Starting phenix.real_space_refine on Wed Aug 5 16:14:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xk4_38415/08_2026/8xk4_38415.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xk4_38415/08_2026/8xk4_38415.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xk4_38415/08_2026/8xk4_38415.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xk4_38415/08_2026/8xk4_38415.map" model { file = "/net/cci-nas-00/data/ceres_data/8xk4_38415/08_2026/8xk4_38415.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xk4_38415/08_2026/8xk4_38415.cif" } resolution = 2.94 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= 0.081 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 5734 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 3 7.51 5 P 22 5.49 5 S 29 5.16 5 C 3791 2.51 5 N 1075 2.21 5 O 1128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s 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: 6048 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5589 Classifications: {'peptide': 689} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 23, 'TRANS': 665} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 2, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 255 Classifications: {'DNA': 12} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 11} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 179 Classifications: {'DNA': 9} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {' MN': 1} Classifications: {'DNA': 1, 'undetermined': 1} Modifications used: {'p5*END': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.64, per 1000 atoms: 0.27 Number of scatterers: 6048 At special positions: 0 Unit cell: (75.739, 89.355, 110.63, 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 3 24.99 S 29 16.00 P 22 15.00 O 1128 8.00 N 1075 7.00 C 3791 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: 0.56 Conformation dependent library (CDL) restraints added in 322.9 milliseconds 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1312 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 9 sheets defined 33.4% alpha, 19.9% beta 8 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 36 through 48 Processing helix chain 'A' and resid 85 through 105 removed outlier: 3.538A pdb=" N ARG A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 165 removed outlier: 3.654A pdb=" N MET A 163 " --> pdb=" O THR A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 288 removed outlier: 3.704A pdb=" N TRP A 282 " --> pdb=" O CYS A 278 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN A 285 " --> pdb=" O ARG A 281 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA A 288 " --> pdb=" O GLN A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 329 removed outlier: 4.200A pdb=" N GLY A 329 " --> pdb=" O VAL A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 354 Processing helix chain 'A' and resid 358 through 375 removed outlier: 3.583A pdb=" N ILE A 362 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR A 363 " --> pdb=" O LYS A 359 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE A 365 " --> pdb=" O ASP A 361 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL A 368 " --> pdb=" O GLN A 364 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA A 375 " --> pdb=" O LYS A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.807A pdb=" N LYS A 387 " --> pdb=" O THR A 384 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER A 388 " --> pdb=" O SER A 385 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE A 389 " --> pdb=" O THR A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 389' Processing helix chain 'A' and resid 394 through 400 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 Processing helix chain 'A' and resid 422 through 428 Processing helix chain 'A' and resid 432 through 442 removed outlier: 3.505A pdb=" N GLY A 442 " --> pdb=" O LYS A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 468 removed outlier: 3.666A pdb=" N ILE A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 488 Processing helix chain 'A' and resid 491 through 508 removed outlier: 4.115A pdb=" N THR A 495 " --> pdb=" O SER A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 585 Processing helix chain 'A' and resid 602 through 611 removed outlier: 3.552A pdb=" N VAL A 606 " --> pdb=" O HIS A 602 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU A 607 " --> pdb=" O THR A 603 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A 609 " --> pdb=" O LEU A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 614 No H-bonds generated for 'chain 'A' and resid 612 through 614' Processing helix chain 'A' and resid 