: 36 4.59 - 6.12: 6 6.12 - 7.65: 5 Bond angle restraints: 8856 Sorted by residual: angle pdb=" N PRO A 474 " pdb=" CA PRO A 474 " pdb=" CB PRO A 474 " ideal model delta sigma weight residual 103.25 110.90 -7.65 1.05e+00 9.07e-01 5.30e+01 angle pdb=" N ILE A 550 " pdb=" CA ILE A 550 " pdb=" C ILE A 550 " ideal model delta sigma weight residual 111.91 105.62 6.29 8.90e-01 1.26e+00 4.99e+01 angle pdb=" N3 DT B 14 " pdb=" C4 DT B 14 " pdb=" O4 DT B 14 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" O5' C C 5 " pdb=" C5' C C 5 " pdb=" C4' C C 5 " ideal model delta sigma weight residual 109.40 112.71 -3.31 8.00e-01 1.56e+00 1.72e+01 angle pdb=" N3 DT B 6 " pdb=" C4 DT B 6 " pdb=" O4 DT B 6 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 ... (remaining 8851 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.64: 3584 27.64 - 55.27: 192 55.27 - 82.91: 30 82.91 - 110.54: 4 110.54 - 138.18: 1 Dihedral angle restraints: 3811 sinusoidal: 1776 harmonic: 2035 Sorted by residual: dihedral pdb=" CA ASN A 54 " pdb=" C ASN A 54 " pdb=" N GLN A 55 " pdb=" CA GLN A 55 " ideal model delta harmonic sigma weight residual 180.00 -160.67 -19.33 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" C4' DT B 13 " pdb=" C3' DT B 13 " pdb=" O3' DT B 13 " pdb=" P DT B 14 " ideal model delta sinusoidal sigma weight residual 220.00 81.82 138.18 1 3.50e+01 8.16e-04 1.37e+01 dihedral pdb=" CA GLN A 76 " pdb=" C GLN A 76 " pdb=" N LYS A 77 " pdb=" CA LYS A 77 " ideal model delta harmonic sigma weight residual 180.00 163.18 16.82 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 3808 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 729 0.043 - 0.087: 187 0.087 - 0.130: 69 0.130 - 0.173: 15 0.173 - 0.217: 2 Chirality restraints: 1002 Sorted by residual: chirality pdb=" CB ILE A 619 " pdb=" CA ILE A 619 " pdb=" CG1 ILE A 619 " pdb=" CG2 ILE A 619 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA PRO A 474 " pdb=" N PRO A 474 " pdb=" C PRO A 474 " pdb=" CB PRO A 474 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.97e-01 chirality pdb=" C2' C C 5 " pdb=" C3' C C 5 " pdb=" O2' C C 5 " pdb=" C1' C C 5 " both_signs ideal model delta sigma weight residual False -2.62 -2.78 0.17 2.00e-01 2.50e+01 6.93e-01 ... (remaining 999 not shown) Planarity restraints: 1013 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT B 1 " 0.029 2.00e-02 2.50e+03 1.48e-02 5.49e+00 pdb=" N1 DT B 1 " -0.034 2.00e-02 2.50e+03 pdb=" C2 DT B 1 " -0.004 2.00e-02 2.50e+03 pdb=" O2 DT B 1 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DT B 1 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DT B 1 " 0.003 2.00e-02 2.50e+03 pdb=" O4 DT B 1 " 0.013 2.00e-02 2.50e+03 pdb=" C5 DT B 1 " -0.004 2.00e-02 2.50e+03 pdb=" C7 DT B 1 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DT B 1 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 49 " -0.026 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO A 50 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 50 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 50 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 705 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.78e+00 pdb=" N PRO A 706 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 706 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 706 " -0.019 5.00e-02 4.00e+02 ... (remaining 1010 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 158 2.69 - 3.24: 5711 3.24 - 3.79: 9694 3.79 - 4.35: 13469 4.35 - 4.90: 21861 Nonbonded interactions: 50893 Sorted by model distance: nonbonded pdb=" CG1 VAL A 737 " pdb="MN MN A 801 " model vdw 2.132 2.740 nonbonded pdb=" OE1 GLN A 510 " pdb=" OG1 THR A 732 " model vdw 2.241 3.040 nonbonded pdb=" NZ LYS A 269 " pdb=" O2 DT B 6 " model vdw 2.248 3.120 nonbonded pdb=" OE1 GLN A 435 " pdb=" NE2 GLN A 723 " model vdw 2.259 3.120 nonbonded pdb=" OH TYR A 434 " pdb=" OP3 DT B 1 " model vdw 2.277 3.040 ... (remaining 50888 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.560 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 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 