Starting phenix.real_space_refine on Thu Jul 2 22:30:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xk4_38415/07_2026/8xk4_38415.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xk4_38415/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8xk4_38415/07_2026/8xk4_38415.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xk4_38415/07_2026/8xk4_38415.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xk4_38415/07_2026/8xk4_38415.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xk4_38415/07_2026/8xk4_38415.map" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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, 0 Ad-hoc single atom residues: {' MN': 1} Chain breaks: 1 Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 20 Ad-hoc single atom residues: {' MN': 1} Classifications: {'DNA': 1} Modifications used: {'p5*END': 1} Chain breaks: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' MN': 1} Chain breaks: 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: 1.25, per 1000 atoms: 0.21 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: 0.34 Conformation dependent library (CDL) restraints added in 235.1 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: 0.44 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: 0.72 Time building geometry restraints manager: 0.47 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: 217 3.22 - 4.83: 29 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 3.060 nonbonded pdb=" O VAL A 737 " pdb="MN MN B 101 " model vdw 1.761 3.060 nonbonded pdb=" OP1 DT B 1 " pdb="MN MN B 101 " model vdw 1.807 3.060 nonbonded pdb=" OD1 ASP A 713 " pdb="MN MN C 101 " model vdw 1.941 3.060 nonbonded pdb=" OP1 DA B 3 " pdb="MN MN B 101 " model vdw 2.096 3.060 ... (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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.970 Find NCS groups from input model: 0.010 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:5.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.960 ------------------------------------------------------------------------------- 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 : 0.652 8.046 8499 Z= 0.430 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 0.65246 / 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 : 0.185 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: 0.4062 time to fit residues: 56.8105 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 : 0.138 ------------------------------------------------------------------------------- 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: 0.6980 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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 = 0.4106 r_free = 0.4106 target = 0.189219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.152546 restraints weight = 6233.915| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 1.81 r_work: 0.3440 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6220 Z= 0.158 Angle : 0.588 5.911 8499 Z= 0.333 Chirality : 0.046 0.223 947 Planarity : 0.005 0.054 1002 Dihedral : 12.813 137.772 978 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.99 % Allowed : 12.91 % Favored : 85.10 % 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: -0.71 (0.32), residues: 681 helix: -0.22 (0.37), residues: 214 sheet: 1.04 (0.44), residues: 152 loop : -1.40 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 105 TYR 0.015 0.001 TYR A 37 PHE 0.023 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 0.00339 / 0.16 ( 6220) covalent geometry : angle 0.58837 / 0.33 ( 8499) hydrogen bonds : bond 0.05149 / 3.21 ( 239) hydrogen bonds : angle 5.15248 / 3.66 ( 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: 12 poor density : 96 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: A 56 HIS cc_start: 0.7653 (m-70) cc_final: 0.7156 (m170) REVERT: A 310 ASP cc_start: 0.6872 (m-30) cc_final: 0.6546 (m-30) REVERT: A 371 LYS cc_start: 0.8169 (tppt) cc_final: 0.7859 (mmmt) REVERT: A 539 MET cc_start: 0.7994 (mpp) cc_final: 0.7550 (mmt) REVERT: A 540 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7834 (tpp) REVERT: A 663 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.7186 (tt0) outliers start: 12 outliers final: 3 residues processed: 101 average time/residue: 0.3671 time to fit residues: 39.1931 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 : 0.140 ------------------------------------------------------------------------------- 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: 0.9980 chunk 7 optimal weight: 0.0670 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.0020 chunk 36 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.5728 ------------------------------------------------------------------------------- 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 = 0.4063 r_free = 0.4063 target = 0.185854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.148431 restraints weight = 6193.030| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 1.75 r_work: 0.3447 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6220 Z= 0.124 Angle : 0.530 5.470 8499 Z= 0.303 Chirality : 0.043 0.216 947 Planarity : 0.004 0.041 1002 Dihedral : 12.707 136.237 978 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.65 % Allowed : 15.07 % Favored : 82.28 % 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: -0.57 (0.33), residues: 681 helix: -0.02 (0.37), residues: 217 sheet: 1.19 (0.46), residues: 143 loop : -1.37 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 105 TYR 0.009 0.001 TYR A 185 PHE 0.021 0.001 PHE A 351 TRP 0.007 0.001 TRP A 282 HIS 0.005 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 ( 6220) covalent geometry : angle 0.52963 / 0.30 ( 8499) hydrogen bonds : bond 0.04424 / 2.79 ( 239) hydrogen bonds : angle 4.82259 / 3.44 ( 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 110 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.129 Fit side-chains REVERT: A 56 HIS cc_start: 0.7704 (m-70) cc_final: 0.7202 (m170) REVERT: A 274 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7916 (mmtm) REVERT: A 310 ASP cc_start: 0.6769 (m-30) cc_final: 0.6433 (m-30) REVERT: A 371 LYS cc_start: 0.8161 (tppt) cc_final: 0.7873 (mmmt) REVERT: A 539 MET cc_start: 0.7986 (mpp) cc_final: 0.7699 (mmt) REVERT: A 731 GLN cc_start: 0.7325 (mm-40) cc_final: 0.7092 (tp-100) outliers start: 16 outliers final: 5 residues processed: 103 average time/residue: 0.3451 time to fit residues: 37.8259 Evaluate side-chains 91 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.131 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 57 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.4035 r_free = 0.4035 target = 0.182837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.149102 restraints weight = 6257.318| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 1.66 r_work: 0.3391 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6220 Z= 0.158 Angle : 0.556 5.790 8499 Z= 0.314 Chirality : 0.045 0.227 947 Planarity : 0.004 0.044 1002 Dihedral : 12.734 134.632 978 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.98 % Allowed : 15.89 % Favored : 81.13 % 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: -0.63 (0.32), residues: 681 helix: 0.01 (0.36), residues: 220 sheet: 1.16 (0.46), residues: 143 loop : -1.49 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 275 TYR 0.008 0.001 TYR A 336 PHE 0.018 0.002 PHE A 351 TRP 0.005 0.001 TRP A 282 HIS 0.007 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 ( 6220) covalent geometry : angle 0.55634 / 0.31 ( 8499) hydrogen bonds : bond 0.04481 / 2.81 ( 239) hydrogen bonds : angle 4.80452 / 3.41 ( 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 106 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.182 Fit side-chains REVERT: A 73 MET cc_start: 0.7375 (OUTLIER) cc_final: 0.6382 (mpt) REVERT: A 274 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7944 (mmtm) REVERT: A 310 ASP cc_start: 0.6854 (m-30) cc_final: 0.6529 (m-30) REVERT: A 371 LYS cc_start: 0.8141 (tppt) cc_final: 0.7833 (mmmt) REVERT: A 432 ARG cc_start: 0.6376 (mtm-85) cc_final: 0.6127 (mtp85) REVERT: A 539 MET cc_start: 0.8086 (mpp) cc_final: 0.7804 (mmt) REVERT: A 731 GLN cc_start: 0.7330 (mm-40) cc_final: 0.7072 (tp-100) outliers start: 18 outliers final: 9 residues processed: 96 average time/residue: 0.3494 time to fit residues: 35.6438 Evaluate side-chains 92 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 73 MET 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: 3.9990 chunk 6 optimal weight: 6.9990 chunk 51 optimal weight: 0.0970 chunk 18 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 9 optimal weight: 0.0170 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 56 HIS 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 = 0.4036 r_free = 0.4036 target = 0.183118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.144284 restraints weight = 6398.092| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.68 r_work: 0.3378 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6220 Z= 0.131 Angle : 0.539 6.881 8499 Z= 0.304 Chirality : 0.044 0.228 947 Planarity : 0.004 0.041 1002 Dihedral : 12.730 134.670 978 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.48 % Allowed : 17.22 % Favored : 80.30 % 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 (0.32), residues: 681 helix: 0.08 (0.36), residues: 220 sheet: 1.17 (0.46), residues: 143 loop : -1.40 (0.33), residues: 318 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 0.017 0.001 PHE A 351 TRP 0.006 0.001 TRP A 282 HIS 0.004 0.001 HIS A 590 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 6220) covalent geometry : angle 0.53855 / 0.30 ( 8499) hydrogen bonds : bond 0.04108 / 2.59 ( 239) hydrogen bonds : angle 4.74389 / 3.38 ( 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 101 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.137 Fit side-chains REVERT: A 73 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.6407 (mpt) REVERT: A 274 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7460 (mppt) REVERT: A 310 ASP cc_start: 0.6906 (m-30) cc_final: 0.6559 (m-30) REVERT: A 371 LYS cc_start: 0.8139 (tppt) cc_final: 0.7812 (mmmt) REVERT: A 432 ARG cc_start: 0.6296 (mtm-85) cc_final: 0.6055 (mtp85) REVERT: A 719 TYR cc_start: 0.7967 (OUTLIER) cc_final: 0.7373 (t80) REVERT: A 731 GLN cc_start: 0.7334 (mm-40) cc_final: 0.7088 (tp-100) outliers start: 15 outliers final: 9 residues processed: 93 average time/residue: 0.3604 time to fit residues: 35.7306 Evaluate side-chains 92 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.171 ------------------------------------------------------------------------------- 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 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 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 719 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 27 optimal weight: 0.4980 chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 ASN A 56 HIS 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 = 0.4009 r_free = 0.4009 target = 0.180376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.142043 restraints weight = 6232.200| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 1.89 r_work: 0.3451 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6220 Z= 0.160 Angle : 0.565 5.847 8499 Z= 0.315 Chirality : 0.045 0.228 947 Planarity : 0.004 0.045 1002 Dihedral : 12.787 135.059 978 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.15 % Allowed : 17.72 % 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: -0.65 (0.32), residues: 681 helix: -0.05 (0.35), residues: 220 sheet: 1.15 (0.46), residues: 143 loop : -1.47 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 275 TYR 0.009 0.001 TYR A 440 PHE 0.018 0.002 PHE A 319 TRP 0.005 0.001 TRP A 282 HIS 0.004 0.001 HIS A 710 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 6220) covalent geometry : angle 0.56457 / 0.32 ( 8499) hydrogen bonds : bond 0.04462 / 2.80 ( 239) hydrogen bonds : angle 4.74582 / 3.37 ( 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 103 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.212 Fit side-chains REVERT: A 73 MET cc_start: 0.7438 (OUTLIER) cc_final: 0.6545 (mpt) REVERT: A 274 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7529 (mppt) REVERT: A 310 ASP cc_start: 0.6937 (m-30) cc_final: 0.6608 (m-30) REVERT: A 351 PHE cc_start: 0.8166 (OUTLIER) cc_final: 0.7962 (m-80) REVERT: A 371 LYS cc_start: 0.8205 (tppt) cc_final: 0.7910 (mmmt) REVERT: A 432 ARG cc_start: 0.6377 (mtm-85) cc_final: 0.6164 (mtp85) REVERT: A 643 ARG cc_start: 0.7603 (ttm-80) cc_final: 0.7218 (mtm180) REVERT: A 719 TYR cc_start: 0.8187 (OUTLIER) cc_final: 0.7623 (t80) outliers start: 19 outliers final: 10 residues processed: 95 average time/residue: 0.3773 time to fit residues: 38.1172 Evaluate side-chains 96 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.168 ------------------------------------------------------------------------------- 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 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 351 PHE 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 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: 4.9990 chunk 48 optimal weight: 0.0970 chunk 5 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 ASN 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 = 0.4018 r_free = 0.4018 target = 0.180779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.143999 restraints weight = 6282.005| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.77 r_work: 0.3363 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6220 Z= 0.188 Angle : 0.598 5.740 8499 Z= 0.331 Chirality : 0.046 0.266 947 Planarity : 0.004 0.049 1002 Dihedral : 12.893 135.854 978 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.64 % Allowed : 18.05 % Favored : 78.31 % 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: -0.86 (0.32), residues: 681 helix: -0.17 (0.35), residues: 222 sheet: 1.10 (0.46), residues: 137 loop : -1.62 