681 through 693 removed outlier: 3.622A pdb=" N SER A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 721 removed outlier: 3.639A pdb=" N ARG A 721 " --> pdb=" O THR A 717 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5 Processing sheet with id=AA2, first strand: chain 'A' and resid 7 through 13 removed outlier: 5.151A pdb=" N ILE A 144 " --> pdb=" O SER A 10 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL A 127 " --> pdb=" O GLN A 122 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLN A 122 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ILE A 129 " --> pdb=" O GLN A 120 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N GLN A 120 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLU A 131 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.785A pdb=" N VAL A 23 " --> pdb=" O GLU A 74 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLU A 74 " --> pdb=" O VAL A 23 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 187 Processing sheet with id=AA5, first strand: chain 'A' and resid 230 through 232 removed outlier: 4.065A pdb=" N ILE A 231 " --> pdb=" O TYR A 242 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N TYR A 242 " --> pdb=" O ILE A 231 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 308 through 311 removed outlier: 3.618A pdb=" N THR A 646 " --> pdb=" O CYS A 657 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N CYS A 522 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N HIS A 594 " --> pdb=" O CYS A 522 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE A 524 " --> pdb=" O HIS A 594 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ASP A 596 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ILE A 526 " --> pdb=" O ASP A 596 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 322 through 323 Processing sheet with id=AA8, first strand: chain 'A' and resid 378 through 382 removed outlier: 6.584A pdb=" N VAL A 417 " --> pdb=" O GLN A 450 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 528 through 531 removed outlier: 4.571A pdb=" N SER A 535 " --> pdb=" O LEU A 559 " (cutoff:3.500A) 220 hydrogen bonds defined for protein. 609 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 19 hydrogen bonds 38 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 1.22 Time building geometry restraints manager: 0.74 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: 1617 1.33 - 1.45: 1195 1.45 - 1.57: 3312 1.57 - 1.69: 45 1.69 - 1.81: 51 Bond restraints: 6220 Sorted by residual: bond pdb=" P DC B 102 " pdb=" OP3 DC B 102 " ideal model delta sigma weight residual 1.480 1.606 -0.126 2.00e-02 2.50e+03 4.00e+01 bond pdb=" P DT C 7 " pdb=" OP3 DT C 7 " ideal model delta sigma weight residual 1.480 1.606 -0.126 2.00e-02 2.50e+03 3.94e+01 bond pdb=" P DT B 1 " pdb=" OP3 DT B 1 " ideal model delta sigma weight residual 1.480 1.600 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" C3' DT B 6 " pdb=" C2' DT B 6 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.00e+01 bond pdb=" P DT B 1 " pdb=" O5' DT B 1 " ideal model delta sigma weight residual 1.593 1.624 -0.031 1.00e-02 1.00e+04 9.53e+00 ... (remaining 6215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 8238 1.61 - 3.22: 216 3.22 - 4.83: 30 4.83 - 6.44: 11 6.44 - 8.05: 4 Bond angle restraints: 8499 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 103.25 111.30 -8.05 1.05e+00 9.07e-01 5.87e+01 angle pdb=" N3 DT B 6 " pdb=" C4 DT B 6 " pdb=" O4 DT B 6 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 angle pdb=" C PHE A 319 " pdb=" N HIS A 320 " pdb=" CA HIS A 320 " ideal model delta sigma weight residual 121.54 129.53 -7.99 1.91e+00 2.74e-01 1.75e+01 angle pdb=" N3 DT B 9 " pdb=" C4 DT B 9 " pdb=" O4 DT B 9 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT C 10 " pdb=" C4 DT C 10 " pdb=" O4 DT C 10 " ideal model delta sigma weight residual 119.90 122.32 -2.42 6.00e-01 2.78e+00 1.62e+01 ... (remaining 8494 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.68: 3463 27.68 - 55.35: 160 55.35 - 83.03: 13 83.03 - 110.71: 3 110.71 - 138.38: 1 Dihedral angle restraints: 3640 sinusoidal: 1612 harmonic: 2028 Sorted by residual: dihedral pdb=" CA LYS A 77 " pdb=" C LYS A 77 " pdb=" N ARG A 78 " pdb=" CA ARG A 78 " ideal model delta harmonic sigma weight residual -180.00 -156.88 -23.12 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA LEU A 270 " pdb=" C LEU A 270 " pdb=" N SER A 271 " pdb=" CA SER A 271 " ideal model delta harmonic sigma weight residual -180.00 -160.71 -19.29 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA ILE A 374 " pdb=" C ILE A 374 " pdb=" N ALA A 375 " pdb=" CA