0.091 6446 Z= 0.200 Angle : 0.625 7.646 8856 Z= 0.417 Chirality : 0.047 0.217 1002 Planarity : 0.004 0.040 1013 Dihedral : 16.621 138.177 2495 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.56 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.92 (0.32), residues: 684 helix: 0.12 (0.34), residues: 239 sheet: 0.48 (0.42), residues: 151 loop : -1.83 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 275 TYR 0.008 0.001 TYR A 363 PHE 0.010 0.001 PHE A 86 TRP 0.013 0.002 TRP A 43 HIS 0.004 0.001 HIS A 590 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.20 ( 6446) covalent geometry : angle 0.62468 / 0.42 ( 8856) hydrogen bonds : bond 0.14211 / 8.06 ( 254) hydrogen bonds : angle 7.12257 / 4.88 ( 725) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 163 MET cc_start: 0.4887 (mtt) cc_final: 0.4604 (mtm) REVERT: A 493 TYR cc_start: 0.6802 (t80) cc_final: 0.6548 (t80) REVERT: A 667 MET cc_start: 0.7941 (ttt) cc_final: 0.7643 (ttt) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.4519 time to fit residues: 47.7053 Evaluate side-chains 73 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 GLN A 126 GLN A 257 GLN A 379 ASN A 638 ASN A 644 GLN A 674 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.211909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.169291 restraints weight = 6278.900| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 2.97 r_work: 0.3689 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6446 Z= 0.157 Angle : 0.630 7.349 8856 Z= 0.344 Chirality : 0.046 0.205 1002 Planarity : 0.004 0.035 1013 Dihedral : 16.506 138.505 1140 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 3.14 % Allowed : 10.41 % Favored : 86.45 % 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: -0.81 (0.32), residues: 684 helix: 0.36 (0.34), residues: 242 sheet: 0.42 (0.41), residues: 159 loop : -1.92 (0.33), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 143 TYR 0.012 0.001 TYR A 307 PHE 0.013 0.002 PHE A 351 TRP 0.012 0.001 TRP A 282 HIS 0.004 0.001 HIS A 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 ( 6446) covalent geometry : angle 0.62973 / 0.34 ( 8856) hydrogen bonds : bond 0.05875 / 3.53 ( 254) hydrogen bonds : angle 5.41535 / 3.82 ( 725) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: A 38 HIS cc_start: 0.6456 (OUTLIER) cc_final: 0.5826 (p90) REVERT: A 163 MET cc_start: 0.5538 (mtt) cc_final: 0.5034 (mtm) REVERT: A 259 GLN cc_start: 0.7374 (OUTLIER) cc_final: 0.6904 (tt0) REVERT: A 291 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.7104 (mmp-170) REVERT: A 439 GLN cc_start: 0.6581 (mt0) cc_final: 0.6331 (mt0) REVERT: A 493 TYR cc_start: 0.7480 (t80) cc_final: 0.7096 (t80) outliers start: 19 outliers final: 6 residues processed: 90 average time/residue: 0.4635 time to fit residues: 44.0272 Evaluate side-chains 92 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 725 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 35 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 3 optimal weight: 10.0000 chunk 46 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 257 GLN A 638 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.210134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.167613 restraints weight = 6278.725| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 3.01 r_work: 0.3668 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6446 Z= 0.174 Angle : 0.644 7.288 8856 Z= 0.354 Chirality : 0.046 0.180 1002 Planarity : 0.004 0.035 1013 Dihedral : 16.554 137.150 1140 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.81 % Allowed : 13.88 % Favored : 83.31 % 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: -0.87 (0.31), residues: 684 helix: 0.35 (0.34), residues: 242 sheet: 0.47 (0.42), residues: 153 loop : -2.00 (0.33), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 182 TYR 0.015 0.001 TYR A 307 PHE 0.014 0.002 PHE A 253 TRP 0.013 0.001 TRP A 282 HIS 0.005 0.001 HIS A 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 ( 6446) covalent geometry : angle 0.64416 / 0.35 ( 8856) hydrogen