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 291 TYR 0.009 0.001 TYR A 440 PHE 0.020 0.002 PHE A 319 TRP 0.005 0.001 TRP A 512 HIS 0.005 0.001 HIS A 710 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 ( 6220) covalent geometry : angle 0.59821 / 0.33 ( 8499) hydrogen bonds : bond 0.04706 / 2.97 ( 239) hydrogen bonds : angle 4.79550 / 3.41 ( 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 105 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.160 Fit side-chains REVERT: A 73 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.6511 (mpt) REVERT: A 274 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7511 (mppt) REVERT: A 310 ASP cc_start: 0.7020 (m-30) cc_final: 0.6670 (m-30) REVERT: A 371 LYS cc_start: 0.8179 (tppt) cc_final: 0.7867 (mmmt) REVERT: A 432 ARG cc_start: 0.6453 (mtm-85) cc_final: 0.6204 (mtp85) REVERT: A 643 ARG cc_start: 0.7600 (ttm-80) cc_final: 0.7155 (mtt180) REVERT: A 719 TYR cc_start: 0.8266 (OUTLIER) cc_final: 0.7654 (t80) outliers start: 22 outliers final: 10 residues processed: 97 average time/residue: 0.3891 time to fit residues: 40.1148 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 : 0.207 ------------------------------------------------------------------------------- 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 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 539 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 24 optimal weight: 0.0030 chunk 8 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 overall best weight: 0.7792 ------------------------------------------------------------------------------- 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 = 0.4021 r_free = 0.4021 target = 0.181669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.144276 restraints weight = 6263.841| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 1.76 r_work: 0.3471 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6220 Z= 0.130 Angle : 0.539 5.904 8499 Z= 0.304 Chirality : 0.044 0.282 947 Planarity : 0.004 0.045 1002 Dihedral : 12.801 135.250 976 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.98 % Allowed : 19.04 % Favored : 77.98 % 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: -0.07 (0.35), residues: 226 sheet: 1.43 (0.48), residues: 127 loop : -1.59 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 291 TYR 0.007 0.001 TYR A 440 PHE 0.014 0.001 PHE A 319 TRP 0.007 0.001 TRP A 282 HIS 0.003 0.001 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 6220) covalent geometry : angle 0.53916 / 0.30 ( 8499) hydrogen bonds : bond 0.03967 / 2.53 ( 239) hydrogen bonds : angle 4.60874 / 3.26 ( 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 101 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.143 Fit side-chains REVERT: A 73 MET cc_start: 0.7445 (OUTLIER) cc_final: 0.6553 (mpt) REVERT: A 274 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7497 (mppt) REVERT: A 310 ASP cc_start: 0.6954 (m-30) cc_final: 0.6597 (m-30) REVERT: A 371 LYS cc_start: 0.8197 (tppt) cc_final: 0.7937 (mmmt) REVERT: A 432 ARG cc_start: 0.6515 (mtm-85) cc_final: 0.6282 (mtp85) REVERT: A 643 ARG cc_start: 0.7649 (ttm-80) cc_final: 0.7209 (mtt180) REVERT: A 719 TYR cc_start: 0.8231 (OUTLIER) cc_final: 0.7605 (t80) outliers start: 18 outliers final: 9 residues processed: 95 average time/residue: 0.3759 time to fit residues: 37.9537 Evaluate side-chains 90 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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 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 353 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 65 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 36 optimal weight: 0.0060 chunk 54 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4033 r_free = 0.4033 target = 0.182611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.146424 restraints weight = 6306.474| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 1.65 r_work: 0.3477 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6220 Z= 0.126 Angle : 0.537 5.684 8499 Z= 0.304 Chirality : 0.044 0.229 947 Planarity : 0.004 0.043 1002 Dihedral : 12.738 134.782 976 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.99 % Allowed : 20.53 % Favored : 77.48 % 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: -0.65 (0.32), residues: 681 helix: -0.05 (0.35), residues: 227 sheet: 1.49 (0.48), residues: 127 loop : -1.53 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 291 TYR 0.011 0.001 TYR A 613 PHE 0.014 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 0.00266 / 0.13 ( 6220) covalent geometry : angle 0.53651 / 0.30 ( 8499) hydrogen bonds : bond 0.03862 / 2.45 ( 239) hydrogen bonds : angle 4.71578 / 