ALA A 375 " ideal model delta harmonic sigma weight residual 180.00 161.13 18.87 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 3637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 919 0.109 - 0.217: 25 0.217 - 0.326: 1 0.326 - 0.435: 0 0.435 - 0.543: 2 Chirality restraints: 947 Sorted by residual: chirality pdb=" P DT C 7 " pdb=" OP1 DT C 7 " pdb=" OP2 DT C 7 " pdb=" O5' DT C 7 " both_signs ideal model delta sigma weight residual True 2.34 2.88 -0.54 2.00e-01 2.50e+01 7.38e+00 chirality pdb=" P DC B 102 " pdb=" OP1 DC B 102 " pdb=" OP2 DC B 102 " pdb=" O5' DC B 102 " both_signs ideal model delta sigma weight residual True 2.34 -2.84 -0.51 2.00e-01 2.50e+01 6.44e+00 chirality pdb=" P DT B 1 " pdb=" OP1 DT B 1 " pdb=" OP2 DT B 1 " pdb=" O5' DT B 1 " both_signs ideal model delta sigma weight residual True 2.34 2.61 -0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 944 not shown) Planarity restraints: 1002 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 257 " 0.064 5.00e-02 4.00e+02 9.53e-02 1.45e+01 pdb=" N PRO A 258 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO A 258 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 258 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT B 1 " 0.032 2.00e-02 2.50e+03 1.62e-02 6.60e+00 pdb=" N1 DT B 1 " -0.035 2.00e-02 2.50e+03 pdb=" C2 DT B 1 " 0.003 2.00e-02 2.50e+03 pdb=" O2 DT B 1 " -0.009 2.00e-02 2.50e+03 pdb=" N3 DT B 1 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DT B 1 " 0.007 2.00e-02 2.50e+03 pdb=" O4 DT B 1 " 0.014 2.00e-02 2.50e+03 pdb=" C5 DT B 1 " 0.002 2.00e-02 2.50e+03 pdb=" C7 DT B 1 " -0.009 2.00e-02 2.50e+03 pdb=" C6 DT B 1 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 510 " -0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO A 511 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 511 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 511 " -0.022 5.00e-02 4.00e+02 ... (remaining 999 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 18 2.38 - 3.01: 2986 3.01 - 3.64: 8479 3.64 - 4.27: 13700 4.27 - 4.90: 23035 Nonbonded interactions: 48218 Sorted by model distance: nonbonded pdb=" OP2 DT C 7 " pdb="MN MN C 101 " model vdw 1.749 2.320 nonbonded pdb=" O VAL A 737 " pdb="MN MN B 101 " model vdw 1.761 2.320 nonbonded pdb=" OP1 DT B 1 " pdb="MN MN B 101 " model vdw 1.807 2.320 nonbonded pdb=" OD1 ASP A 713 " pdb="MN MN C 101 " model vdw 1.941 2.320 nonbonded pdb=" OP1 DA B 3 " pdb="MN MN B 101 " model vdw 2.096 2.320 ... (remaining 48213 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: 1.270 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.300 Find NCS groups from input model: 0.120 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:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 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 : 0.005 0.126 6220 Z= 0.281 Angle : 0.654 8.046 8499 Z= 0.431 Chirality : 0.051 0.543 947 Planarity : 0.005 0.095 1002 Dihedral : 15.225 138.384 2328 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.67 % Favored : 96.04 % 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: -1.05 (0.32), residues: 681 helix: -0.48 (0.37), residues: 203 sheet: 0.78 (0.45), residues: 146 loop : -1.52 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 105 TYR 0.018 0.001 TYR A 352 PHE 0.024 0.001 PHE A 319 TRP 0.012 0.001 TRP A 43 HIS 0.007 0.001 HIS A 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.28 ( 6220) covalent geometry : angle 0.65354 / 0.43 ( 8499) hydrogen bonds : bond 0.19063 / 11.15 ( 239) hydrogen bonds : angle 7.20322 / 5.07 ( 647) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.216 Fit side-chains REVERT: A 56 HIS cc_start: 0.7119 (m-70) cc_final: 0.6586 (m170) REVERT: A 310 ASP cc_start: 0.6192 (m-30) cc_final: 0.5751 (m-30) REVERT: A 539 MET cc_start: 0.7246 (mpp) cc_final: 0.6890 (mmt) REVERT: A 639 THR cc_start: 0.8538 (m) cc_final: 0.8309 (p) outliers start: 0 outliers final: 1 residues processed: 133 average time/residue: 0.5200 time to fit residues: 72.5842 Evaluate side-chains 88 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 87 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 44 GLN A 183 GLN A 259 GLN A 461 GLN A 548 HIS ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.186179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.147718 restraints weight = 6271.909| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 1.89 r_work: 0.3430 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6220 Z= 0.159 Angle : 0.591 5.956 8499 Z= 0.335 Chirality : 0.046 0.234 947 Planarity : 0.005 0.055 1002 Dihedral : 12.861 137.310 978 