bonds : bond 0.05515 / 3.21 ( 254) hydrogen bonds : angle 5.23927 / 3.70 ( 725) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: A 38 HIS cc_start: 0.6448 (OUTLIER) cc_final: 0.5802 (p90) REVERT: A 163 MET cc_start: 0.5614 (mtt) cc_final: 0.5099 (mtm) REVERT: A 259 GLN cc_start: 0.7383 (OUTLIER) cc_final: 0.7028 (tt0) REVERT: A 291 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7134 (mmp-170) REVERT: A 439 GLN cc_start: 0.6507 (mt0) cc_final: 0.6191 (mt0) REVERT: A 458 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7289 (mt-10) REVERT: A 493 TYR cc_start: 0.7559 (t80) cc_final: 0.7153 (t80) REVERT: A 667 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7741 (ttt) outliers start: 17 outliers final: 7 residues processed: 90 average time/residue: 0.4823 time to fit residues: 45.6551 Evaluate side-chains 90 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 MET Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 667 MET Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 725 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 0.0010 chunk 49 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 34 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 11 optimal weight: 0.0470 overall best weight: 1.4088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 257 GLN A 638 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.210207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.167929 restraints weight = 6341.024| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 2.94 r_work: 0.3670 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6446 Z= 0.167 Angle : 0.642 7.929 8856 Z= 0.352 Chirality : 0.046 0.180 1002 Planarity : 0.004 0.032 1013 Dihedral : 16.582 138.055 1140 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 3.47 % Allowed : 16.03 % Favored : 80.50 % 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: -0.81 (0.31), residues: 684 helix: 0.48 (0.34), residues: 241 sheet: 0.50 (0.42), residues: 153 loop : -2.03 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 143 TYR 0.014 0.001 TYR A 307 PHE 0.012 0.002 PHE A 253 TRP 0.013 0.001 TRP A 282 HIS 0.005 0.001 HIS A 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 ( 6446) covalent geometry : angle 0.64234 / 0.35 ( 8856) hydrogen bonds : bond 0.05250 / 3.07 ( 254) hydrogen bonds : angle 5.08126 / 3.62 ( 725) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 38 HIS cc_start: 0.6416 (OUTLIER) cc_final: 0.5764 (p90) REVERT: A 163 MET cc_start: 0.5690 (mtt) cc_final: 0.5102 (mtm) REVERT: A 259 GLN cc_start: 0.7384 (OUTLIER) cc_final: 0.7108 (tt0) REVERT: A 291 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7197 (mmp-170) REVERT: A 439 GLN cc_start: 0.6652 (mt0) cc_final: 0.6231 (mt0) REVERT: A 458 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7208 (mt-10) REVERT: A 493 TYR cc_start: 0.7515 (t80) cc_final: 0.7116 (t80) outliers start: 21 outliers final: 5 residues processed: 88 average time/residue: 0.4364 time to fit residues: 40.7156 Evaluate side-chains 85 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 MET Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 671 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 21 optimal weight: 0.0970 chunk 68 optimal weight: 0.3980 chunk 69 optimal weight: 6.9990 chunk 47 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 ASN A 638 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.212831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.170608 restraints weight = 6441.797| |-----------------------------------------------------------------------------| r_work (start): 0.4059 rms_B_bonded: 2.87 r_work: 0.3716 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6446 Z= 0.124 Angle : 0.601 7.891 8856 Z= 0.331 Chirality : 0.044 0.177 1002 Planarity : 0.004 0.032 1013 Dihedral : 16.565 137.726 1140 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.48 % Allowed : 18.51 % Favored : 79.01 % 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: -0.67 (0.31), residues: 684 helix: 0.61 (0.34), residues: 238 sheet: 0.72 (0.41), residues: 