3.37 ( 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 95 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.160 Fit side-chains REVERT: A 73 MET cc_start: 0.7428 (OUTLIER) cc_final: 0.6537 (mpt) REVERT: A 274 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7410 (mppt) REVERT: A 310 ASP cc_start: 0.6946 (m-30) cc_final: 0.6592 (m-30) REVERT: A 371 LYS cc_start: 0.8162 (tppt) cc_final: 0.7922 (mmmt) REVERT: A 432 ARG cc_start: 0.6542 (mtm-85) cc_final: 0.6316 (mtp85) REVERT: A 643 ARG cc_start: 0.7652 (ttm-80) cc_final: 0.7212 (mtt180) REVERT: A 719 TYR cc_start: 0.8218 (OUTLIER) cc_final: 0.7618 (t80) outliers start: 12 outliers final: 6 residues processed: 90 average time/residue: 0.3494 time to fit residues: 33.5441 Evaluate side-chains 89 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.133 ------------------------------------------------------------------------------- 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 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 436 LEU Chi-restraints excluded: chain A residue 689 VAL 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: 0.0030 chunk 11 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 27 optimal weight: 0.0060 chunk 13 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 overall best weight: 0.7408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4034 r_free = 0.4034 target = 0.182655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.146830 restraints weight = 6241.507| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.70 r_work: 0.3432 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6220 Z= 0.128 Angle : 0.545 8.566 8499 Z= 0.304 Chirality : 0.044 0.227 947 Planarity : 0.004 0.043 1002 Dihedral : 12.713 134.498 976 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.32 % Allowed : 20.86 % 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: -0.56 (0.32), residues: 681 helix: 0.02 (0.35), residues: 226 sheet: 1.49 (0.48), residues: 133 loop : -1.50 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 291 TYR 0.006 0.001 TYR A 440 PHE 0.033 0.001 PHE A 86 TRP 0.009 0.001 TRP A 512 HIS 0.003 0.001 HIS A 710 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 6220) covalent geometry : angle 0.54506 / 0.30 ( 8499) hydrogen bonds : bond 0.03798 / 2.42 ( 239) hydrogen bonds : angle 4.67270 / 3.32 ( 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: 14 poor density : 77 time to evaluate : 0.211 Fit side-chains REVERT: A 73 MET cc_start: 0.7438 (OUTLIER) cc_final: 0.6517 (mpt) REVERT: A 274 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7491 (mppt) REVERT: A 310 ASP cc_start: 0.6950 (m-30) cc_final: 0.6598 (m-30) REVERT: A 371 LYS cc_start: 0.8180 (tppt) cc_final: 0.7937 (mmmt) REVERT: A 432 ARG cc_start: 0.6494 (mtm-85) cc_final: 0.6272 (mtp85) REVERT: A 643 ARG cc_start: 0.7646 (ttm-80) cc_final: 0.7197 (mtt180) REVERT: A 719 TYR cc_start: 0.8205 (OUTLIER) cc_final: 0.7649 (t80) outliers start: 14 outliers final: 6 residues processed: 85 average time/residue: 0.3847 time to fit residues: 34.7448 Evaluate side-chains 84 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.168 ------------------------------------------------------------------------------- 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 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 436 LEU Chi-restraints excluded: chain A residue 689 VAL 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: 7.9990 chunk 42 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 ASN 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 = 0.3998 r_free = 0.3998 target = 0.179150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.141302 restraints weight = 6224.291| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 1.80 r_work: 0.3434 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 6220 Z= 0.180 Angle : 0.601 7.796 8499 Z= 0.331 Chirality : 0.047 0.243 947 Planarity : 0.004 0.049 1002 Dihedral : 12.832 135.361 976 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.82 % Allowed : 21.52 % Favored : 76.66 % 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: -0.05 (0.35), residues: 223 sheet: 1.34 (0.47), residues: 133 loop : -1.60 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 291 TYR 0.011 0.001 TYR A 613 PHE 0.025 0.002 PHE A 86 TRP 0.007 0.001 TRP A 512 HIS 0.005 0.001 HIS A 710 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 ( 6220) covalent geometry : angle 0.60094 / 0.33 ( 8499) hydrogen bonds : bond 0.04572 / 2.89 ( 239) hydrogen bonds : angle 4.84120 / 3.44 ( 647) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1950.42 seconds wall clock time: 33 minutes 50.85 seconds (2030.85 seconds total)