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.15 % Allowed : 12.58 % Favored : 85.26 % 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: -0.76 (0.32), residues: 681 helix: -0.26 (0.37), residues: 215 sheet: 1.01 (0.44), residues: 152 loop : -1.45 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 105 TYR 0.016 0.001 TYR A 37 PHE 0.024 0.002 PHE A 351 TRP 0.008 0.001 TRP A 282 HIS 0.006 0.001 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 ( 6220) covalent geometry : angle 0.59086 / 0.33 ( 8499) hydrogen bonds : bond 0.05202 / 3.25 ( 239) hydrogen bonds : angle 5.16708 / 3.67 ( 647) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: A 56 HIS cc_start: 0.7686 (m-70) cc_final: 0.7194 (m170) REVERT: A 310 ASP cc_start: 0.6866 (m-30) cc_final: 0.6545 (m-30) REVERT: A 371 LYS cc_start: 0.8176 (tppt) cc_final: 0.7885 (mmmt) REVERT: A 539 MET cc_start: 0.8005 (mpp) cc_final: 0.7570 (mmt) REVERT: A 540 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7847 (tpp) REVERT: A 663 GLN cc_start: 0.7578 (OUTLIER) cc_final: 0.7188 (tt0) outliers start: 13 outliers final: 3 residues processed: 101 average time/residue: 0.4303 time to fit residues: 46.0563 Evaluate side-chains 93 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 663 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 0.0370 chunk 13 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 461 GLN A 548 HIS ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.184735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.147840 restraints weight = 6192.134| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.67 r_work: 0.3458 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6220 Z= 0.127 Angle : 0.536 5.411 8499 Z= 0.306 Chirality : 0.043 0.231 947 Planarity : 0.004 0.041 1002 Dihedral : 12.745 136.217 978 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.32 % Allowed : 14.74 % Favored : 82.95 % 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: -0.53 (0.33), residues: 681 helix: 0.02 (0.37), residues: 216 sheet: 1.16 (0.46), residues: 143 loop : -1.33 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 105 TYR 0.009 0.001 TYR A 185 PHE 0.020 0.001 PHE A 351 TRP 0.007 0.001 TRP A 282 HIS 0.006 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 ( 6220) covalent geometry : angle 0.53598 / 0.31 ( 8499) hydrogen bonds : bond 0.04546 / 2.87 ( 239) hydrogen bonds : angle 4.86375 / 3.47 ( 647) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.148 Fit side-chains REVERT: A 56 HIS cc_start: 0.7643 (m-70) cc_final: 0.7150 (m170) REVERT: A 73 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.6469 (mpt) REVERT: A 274 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7902 (mmtm) REVERT: A 310 ASP cc_start: 0.6746 (m-30) cc_final: 0.6409 (m-30) REVERT: A 371 LYS cc_start: 0.8132 (tppt) cc_final: 0.7821 (mmmt) REVERT: A 539 MET cc_start: 0.7981 (mpp) cc_final: 0.7557 (mmt) REVERT: A 731 GLN cc_start: 0.7291 (mm-40) cc_final: 0.7031 (tp-100) outliers start: 14 outliers final: 5 residues processed: 100 average time/residue: 0.4309 time to fit residues: 45.7716 Evaluate side-chains 92 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 602 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 12 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 461 GLN A 548 HIS ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.183672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.146928 restraints weight = 6203.256| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.51 r_work: 0.3342 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 6220 Z= 0.200 Angle : 0.615 6.849 8499 Z= 0.341 Chirality : 0.047 0.240 947 Planarity : 0.004 0.048 1002 Dihedral : 12.877 135.485 978 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.64 % Allowed : 14.57 % Favored : 81.79 % 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 (0.32), residues: 681 helix: -0.09 (0.36), residues: 212 sheet: 1.06 (0.46), residues: 143 loop : -1.65 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 275 TYR 0.010 0.001 TYR A 440 PHE 0.021 0.002 PHE A 351 TRP 0.007 0.002 TRP A 512 HIS 0.008 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 ( 6220) covalent geometry : angle 0.61536 / 0.34 ( 8499) hydrogen bonds : bond 0.05102 / 3.19 ( 239) hydrogen bonds : angle 4.97231 / 3.53 ( 647) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.134 Fit side-chains REVERT: A 73 MET cc_start: 0.7429 (OUTLIER) cc_final: 0.6484 (mpt) REVERT: A 274 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7968 (mmtm) REVERT: A 292 HIS cc_start: 0.8034 (m170) cc_final: 0.7795 (m-70) REVERT: A 310 ASP