151 loop : -2.03 (0.32), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 171 TYR 0.008 0.001 TYR A 307 PHE 0.009 0.001 PHE A 351 TRP 0.013 0.001 TRP A 282 HIS 0.006 0.001 HIS A 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 6446) covalent geometry : angle 0.60135 / 0.33 ( 8856) hydrogen bonds : bond 0.04841 / 2.96 ( 254) hydrogen bonds : angle 4.95880 / 3.53 ( 725) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: A 38 HIS cc_start: 0.6599 (OUTLIER) cc_final: 0.5917 (p90) REVERT: A 163 MET cc_start: 0.5673 (mtt) cc_final: 0.5155 (mtm) REVERT: A 259 GLN cc_start: 0.7367 (OUTLIER) cc_final: 0.6888 (tt0) REVERT: A 439 GLN cc_start: 0.6592 (mt0) cc_final: 0.6179 (mt0) REVERT: A 458 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7176 (mt-10) REVERT: A 615 ILE cc_start: 0.5390 (mt) cc_final: 0.4979 (mt) outliers start: 15 outliers final: 5 residues processed: 90 average time/residue: 0.4872 time to fit residues: 46.3066 Evaluate side-chains 84 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 671 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 34 optimal weight: 9.9990 chunk 49 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 60 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 161 GLN A 257 GLN A 638 ASN A 710 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.209380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.166825 restraints weight = 6322.228| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 3.05 r_work: 0.3647 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6446 Z= 0.174 Angle : 0.648 8.386 8856 Z= 0.353 Chirality : 0.046 0.190 1002 Planarity : 0.004 0.031 1013 Dihedral : 16.576 137.419 1140 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.98 % Allowed : 19.17 % Favored : 77.85 % 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: -0.77 (0.31), residues: 684 helix: 0.53 (0.34), residues: 240 sheet: 0.63 (0.42), residues: 151 loop : -2.08 (0.32), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 175 TYR 0.016 0.001 TYR A 307 PHE 0.010 0.002 PHE A 86 TRP 0.011 0.001 TRP A 282 HIS 0.005 0.001 HIS A 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 ( 6446) covalent geometry : angle 0.64764 / 0.35 ( 8856) hydrogen bonds : bond 0.05074 / 2.95 ( 254) hydrogen bonds : angle 5.01665 / 3.56 ( 725) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: A 38 HIS cc_start: 0.6608 (OUTLIER) cc_final: 0.5894 (p90) REVERT: A 163 MET cc_start: 0.5603 (mtt) cc_final: 0.5156 (mtm) REVERT: A 259 GLN cc_start: 0.7391 (OUTLIER) cc_final: 0.7103 (tt0) REVERT: A 291 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.6972 (mmp80) REVERT: A 458 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7150 (mt-10) REVERT: A 615 ILE cc_start: 0.5532 (OUTLIER) cc_final: 0.5093 (mt) outliers start: 18 outliers final: 5 residues processed: 88 average time/residue: 0.4955 time to fit residues: 45.9974 Evaluate side-chains 83 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 575 GLN Chi-restraints excluded: chain A residue 608 LYS Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 623 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 23 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 ASN A 644 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.208801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.179866 restraints weight = 6284.262| |-----------------------------------------------------------------------------| r_work (start): 0.4181 rms_B_bonded: 1.73 r_work: 0.3650 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 6446 Z= 0.194 Angle : 0.682 8.966 8856 Z= 0.370 Chirality : 0.047 0.193 1002 Planarity : 0.004 0.033 1013 Dihedral : 16.621 137.757 1140 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.81 % Allowed : 20.17 % Favored : 77.02 % 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: -0.84 (0.31), residues: 684 helix: 0.52 (0.34), residues: 237 sheet: 0.57 (0.42), residues: 151 loop : -2.13 (0.32), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 175 TYR 0.019 0.002 TYR A 307 PHE 0.015 0.002 PHE A 319 TRP 0.012 