cc_start: 0.6944 (m-30) cc_final: 0.6627 (m-30) REVERT: A 371 LYS cc_start: 0.8220 (tppt) cc_final: 0.7889 (mmmt) outliers start: 22 outliers final: 11 residues processed: 103 average time/residue: 0.3785 time to fit residues: 41.3935 Evaluate side-chains 92 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 602 HIS Chi-restraints excluded: chain A residue 638 ASN Chi-restraints excluded: chain A residue 689 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 60 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 56 HIS A 461 GLN A 548 HIS ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.179926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.142032 restraints weight = 6398.244| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.68 r_work: 0.3374 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6220 Z= 0.160 Angle : 0.580 7.585 8499 Z= 0.324 Chirality : 0.045 0.244 947 Planarity : 0.004 0.046 1002 Dihedral : 12.888 135.450 978 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.15 % Allowed : 16.72 % Favored : 80.13 % 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: -0.76 (0.32), residues: 681 helix: -0.02 (0.36), residues: 212 sheet: 1.10 (0.46), residues: 143 loop : -1.60 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 291 TYR 0.016 0.001 TYR A 37 PHE 0.021 0.002 PHE A 351 TRP 0.007 0.001 TRP A 282 HIS 0.005 0.001 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 ( 6220) covalent geometry : angle 0.58015 / 0.32 ( 8499) hydrogen bonds : bond 0.04481 / 2.81 ( 239) hydrogen bonds : angle 4.88751 / 3.48 ( 647) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.219 Fit side-chains REVERT: A 274 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7441 (mppt) REVERT: A 310 ASP cc_start: 0.6923 (m-30) cc_final: 0.6597 (m-30) REVERT: A 371 LYS cc_start: 0.8187 (tppt) cc_final: 0.7864 (mmmt) REVERT: A 643 ARG cc_start: 0.7599 (ttm-80) cc_final: 0.7147 (mtt180) REVERT: A 719 TYR cc_start: 0.8161 (OUTLIER) cc_final: 0.7554 (t80) outliers start: 19 outliers final: 8 residues processed: 95 average time/residue: 0.4151 time to fit residues: 41.9002 Evaluate side-chains 90 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 602 HIS Chi-restraints excluded: chain A residue 638 ASN Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 719 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 40 optimal weight: 0.0470 chunk 2 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 overall best weight: 1.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 56 HIS A 120 GLN A 548 HIS ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.178654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.142232 restraints weight = 6229.138| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.78 r_work: 0.3354 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 6220 Z= 0.173 Angle : 0.577 5.463 8499 Z= 0.323 Chirality : 0.046 0.245 947 Planarity : 0.004 0.047 1002 Dihedral : 12.900 135.423 976 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.31 % Allowed : 17.55 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.32), residues: 681 helix: -0.11 (0.36), residues: 219 sheet: 1.06 (0.46), residues: 143 loop : -1.61 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 275 TYR 0.008 0.001 TYR A 440 PHE 0.018 0.002 PHE A 319 TRP 0.005 0.001 TRP A 282 HIS 0.005 0.001 HIS A 710 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 ( 6220) covalent geometry : angle 0.57726 / 0.32 ( 8499) hydrogen bonds : bond 0.04635 / 2.91 ( 239) hydrogen bonds : angle 4.84242 / 3.43 ( 647) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.246 Fit side-chains REVERT: A 274 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7521 (mppt) REVERT: A 310 ASP cc_start: 0.7060 (m-30) cc_final: 0.6709 (m-30) REVERT: A 371 LYS cc_start: 0.8218 (tppt) cc_final: 0.7930 (mmmt) REVERT: A 643 ARG cc_start: 0.7658 (ttm-80) cc_final: 0.7210 (mtt180) REVERT: A 719 TYR cc_start: 0.8265 (OUTLIER) cc_final: 0.7662 (t80) outliers start: 20 outliers final: 11 residues processed: 100 average time/residue: 0.4398 time to fit residues: 46.7123 Evaluate side-chains 96 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 551 GLN Chi-restraints excluded: chain A residue 602 HIS Chi-restraints excluded: chain A residue 638 ASN Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 719 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 16 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 1 optimal weight: 0.0570 overall best weight: 1.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 548 HIS ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.179125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.140684 restraints weight = 6265.696| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.75 r_work: 0.3368 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 6220 Z= 0.200 Angle : 0.620 6.112 8499 Z= 0.344 Chirality : 0.047 0.283 947 Planarity : 0.005 0.050 1002 Dihedral : 13.031 136.068 976 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.81 % Allowed : 18.05 % Favored : 78.15 % 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: -1.01 (0.32), residues: 681 helix: -0.26 (0.35), residues: 222 sheet: 0.96 (0.46), residues: 137 loop : -1.73 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 291 TYR 0.010 0.001 TYR A 440 PHE 0.024 0.002 PHE A 319 TRP 0.005 0.001 TRP A 512 HIS 0.007 0.001 HIS A 710 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 ( 6220) covalent geometry : angle 0.62009 / 0.34 ( 8499) hydrogen bonds : bond 0.04989 / 3.14 ( 239) hydrogen bonds : angle 4.94283 / 3.50 ( 647) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 0.222 Fit side-chains REVERT: A 274 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7554 (mppt) REVERT: A 310 ASP cc_start: 0.7003 (m-30) cc_final: 0.6656 (m-30) REVERT: A 371 LYS cc_start: 0.8204 (tppt) cc_final: 0.7895 (mmmt) REVERT: A 643 ARG cc_start: 0.7666 (ttm-80) cc_final: 0.7231 (mtt180) REVERT: A 678 LYS cc_start: 0.8093 (pmmt) cc_final: 0.7416 (tppt) REVERT: A 719 TYR cc_start: 0.8335 (OUTLIER) cc_final: 0.7801 (t80) outliers start: 23 outliers final: 10 residues processed: 101 average time/residue: 0.4402 time to fit residues: 47.1219 Evaluate side-chains 91 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 551 GLN Chi-restraints excluded: chain A residue 602 HIS Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 719 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 4.9990 chunk 25 optimal weight: 0.0770 chunk 21 optimal weight: 0.4980 chunk 55 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 24 optimal weight: 0.0670 chunk 8 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 38 optimal weight: 0.0980 chunk 30 optimal weight: 1.9990 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 289 GLN A 548 HIS ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.183530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.144932 restraints weight = 6215.815| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 1.92 r_work: 0.3436 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6220 Z= 0.115 Angle : 0.525 5.884 8499 Z= 0.299 Chirality : 0.044 0.250 947 Planarity : 0.004 0.044 1002 Dihedral : 12.892 135.096 976 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.66 % Allowed : 20.70 % Favored : 77.65 % 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: -0.82 (0.32), residues: 681 helix: -0.14 (0.35), residues: 227 sheet: 1.33 (0.47), residues: 127 loop : -1.64 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 291 TYR 0.006 0.001 TYR A 440 PHE 0.012 0.001 PHE A 319 TRP 0.009 0.001 TRP A 512 HIS 0.003 0.001 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 ( 6220) covalent geometry : angle 0.52537 / 0.30 ( 8499) hydrogen bonds : bond 0.03835 / 2.43 ( 239) hydrogen bonds : angle 4.65105 / 3.30 ( 647) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.222 Fit side-chains REVERT: A 274 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7525 (mppt) REVERT: A 310 ASP cc_start: 0.7003 (m-30) cc_final: 0.6656 (m-30) REVERT: A 371 LYS cc_start: 0.8186 (tppt) cc_final: 0.7933 (mmmt) REVERT: A 643 ARG cc_start: 0.7713 (ttm-80) cc_final: 0.7263 (mtt180) REVERT: A 719 TYR cc_start: 0.8209 (OUTLIER) cc_final: 0.7558 (t80) outliers start: 10 outliers final: 5 residues processed: 96 average time/residue: 0.4190 time to fit residues: 42.8440 Evaluate side-chains 88 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 602 HIS Chi-restraints excluded: chain A residue 719 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 65 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 36 optimal weight: 0.0870 chunk 54 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 0.0970 chunk 31 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 overall best weight: 0.5756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 GLN A 548 HIS ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.181552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.143891 restraints weight = 6302.231| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 1.83 r_work: 0.3397 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6220 Z= 0.120 Angle : 0.531 7.913 8499 Z= 0.299 Chirality : 0.044 0.247 947 Planarity : 0.004 0.042 1002 