0.001 TRP A 282 HIS 0.005 0.001 HIS A 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 ( 6446) covalent geometry : angle 0.68164 / 0.37 ( 8856) hydrogen bonds : bond 0.05121 / 2.95 ( 254) hydrogen bonds : angle 5.05953 / 3.58 ( 725) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: A 163 MET cc_start: 0.5634 (mtt) cc_final: 0.5185 (mtm) REVERT: A 175 ARG cc_start: 0.5797 (ttm170) cc_final: 0.5405 (ttt90) REVERT: A 259 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.7144 (tt0) REVERT: A 458 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7172 (mt-10) REVERT: A 615 ILE cc_start: 0.5605 (OUTLIER) cc_final: 0.5169 (mt) outliers start: 17 outliers final: 10 residues processed: 83 average time/residue: 0.4503 time to fit residues: 39.6943 Evaluate side-chains 86 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 575 GLN Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 608 LYS Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 725 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 68 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 29 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 46 optimal weight: 0.3980 chunk 15 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 356 HIS A 379 ASN A 638 ASN A 644 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.212053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.169928 restraints weight = 6332.657| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 2.91 r_work: 0.3702 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6446 Z= 0.131 Angle : 0.621 9.373 8856 Z= 0.342 Chirality : 0.045 0.191 1002 Planarity : 0.004 0.030 1013 Dihedral : 16.591 137.365 1140 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.48 % Allowed : 21.82 % Favored : 75.70 % 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: -0.69 (0.32), residues: 684 helix: 0.62 (0.35), residues: 239 sheet: 0.72 (0.42), residues: 151 loop : -2.07 (0.32), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 175 TYR 0.012 0.001 TYR A 130 PHE 0.012 0.001 PHE A 319 TRP 0.014 0.001 TRP A 282 HIS 0.004 0.001 HIS A 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 6446) covalent geometry : angle 0.62096 / 0.34 ( 8856) hydrogen bonds : bond 0.04684 / 2.83 ( 254) hydrogen bonds : angle 4.97132 / 3.51 ( 725) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.151 Fit side-chains revert: symmetry clash REVERT: A 38 HIS cc_start: 0.6387 (OUTLIER) cc_final: 0.5703 (p90) REVERT: A 163 MET cc_start: 0.5606 (mtt) cc_final: 0.5164 (mtm) REVERT: A 175 ARG cc_start: 0.5898 (ttm170) cc_final: 0.5419 (ttt90) REVERT: A 259 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.7164 (tt0) REVERT: A 458 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7163 (mt-10) REVERT: A 615 ILE cc_start: 0.5591 (mt) cc_final: 0.5178 (mt) outliers start: 15 outliers final: 6 residues processed: 85 average time/residue: 0.3528 time to fit residues: 32.0571 Evaluate side-chains 82 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 HIS Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 575 GLN Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 708 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 54 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 0.0870 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 379 ASN A 638 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.212754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.170796 restraints weight = 6359.268| |-----------------------------------------------------------------------------| r_work (start): 0.4056 rms_B_bonded: 2.89 r_work: 0.3711 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6446 Z= 0.129 Angle : 0.621 11.361 8856 Z= 0.341 Chirality : 0.044 0.202 1002 Planarity : 0.004 0.029 1013 Dihedral : 16.557 136.771 1140 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.15 % Allowed : 22.64 % Favored : 75.21 % 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: -0.66 (0.32), residues: 684 helix: 0.65 (0.35), residues: 237 sheet: 0.83 (0.42), residues: 151 loop : -2.10 (0.32), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 175 TYR 0.009 0.001 TYR A 130 PHE 0.009 0.001 PHE A 86 TRP 0.014 0.001 TRP A 282 HIS 0.004 0.001 HIS A 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 6446) covalent geometry : angle 0.62063 / 0.34 ( 8856) hydrogen bonds : bond 0.04598 / 2.80 ( 254) hydrogen bonds : angle 4.92698 / 3.47 ( 725) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: A 163 MET cc_start: 0.5599 (mtt) cc_final: 0.5172 (mtm) REVERT: A 175 ARG cc_start: 0.5927 (ttt180) cc_final: 0.5624 (ttt90) REVERT: A 259 GLN cc_start: 0.7385 (OUTLIER) cc_final: 0.7088 (tt0) REVERT: A 458 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7118 (mt-10) outliers start: 13 outliers final: 5 residues processed: 81 average time/residue: 0.3888 time to fit residues: 33.7086 Evaluate side-chains 79 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 575 GLN Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 708 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 56 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 ASN A 644 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.209360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.164016 restraints weight = 6257.669| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 2.45 r_work: 0.3714 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6446 Z= 0.192 Angle : 0.685 10.507 8856 Z= 0.370 Chirality : 0.047 0.202 1002 Planarity : 0.004 0.034 1013 Dihedral : 16.589 136.956 1140 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 1.32 % Allowed : 23.31 % Favored : 75.37 % 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: -0.79 (0.32), residues: 684 helix: 0.56 (0.35), residues: 237 sheet: 0.69 (0.42), residues: 151 loop : -2.16 (0.32), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 275 TYR 0.018 0.002 TYR A 307 PHE 0.011 0.002 PHE A 86 TRP 0.010 0.002 TRP A 282 HIS 0.005 0.001 HIS A 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 ( 6446) covalent geometry : angle 0.68538 / 0.37 ( 8856) hydrogen bonds : bond 0.04904 / 2.83 ( 254) hydrogen bonds : angle 5.03492 / 3.54 ( 725) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: A 163 MET cc_start: 0.5566 (mtt) cc_final: 0.5130 (mtm) REVERT: A 175 ARG cc_start: 0.5991 (ttt180) cc_final: 0.5609 (ttt90) REVERT: A 259 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.7051 (tt0) REVERT: A 458 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7079 (mt-10) outliers start: 8 outliers final: 4 residues processed: 78 average time/residue: 0.4046 time to fit residues: 33.5706 Evaluate side-chains 79 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 GLN Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 575 GLN Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 708 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 65 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 379 ASN A 581 HIS A 638 ASN A 644 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.211674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.167856 restraints weight = 6344.984| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 2.42 r_work: 0.3748 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6446 Z= 0.136 Angle : 0.641 12.235 8856 Z= 0.349 Chirality : 0.045 0.212 1002 Planarity : 0.004 0.030 1013 Dihedral : 16.591 137.060 1140 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 1.98 % Allowed : 22.64 % Favored : 75.37 % 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: -0.63 (0.32), residues: 684 helix: 0.63 (0.35), residues: 239 sheet: 0.82 (0.42), residues: 156 loop : -2.10 (0.32), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 175 TYR 0.009 0.001 TYR A 307 PHE 0.008 0.001 PHE A 61 TRP 0.014 0.001 TRP A 282 HIS 0.005 0.001 HIS A 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 ( 6446) covalent geometry : angle 0.64076 / 0.35 ( 8856) hydrogen bonds : bond 0.04576 / 2.75 ( 254) hydrogen bonds : angle 4.94296 / 3.48 ( 725) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1979.12 seconds wall clock time: 34 minutes 27.28 seconds (2067.28 seconds total)