Dihedral : 12.787 134.561 976 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.66 % Allowed : 21.03 % Favored : 77.32 % 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: -0.72 (0.32), residues: 681 helix: -0.09 (0.35), residues: 227 sheet: 1.43 (0.47), residues: 127 loop : -1.57 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 291 TYR 0.007 0.001 TYR A 440 PHE 0.013 0.001 PHE A 319 TRP 0.010 0.001 TRP A 512 HIS 0.003 0.001 HIS A 710 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 ( 6220) covalent geometry : angle 0.53118 / 0.30 ( 8499) hydrogen bonds : bond 0.03828 / 2.41 ( 239) hydrogen bonds : angle 4.75682 / 3.39 ( 647) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.234 Fit side-chains REVERT: A 274 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7358 (mppt) REVERT: A 310 ASP cc_start: 0.7018 (m-30) cc_final: 0.6660 (m-30) REVERT: A 371 LYS cc_start: 0.8171 (tppt) cc_final: 0.7917 (mmmt) REVERT: A 643 ARG cc_start: 0.7673 (ttm-80) cc_final: 0.7224 (mtt180) REVERT: A 678 LYS cc_start: 0.8102 (pmmt) cc_final: 0.7425 (tppt) REVERT: A 719 TYR cc_start: 0.8184 (OUTLIER) cc_final: 0.7590 (t80) outliers start: 10 outliers final: 5 residues processed: 89 average time/residue: 0.4392 time to fit residues: 41.5298 Evaluate side-chains 83 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 602 HIS Chi-restraints excluded: chain A residue 719 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 36 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 GLN A 548 HIS ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.184932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.147098 restraints weight = 6168.899| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.81 r_work: 0.3415 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6220 Z= 0.128 Angle : 0.531 5.837 8499 Z= 0.301 Chirality : 0.044 0.243 947 Planarity : 0.004 0.044 1002 Dihedral : 12.783 134.342 976 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.66 % Allowed : 21.36 % Favored : 76.99 % 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: 681 helix: -0.06 (0.35), residues: 227 sheet: 1.46 (0.47), residues: 127 loop : -1.57 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 291 TYR 0.012 0.001 TYR A 613 PHE 0.015 0.001 PHE A 319 TRP 0.008 0.001 TRP A 512 HIS 0.003 0.001 HIS A 710 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 ( 6220) covalent geometry : angle 0.53103 / 0.30 ( 8499) hydrogen bonds : bond 0.03811 / 2.41 ( 239) hydrogen bonds : angle 4.73624 / 3.37 ( 647) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.205 Fit side-chains REVERT: A 274 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7347 (mppt) REVERT: A 310 ASP cc_start: 0.7020 (m-30) cc_final: 0.6656 (m-30) REVERT: A 351 PHE cc_start: 0.7753 (m-80) cc_final: 0.7503 (m-80) REVERT: A 371 LYS cc_start: 0.8175 (tppt) cc_final: 0.7917 (mmmt) REVERT: A 643 ARG cc_start: 0.7656 (ttm-80) cc_final: 0.7219 (mtt180) REVERT: A 678 LYS cc_start: 0.8078 (pmmt) cc_final: 0.7415 (tppt) REVERT: A 719 TYR cc_start: 0.8180 (OUTLIER) cc_final: 0.7587 (t80) outliers start: 10 outliers final: 4 residues processed: 90 average time/residue: 0.4428 time to fit residues: 42.4224 Evaluate side-chains 83 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 719 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 23 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 7 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 548 HIS ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.177398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.137955 restraints weight = 6238.746| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.80 r_work: 0.3322 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 6220 Z= 0.249 Angle : 0.665 6.339 8499 Z= 0.365 Chirality : 0.050 0.239 947 Planarity : 0.005 0.052 1002 Dihedral : 13.065 135.943 976 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.32 % Allowed : 21.85 % Favored : 76.82 % 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: -1.08 (0.31), residues: 681 helix: -0.35 (0.35), residues: 220 sheet: 1.19 (0.46), residues: 127 loop : -1.79 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 291 TYR 0.010 0.002 TYR A 440 PHE 0.028 0.003 PHE A 319 TRP 0.008 0.002 TRP A 512 HIS 0.007 0.001 HIS A 710 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.25 ( 6220) covalent geometry : angle 0.66515 / 0.36 ( 8499) hydrogen bonds : bond 0.05405 / 3.39 ( 239) hydrogen bonds : angle 5.12759 / 3.64 ( 647) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2286.34 seconds wall clock time: 39 minutes 36.94 seconds (2376.94 seconds total)